From - Thu Dec 23 10:42:56 1999 Received: from dodo.cpmc.columbia.edu (dodo.cpmc.columbia.edu [156.111.190.78]) by buda.ipbs.fr (8.9.3/8.9.3) with ESMTP id KAA10319 for ; Thu, 23 Dec 1999 10:41:25 +0100 Received: (from phd@localhost) by dodo.cpmc.columbia.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) id EAA20843 for gouet@ipbs.fr; Thu, 23 Dec 1999 04:37:21 -0500 (EST) Date: Thu, 23 Dec 1999 04:37:21 -0500 (EST) From: phd@dodo.cpmc.columbia.edu (PredictProtein) Message-Id: <199912230937.EAA20843@dodo.cpmc.columbia.edu> To: gouet@ipbs.fr Subject: PredictProtein Status: X-Mozilla-Status: 0001 Content-Length: 102467 The following information has been received by the server: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________________________________________________________ reference predict_h11817647 (Dec 23, 1999 04:29:56) PPhdr from: gouet@ipbs.fr PPhdr resp: MAIL PPhdr orig: HTML PPhdr want: ASCII PPhdr password(###) prediction of: - default prediction of: - PHDsec PHDacc PHDhtm ProSite SEG ProDom return msf format # default: single protein sequence description=VP2_ROTBU MAYRKRGATVEADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDE VKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQT KLFRIFEPRQLPIYRANGEKELRNRWYWKLKKDTLPDGDYDVREYFLNLYDQVLTEMPDY LLLKDMAVENKNSRDAGKVVDSETASICDAIFQDEETEGAVRRFIAEMRQRVQADRNVVN YPSILHPIDYAFNEYFLQHQLVEPLNNDIIFNYIPERIRNDVNYILNMDRNLPSTARYIR PNLLQDRLNLHDNFESLWDTITTSNYILARSVVPDLKELVSTEAQIQKMSQDLQLEALTI QSETQFLTGINSQAANDCFKTLIAAMLSQRTMSLDFVTTNYMSLISGMWLLTVVPNDMFI RESLVACQLAIVNTIIYPAFGMQRMHYRNGDPQTPFQIAEQQIRKFSGSGIGWHFVNNNQ FRQVVIDGVLNQVLNDNIRNVHVIKQLMQALMQLSRQQFPTMPVDYKRSIQRGILLLSNR LGQLVDLTRLLAYNYETLMACVTMNMQHVQTLTTEKLQLTSVTSLCMLIGNATVIPSPQT LFHYYNVNVNFHSNYNERINDAVAIITAANRLNLYQKKMKAIVEDFLKRLHIFDVARVPD DQMYRLRDRLRLLPVEVRRLDIFNLILMNMDQIERASDKIAQGVIIAYRDMQLERDEMYG YVNIARNLDGFQQINLEELMRTGDYAQITNMLLNNQPVALVGALPFVTDSSVISLIAKLD ATVFAQIVKLRKVDTLKPILYKINSDSNDFYLVANYDWVPTSTTKVYKQVPQQFDFRNSM HMLTSNLTFTVYSDLLAFVSADTVEPINAVAFDNMRIMNEL ________________________________________________________________________________ Result of PROSITE search (Amos Bairoch): ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ please quote: A Bairoch, P Bucher & K Hofmann: The PROSITE database, its status in 1997. Nucl. Acids Res., 1997, 25, 217-221. ________________________________________________________________________________ -------------------------------------------------------- Pattern-ID: ASN_GLYCOSYLATION PS00001 PDOC00001 Pattern-DE: N-glycosylation site Pattern: N[^P][ST][^P] 591 NATV 846 NLTF Pattern-ID: GLYCOSAMINOGLYCAN PS00002 PDOC00002 Pattern-DE: Glycosaminoglycan attachment site Pattern: SG.G 467 SGSG Pattern-ID: CAMP_PHOSPHO_SITE PS00004 PDOC00004 Pattern-DE: cAMP- and cGMP-dependent protein kinase phosphorylation site Pattern: [RK]{2}.[ST] 62 KKST 117 KKQT 151 KKDT 464 RKFS Pattern-ID: PKC_PHOSPHO_SITE PS00005 PDOC00005 Pattern-DE: Protein kinase C phosphorylation site Pattern: [ST].[RK] 37 SDK 42 SKK 64 STK 295 TAR 388 SQR 538 SNR 574 TEK 697 SDK 795 TLK 823 TTK Pattern-ID: CK2_PHOSPHO_SITE PS00006 PDOC00006 Pattern-DE: Casein kinase II phosphorylation site Pattern: [ST].{2}[DE] 42 SKKE 51 SQEE 64 STKE 78 TKEE 154 TLPD 206 SICD 316 SLWD Pattern-ID: TYR_PHOSPHO_SITE PS00007 PDOC00007 Pattern-DE: Tyrosine kinase phosphorylation site Pattern: [RK].{2,3}[DE].{2,3}Y 277 RIRNDVNY 657 RVPDDQMY Pattern-ID: MYRISTYL PS00008 PDOC00008 Pattern-DE: N-myristoylation site Pattern: G[^EDRKHPFYW].{2}[STAGCN][^P] 468 GSGIGW 703 GVIIAY Pattern-ID: LEUCINE_ZIPPER PS00029 PDOC00029 Pattern-DE: Leucine zipper pattern Pattern: L.{6}L.{6}L.{6}L 537 LSNRLGQLVDLTRLLAYNYETL 666 LRDRLRLLPVEVRRLDIFNLIL ________________________________________________________________________________ Result of SEG low-complexity search (JC Wootton & S Federhen): ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ please quote: J C Wootton & S Federhen: Analysis of compositionally biased regions in sequence databases. Meth. in Enzymol. 1996, 266, 554-571. NOTE 1: regions of low-complexity ('simple sequence' or 'compo- sition biased regions') are marked by the letter 'x' in the following output. NOTE 2: The dynamic programming algorithm (MaxHom) does NOT take the SEG information into account, nor do the PHD pre- dictions! !!! --> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! <-- !!! !!! --> WE STRONGLY suggest that you resubmit the regions NOT marked by <-- !!! !!! --> 'x' separately!! <-- !!! !!! --> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! <-- !!! ________________________________________________________________________________ >prot , (#) ppOld, default: single protein sequence description=vp2_rotbu /home/phd/server/work/predict_h11817647 MAYRKRGATVEADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDE VKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQT KLFRIFEPRQLPIYRANGEKELRNRWYWKLKKDTLPDGDYDVREYFLNLYDQVLTEMPDY LLLKDMAVENKNSRDAGKVVDSETASICDAIFQDEETEGAVRRFIAEMRQRVQADRNVVN YPSILHPIDYAFNEYFLQHQLVEPLNNDIIFNYIPERIRNDVNYILNMDRNLPSTARYIR PNLLQDRLNLHDNFESLWDTITTSNYILARSVVPDLKELVSTEAQIQKMSQDLQLEALTI QSETQFLTGINSQAANDCFKTLIAAMLSQRTMSLDFVTTNYMSLISGMWLLTVVPNDMFI RESLVACQLAIVNTIIYPAFGMQRMHYRNGDPQTPFQIAEQQIRKFSGSGIGWHFVNNNQ FRQVVIDGVLNQVLNDNIRNVHVIKQLMQALMQLSRQQFPTMPVDYKRSIQRGILLLSNR LGQLVDLTRLLAYNYETLMACVTMNMQHVQTLTTEKLQLTSVTSLCMLIGNATVIPSPQT LFHYYNVNVNFHSNYNERINDAVAIITAANRLNLYQKKMKAIVEDFLKRLHIFDVARVPD DQMYxxxxxxxxxxxxxxxxxIFNLILMNMDQIERASDKIAQGVIIAYRDMQLERDEMYG YVNIARNLDGFQQINLEELMRTGDYAQITNMLLNNQPVALVGALPFVTDSSVISLIAKLD ATVFAQIVKLRKVDTLKPILYKINSDSNDFYLVANYDWVPTSTTKVYKQVPQQFDFRNSM HMLTSNLTFTVYSDLLAFVSADTVEPINAVAFDNMRIMNEL ________________________________________________________________________________ Result of ProDom domain search (Sonnhammer; Corpet, Gouzy, Kahn): ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - please quote: ELL Sonnhammer & D Kahn, Prot. Sci., 1994, 3, 482-492 ________________________________________________________________________________ --- ------------------------------------------------------------ --- Results from running BLAST against PRODOM domains --- --- PLEASE quote: --- F Corpet, J Gouzy, D Kahn (1998). The ProDom database --- of protein domain families. Nucleic Ac Res 26:323-326. --- --- BEGIN of BLASTP output BLASTP 1.4.7 [16-Oct-94] [Build 12:52:03 Oct 30 1994] Reference: Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990). Basic local alignment search tool. J. Mol. Biol. 215:403-10. Query= prot , (#) ppOld, default: single protein sequence description=vp2_rotbu /home/phd/server/work/predict_h11817647 (881 letters) Database: prodom_99_2 157,167 sequences; 18,560,502 total letters. Searching..................................................done Smallest Sum High Probability Sequences producing High-scoring Segment Pairs: Score P(N) N PD008866 p99.2 (8) VP2(5) O55591(1) Q86218(1) // VP2 PR... 1972 0.0 3 PD000002 p99.2 (2100) ATPF(44) MYSP(31) MYSA(29) // PRO... 108 3.1e-06 1 PD000422 p99.2 (108) TOP1(17) NFH(4) Q20007(3) // PROTE... 91 0.0010 1 PD140913 p99.2 (1) YMT4_YEAST // HYPOTHETICAL 55.4 KD PR... 56 0.0011 5 PD001891 p99.2 (39) GRPE(22) // HEAT SHOCK PROTEIN CHAP... 81 0.017 1 PD000023 p99.2 (401) TPM1(11) Q25893(7) TPM2(6) // PROT... 81 0.018 1 PD074905 p99.2 (1) O42263_XENLA // KINESINRELATED PROTEI... 75 0.019 2 PD031168 p99.2 (3) O06969(1) P54(1) US45(1) // PROTEIN ... 64 0.027 2 PD107575 p99.2 (1) YN8V_YEAST // HYPOTHETICAL 36.4 KD PR... 74 0.051 1 >PD008866 p99.2 (8) VP2(5) O55591(1) Q86218(1) // VP2 PROTEIN RNABINDING MAJOR INTERNAL CORE NUCLEOCAPSID RNA COMPLETE CDS Length = 891 Score = 1972 (903.1 bits), Expect = 0.0, Sum P(3) = 0.0 Identities = 374/423 (88%), Positives = 399/423 (94%) Query: 44 KEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPTFEPKES 103 K++ T +EEIKI D+VK STKEESKQLLEVLKTKEEHQKE+QYEILQKTIPTFEP ES Sbjct: 56 KDKKDTPPEEEIKINDQVKBSTKEESKQLLEVLKTKEEHQKEVQYEILQKTIPTFEPBES 115 Query: 104 ILKKLEDIKPEQAKKQTKLFRIFEPRQLPIYRANGEKELRNRWYWKLKKDTLPDGDYDVR 163 ILKKLEDIKPEQ KKQ KLFR+FEP+QLPIYRANGEKELRNRWYWKLKKD LPDGDYDVR Sbjct: 116 ILKKLEDIKPEQCKKQNKLFRLFEPKQLPIYRANGEKELRNRWYWKLKKDDLPDGDYDVR 175 Query: 164 EYFLNLYDQVLTEMPDYLLLKDMAVENKNSRDAGKVVDSETASICDAIFQDEETEGAVRR 223 EYFLNLYDQVL EMPDYLLLKDMAVENKNSRDAGKVVDSETA ICD IFQDEETEG VRR Sbjct: 176 EYFLNLYDQVLDEMPDYLLLKDMAVENKNSRDAGKVVDSETAEICDEIFQDEETEGYVRR 235 Query: 224 FIAEMRQRVQADRNVVNYPSILHPIDYAFNEYFLQHQLVEPLNNDIIFNYIPERIRNDVN 283 FIA+MRQRVQADRN VNYP+ILHPID+ FNEYFL+HQL+EPL N+IIFNYIPER+RND N Sbjct: 236 FIADMRQRVQADRNTVNYPAILHPIDHEFNEYFLEHQLIEPLTNEIIFNYIPERLRNDPN 295 Query: 284 YILNMDRNLPSTARYIRPNLLQDRLNLHDNFESLWDTITTSNYILARSVVPDLKELVSTE 343 YILNMD NLP+TARYIRP LLQDRLNLHDNFES+WDTIT +NY+LARSVVPDLKELVSTE Sbjct: 296 YILNMDANLPTTARYIRPYLLQDRLNLHDNFESIWDTITHANYVLARSVVPDLKELVSTE 355 Query: 344 AQIQKMSQDLQLEALTIQSETQFLTGINSQAANDCFKTLIAAMLSQRTMSLDFVTTNYMS 403 AQIQKMSQDLQLEALTIQSETQFLTGINSQAANDCFKT+IA MLSQRTMSLDFVTTNYMS Sbjct: 356 AQIQKMSQDLQLEALTIQSETQFLTGINSQAANDCFKTIIATMLSQRTMSLDFVTTNYMS 415 Query: 404 LISGMWLLTVVPNDMFIRESLVACQLAIVNTIIYPAFGMQRMHYRNGDPQTPFQIAEQQI 463 LIS MWL+T+VPNDMFIRESLVACQLA++NTIIYPAFGMQRMHYRNGDP+TPFQIAEQQI Sbjct: 416 LISCMWLMTIVPNDMFIRESLVACQLAVINTIIYPAFGMQRMHYRNGDPRTPFQIAEQQI 475 Query: 464 RKF 466 + F Sbjct: 476 QNF 478 Score = 1904 (872.0 bits), Expect = 0.0, Sum P(3) = 0.0 Identities = 369/407 (90%), Positives = 388/407 (95%) Query: 474 HFVNNNQFRQVVIDGVLNQVLNDNIRNVHVIKQLMQALMQLSRQQFPTMPVDYKRSIQRG 533 HF NNNQFRQVVIDGVLNQ LNDNIRN H++ QLM+ALMQLSRQQFPT P+DYKRS+QRG Sbjct: 485 HFCNNNQFRQVVIDGVLNQTLNDNIRNGHIVNQLMEALMQLSRQQFPTYPIDYKRSVQRG 544 Query: 534 ILLLSNRLGQLVDLTRLLAYNYETLMACVTMNMQHVQTLTTEKLQLTSVTSLCMLIGNAT 593 ILLLSNRLGQLVDLTRL+ YNYETLMAC+TMNMQHVQTLTTEKLQLTSVTSLCMLIGN T Sbjct: 545 ILLLSNRLGQLVDLTRLICYNYETLMACITMNMQHVQTLTTEKLQLTSVTSLCMLIGNTT 604 Query: 594 VIPSPQTLFHYYNVNVNFHSNYNERINDAVAIITAANRLNLYQKKMKAIVEDFLKRLHIF 653 VIP PQTLFHYYN NVNFHSNYNERINDAVAIITAANRL+LYQKKMK+IVEDFLKRLHIF Sbjct: 605 VIPEPQTLFHYYNTNVNFHSNYNERINDAVAIITAANRLDLYQKKMKSIVEDFLKRLHIF 664 Query: 654 DVARVPDDQMYRLRDRLRLLPVEVRRLDIFNLILMNMDQIERASDKIAQGVIIAYRDMQL 713 DV +VPDDQMYRLRDRLR LPVE RRLD+FN+I+ NMDQIERASDKI QGVIIAYRDMQL Sbjct: 665 DVPKVPDDQMYRLRDRLRNLPVERRRLDVFNIIMNNMDQIERASDKICQGVIIAYRDMQL 724 Query: 714 ERDEMYGYVNIARNLDGFQQINLEELMRTGDYAQITNMLLNNQPVALVGALPFVTDSSVI 773 E DEMYGYVNIAR+L+GFQQINLEELMRTGDY+QITNMLLNNQPVALVGA+PFVTDSSVI Sbjct: 725 EYDEMYGYVNIARDLNGFQQINLEELMRTGDYSQITNMLLNNQPVALVGAIPFVTDSSVI 784 Query: 774 SLIAKLDATVFAQIVKLRKVDTLKPILYKINSDSNDFYLVANYDWVPTSTTKVYKQVPQQ 833 SLIAKLDATVFAQIVK RKVDTLKPILYKINSDSNDFYLV NYDWVPTSTTKVYKQVPQQ Sbjct: 785 SLIAKLDATVFAQIVKDRKVDTLKPILYKINSDSNDFYLVHNYDWVPTSTTKVYKQVPQQ 844 Query: 834 FDFRNSMHMLTSNLTFTVYSDLLAFVSADTVEPINAVAFDNMRIMNE 880 FDFR+SMHMLTSNLTFTVY+DLL FVSADTVEPINAVAFDNMRIM E Sbjct: 845 FDFRHSMHMLTSNLTFTVYNDLLKFVSADTVEPINAVAFDNMRIMQE 891 Score = 92 (42.1 bits), Expect = 0.0, Sum P(3) = 0.0 Identities = 18/32 (56%), Positives = 23/32 (71%) Query: 1 MAYRKRGATVEADINNNDRMQEKDDEKQDQNN 32 MAYRKRGA E N+R QEK+DEK+ +N+ Sbjct: 1 MAYRKRGANTEQKDAENERQQEKEDEKEIKND 32 Score = 77 (35.3 bits), Expect = 0.0, Sum P(3) = 0.0 Identities = 16/42 (38%), Positives = 25/42 (59%) Query: 15 NNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIK 56 N + +E + E ++ + QL +KVLSKKE V+TD + K Sbjct: 17 NERQQEKEDEKEIKNDAKKQQLDEKVLSKKENVITDKDVKDK 58 Score = 45 (20.6 bits), Expect = 0.00020, Sum P(2) = 0.00020 Identities = 11/46 (23%), Positives = 21/46 (45%) Query: 214 DEETEGAVRRFIAEMRQRVQADRNVVNYPSILHPIDYAFNEYFLQH 259 D + + A + ++ DR V IL+ I+ N+++L H Sbjct: 780 DSSVISLIAKLDATVFAQIVKDRKVDTLKPILYKINSDSNDFYLVH 825 Score = 43 (19.7 bits), Expect = 0.0, Sum P(3) = 0.0 Identities = 11/49 (22%), Positives = 23/49 (46%) Query: 23 KDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQ 71 KD + ++++D+V +E E +K ++E +K + E Q Sbjct: 56 KDKKDTPPEEEIKINDQVKBSTKEESKQLLEVLKTKEEHQKEVQYEILQ 104 Score = 41 (18.8 bits), Expect = 2.7e-285, Sum P(3) = 2.7e-285 Identities = 8/27 (29%), Positives = 14/27 (51%) Query: 820 PTSTTKVYKQVPQQFDFRNSMHMLTSN 846 P + ++ +Q Q F RN +H +N Sbjct: 464 PRTPFQIAEQQIQNFQVRNWLHFCNNN 490 Score = 38 (17.4 bits), Expect = 0.0, Sum P(3) = 0.0 Identities = 9/39 (23%), Positives = 20/39 (51%) Query: 17 NDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEI 55 ND +++ DEK ++DK + K++ + + +I Sbjct: 31 NDAKKQQLDEKVLSKKENVITDKDVKDKKDTPPEEEIKI 69 Score = 37 (16.9 bits), Expect = 0.0, Sum P(3) = 0.0 Identities = 12/49 (24%), Positives = 22/49 (44%) Query: 5 KRGATVEADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQE 53 ++ A E D + K+D K+ Q + LS K ++ V D ++ Sbjct: 12 QKDAENERQQEKEDEKEIKNDAKKQQLDEKVLSKKENVITDKDVKDKKD 60 Score = 34 (15.6 bits), Expect = 0.0, Sum P(3) = 0.0 Identities = 7/26 (26%), Positives = 14/26 (53%) Query: 5 KRGATVEADINNNDRMQEKDDEKQDQ 30 K+ E +I ND++++ E+ Q Sbjct: 58 KKDTPPEEEIKINDQVKBSTKEESKQ 83 >PD000002 p99.2 (2100) ATPF(44) MYSP(31) MYSA(29) // PROTEIN COILED COIL CHAIN MYOSIN REPEAT HEAVY ATPBINDING FILAMENT HEPTAD Length = 239 Score = 108 (49.5 bits), Expect = 3.1e-06, P = 3.1e-06 Identities = 24/102 (23%), Positives = 59/102 (57%) Query: 18 DRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLK 77 + M+E ++EK+++ ++Q +K + EE + + QEE++ ++E K +EE ++ +E + Sbjct: 15 EEMEELEEEKEEEEEKLQELEKKKKELEEEMEELQEEMEEQEEKMKEEQEEKEEEMEEKE 74 Query: 78 TKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQ 119 + E Q+E E ++ E +E +++E+ E+ +++ Sbjct: 75 EEMEEQEEEMEEQKEEQEEKQEEQEEEQEEMEEEMEEEQEEE 116 Score = 105 (48.1 bits), Expect = 8.2e-06, P = 8.2e-06 Identities = 29/131 (22%), Positives = 62/131 (47%) Query: 11 EADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESK 70 E + ++ +E +++K++Q + + ++ + EE + + QEE + + E +K EE + Sbjct: 72 EKEEEMEEQEEEMEEQKEEQEEKQEEQEEEQEEMEEEMEEEQEEEEEKQEEEKEEMEEEQ 131 Query: 71 QLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTKLFRIFEPRQ 130 + +E ++E QKE E +K E E +++ E+ E ++ K E ++ Sbjct: 132 KEMEEQMEEQEEQKEEMEEEQKKLEQELEELEEEMEEQEEEMEEMEEEMEKQQEEMEEQE 191 Query: 131 LPIYRANGEKE 141 EKE Sbjct: 192 EEKEEQQEEKE 202 Score = 103 (47.2 bits), Expect = 1.6e-05, P = 1.6e-05 Identities = 21/68 (30%), Positives = 39/68 (57%) Query: 18 DRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLK 77 + M+E+++E ++ M+ + + ++EE + QEE + E K+ KEE +Q E K Sbjct: 164 EEMEEQEEEMEEMEEEMEKQQEEMEEQEEEKEEQQEEKEEEQEEKEEQKEEQEQEQEEQK 223 Query: 78 TKEEHQKE 85 +EE Q+E Sbjct: 224 QQEEEQEE 231 Score = 101 (46.3 bits), Expect = 3.0e-05, P = 3.0e-05 Identities = 27/131 (20%), Positives = 66/131 (50%) Query: 11 EADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESK 70 E + ++ +E ++++++ + + ++ ++EE + +EE++ E ++ +EE K Sbjct: 65 EKEEEMEEKEEEMEEQEEEMEEQKEEQEEKQEEQEEEQEEMEEEMEEEQEEEEEKQEEEK 124 Query: 71 QLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTKLFRIFEPRQ 130 + +E + + E Q E Q E ++ + E L++LE+ EQ ++ ++ E +Q Sbjct: 125 EEMEEEQKEMEEQMEEQEEQKEEMEEEQKKLEQELEELEEEMEEQEEEMEEMEEEMEKQQ 184 Query: 131 LPIYRANGEKE 141 + EKE Sbjct: 185 EEMEEQEEEKE 195 Score = 98 (44.9 bits), Expect = 7.9e-05, P = 7.9e-05 Identities = 24/93 (25%), Positives = 52/93 (55%) Query: 27 KQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLKTKEEHQKEI 86 K+ +++ ++ + + EE + +E+++ ++ KK +EE ++L E ++ +EE KE Sbjct: 3 KEQMQEQLKELEEEMEELEEEKEEEEEKLQELEKKKKELEEEMEELQEEMEEQEEKMKEE 62 Query: 87 QYEILQKTIPTFEPKESILKKLEDIKPEQAKKQ 119 Q E ++ E E +++E+ K EQ +KQ Sbjct: 63 QEEKEEEMEEKEEEMEEQEEEMEEQKEEQEEKQ 95 Score = 97 (44.4 bits), Expect = 0.00011, P = 0.00011 Identities = 21/99 (21%), Positives = 58/99 (58%) Query: 21 QEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLKTKE 80 +E+++E++ Q + ++ + EE + + +E+ + +E +K ++E ++L E ++ +E Sbjct: 111 EEQEEEEEKQEEEKEEMEEEQKEMEEQMEEQEEQKEEMEEEQKKLEQELEELEEEMEEQE 170 Query: 81 EHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQ 119 E +E++ E+ ++ E +E ++ E+ + EQ +K+ Sbjct: 171 EEMEEMEEEMEKQQEEMEEQEEEKEEQQEEKEEEQEEKE 209 Score = 96 (44.0 bits), Expect = 0.00015, P = 0.00015 Identities = 22/104 (21%), Positives = 58/104 (55%) Query: 18 DRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLK 77 +++QE + +K++ M+ + + ++EE + + QEE + E K+ EE ++ +E K Sbjct: 29 EKLQELEKKKKELEEEMEELQEEMEEQEEKMKEEQEEKEEEMEEKEEEMEEQEEEMEEQK 88 Query: 78 TKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTK 121 ++E ++E Q E ++ E ++ ++ ++ + E+ +++ K Sbjct: 89 EEQEEKQEEQEEEQEEMEEEMEEEQEEEEEKQEEEKEEMEEEQK 132 Score = 93 (42.6 bits), Expect = 0.00040, P = 0.00040 Identities = 18/74 (24%), Positives = 45/74 (60%) Query: 20 MQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLKTK 79 ++E ++E ++Q M+ ++ + K++E + + +EE + + E K+ +EE ++ E + + Sbjct: 159 LEELEEEMEEQEEEMEEMEEEMEKQQEEMEEQEEEKEEQQEEKEEEQEEKEEQKEEQEQE 218 Query: 80 EEHQKEIQYEILQK 93 +E QK+ + E +K Sbjct: 219 QEEQKQQEEEQEEK 232 Score = 91 (41.7 bits), Expect = 0.00077, P = 0.00077 Identities = 22/119 (18%), Positives = 64/119 (53%) Query: 4 RKRGATVEADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKK 63 +K+ E + + ++++ K++Q + + ++ + EE + +E+ + ++E ++ Sbjct: 37 KKKELEEEMEELQEEMEEQEEKMKEEQEEKEEEMEEKEEEMEEQEEEMEEQKEEQEEKQE 96 Query: 64 STKEESKQLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTKL 122 +EE +++ E ++ ++E ++E Q E ++ + E +++ E+ K E ++Q KL Sbjct: 97 EQEEEQEEMEEEMEEEQEEEEEKQEEEKEEMEEEQKEMEEQMEEQEEQKEEMEEEQKKL 155 Score = 88 (40.3 bits), Expect = 0.0020, P = 0.0020 Identities = 23/109 (21%), Positives = 55/109 (50%) Query: 11 EADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESK 70 E + M+EK++E ++Q M+ + +K+E + QEE++ E ++ +EE + Sbjct: 61 EEQEEKEEEMEEKEEEMEEQEEEMEEQKEEQEEKQEEQEEEQEEMEEEMEEEQEEEEEKQ 120 Query: 71 QLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQ 119 + + +E+ + E Q E ++ E ++ L++ + E+ ++Q Sbjct: 121 EEEKEEMEEEQKEMEEQMEEQEEQKEEMEEEQKKLEQELEELEEEMEEQ 169 Score = 87 (39.8 bits), Expect = 0.0028, P = 0.0028 Identities = 25/121 (20%), Positives = 62/121 (51%) Query: 21 QEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLKTKE 80 +EK++E++ + ++ + EE+ + +E+ + E ++ +EE ++ E ++ +E Sbjct: 22 EEKEEEEEKLQELEKKKKELEEEMEELQEEMEEQEEKMKEEQEEKEEEMEEKEEEMEEQE 81 Query: 81 EHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTKLFRIFEPRQLPIYRANGEK 140 E +E + E +K E +E + +++E+ + E+ +KQ + E Q + E+ Sbjct: 82 EEMEEQKEEQEEKQEEQEEEQEEMEEEMEEEQEEEEEKQEEEKEEMEEEQKEMEEQMEEQ 141 Query: 141 E 141 E Sbjct: 142 E 142 Score = 86 (39.4 bits), Expect = 0.0039, P = 0.0039 Identities = 21/119 (17%), Positives = 63/119 (52%) Query: 1 MAYRKRGATVEADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDE 60 M +K + + ++ + +++ +++Q + ++ + EE + +E+++ ++E Sbjct: 84 MEEQKEEQEEKQEEQEEEQEEMEEEMEEEQEEEEEKQEEEKEEMEEEQKEMEEQMEEQEE 143 Query: 61 VKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQ 119 K+ +EE K+L + L+ EE +E + E+ + + +E + ++ E+ + +Q +K+ Sbjct: 144 QKEEMEEEQKKLEQELEELEEEMEEQEEEMEEMEEEMEKQQEEMEEQEEEKEEQQEEKE 202 Score = 84 (38.5 bits), Expect = 0.0074, P = 0.0074 Identities = 20/105 (19%), Positives = 59/105 (56%) Query: 23 KDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLKTKEEH 82 K+++++ + + +++ ++EE+ +E+ + ++E ++ +E +++ E + +EE Sbjct: 60 KEEQEEKEEEMEEKEEEMEEQEEEMEEQKEEQEEKQEEQEEEQEEMEEEMEEEQEEEEEK 119 Query: 83 QKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTKLFRIFE 127 Q+E + E+ ++ E E ++ E+++ EQ K + +L + E Sbjct: 120 QEEEKEEMEEEQKEMEEQMEEQEEQKEEMEEEQKKLEQELEELEE 164 Score = 83 (38.0 bits), Expect = 0.010, P = 0.010 Identities = 19/102 (18%), Positives = 56/102 (54%) Query: 18 DRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLK 77 + +E++++ Q+ + + ++ + + +E + + +E++K E K+ EE ++ +E + Sbjct: 22 EEKEEEEEKLQELEKKKKELEEEMEELQEEMEEQEEKMKEEQEEKEEEMEEKEEEMEEQE 81 Query: 78 TKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQ 119 + E QKE Q E ++ E E +++ ++ + E+ +++ Sbjct: 82 EEMEEQKEEQEEKQEEQEEEQEEMEEEMEEEQEEEEEKQEEE 123 Score = 81 (37.1 bits), Expect = 0.020, P = 0.019 Identities = 19/109 (17%), Positives = 58/109 (53%) Query: 11 EADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESK 70 E + + +E ++E+++ +M+ ++ + EE ++E++ +E + +EE + Sbjct: 115 EEEEKQEEEKEEMEEEQKEMEEQMEEQEEQKEEMEEEQKKLEQELEELEEEMEEQEEEME 174 Query: 71 QLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQ 119 ++ E ++ ++E +E + E ++ E +E ++ E+ + EQ +++ Sbjct: 175 EMEEEMEKQQEEMEEQEEEKEEQQEEKEEEQEEKEEQKEEQEQEQEEQK 223 Score = 80 (36.6 bits), Expect = 0.027, P = 0.027 Identities = 17/67 (25%), Positives = 38/67 (56%) Query: 18 DRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLK 77 + M+E ++E + Q M+ ++ +++E + QEE + + E ++ +EE KQ E + Sbjct: 171 EEMEEMEEEMEKQQEEMEEQEEEKEEQQEEKEEEQEEKEEQKEEQEQEQEEQKQQEEEQE 230 Query: 78 TKEEHQK 84 K++ +K Sbjct: 231 EKKKQKK 237 Score = 77 (35.3 bits), Expect = 0.071, P = 0.069 Identities = 21/109 (19%), Positives = 53/109 (48%) Query: 11 EADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESK 70 E + M+E+ E ++Q + + + ++++ + EE++ E ++ EE + Sbjct: 118 EKQEEEKEEMEEEQKEMEEQMEEQEEQKEEMEEEQKKLEQELEELEEEMEEQEEEMEEME 177 Query: 71 QLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQ 119 + +E + + E Q+E + E ++ E KE ++ E + EQ +++ Sbjct: 178 EEMEKQQEEMEEQEEEKEEQQEEKEEEQEEKEEQKEEQEQEQEEQKQQE 226 Score = 76 (34.8 bits), Expect = 0.098, P = 0.094 Identities = 18/109 (16%), Positives = 60/109 (55%) Query: 11 EADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESK 70 E + + +EK++ +++Q + ++ +KEE+ + ++ + +E+++ +E+ + Sbjct: 112 EQEEEEEKQEEEKEEMEEEQKEMEEQMEEQEEQKEEMEEEQKKLEQELEELEEEMEEQEE 171 Query: 71 QLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQ 119 ++ E+ + E+ Q+E++ + +K E +E +K E + ++ +++ Sbjct: 172 EMEEMEEEMEKQQEEMEEQEEEKEEQQEEKEEEQEEKEEQKEEQEQEQE 220 >PD000422 p99.2 (108) TOP1(17) NFH(4) Q20007(3) // PROTEIN TOPOISOMERASE I DNA ISOMERASE REPEAT DNABINDING INTERMEDIATE FILAMENT HEPTAD Length = 805 Score = 91 (41.7 bits), Expect = 0.0010, P = 0.0010 Identities = 32/123 (26%), Positives = 54/123 (43%) Query: 32 NRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLKTKEEHQKEIQYEIL 91 N + SD + KKE+ ++ K +++ K TKE+SK+ E+ +KE E Sbjct: 542 NPKKPSDDLFEKKEKDKEPKPKKEKHKEKAKPKTKEKSKKSSNSKAKSEKEKKEKSKEKK 601 Query: 92 QKTIPTFEPKESILKKLEDIKPEQAKKQTKLFRIFEPRQLPIYRANGEKELRNRWYWKLK 151 K K+ KK E+ PE K+ K + + P + E + ++ K K Sbjct: 602 PKPKKKEAKKKKESKKKEEKPPESKSKKEKKEKESPEKSKPEEKEKKESKKKSSKPSKSK 661 Query: 152 KDT 154 K+T Sbjct: 662 KET 664 >PD140913 p99.2 (1) YMT4_YEAST // HYPOTHETICAL 55.4 KD PROTEIN IN MCM1NUP116 INTERGENIC REGION Length = 434 Score = 56 (25.6 bits), Expect = 0.0011, Sum P(5) = 0.0011 Identities = 13/58 (22%), Positives = 31/58 (53%) Query: 62 KKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQ 119 K+ T+ +Q ++ + +EE ++E E ++K + K+ ++ K + +AKK+ Sbjct: 187 KRVTRSTRQQAIDASEEEEEEEEEKVQEAVRKRPQRTKTKKVVVSKTKPNPKTKAKKE 244 Score = 44 (20.2 bits), Expect = 0.0011, Sum P(5) = 0.0011 Identities = 7/26 (26%), Positives = 17/26 (65%) Query: 4 RKRGATVEADINNNDRMQEKDDEKQD 29 +K ++AD+ + R +E+ +E++D Sbjct: 12 KKANEDIDADMESEARDREQSEEEED 37 Score = 40 (18.3 bits), Expect = 0.0011, Sum P(5) = 0.0011 Identities = 12/52 (23%), Positives = 24/52 (46%) Query: 317 LWDTITTSNYILARSVVPDLKELVSTEAQIQKMSQDLQLEALTIQSETQFLT 368 L D + N +L + + + VS + + + +LQ+ T S +F+T Sbjct: 301 LEDKLAGINKLLCDVLCSAINQAVSIKDDFEIILDELQIALDTRGSRNEFIT 352 Score = 38 (17.4 bits), Expect = 0.0011, Sum P(5) = 0.0011 Identities = 8/28 (28%), Positives = 16/28 (57%) Query: 44 KEEVVTDSQEEIKIRDEVKKSTKEESKQ 71 +EE V + +EE + + + T+ S+Q Sbjct: 140 EEEYVEEEEEENEPEKKAIRPTRSSSRQ 167 Score = 36 (16.5 bits), Expect = 0.0083, Sum P(6) = 0.0083 Identities = 8/28 (28%), Positives = 16/28 (57%) Query: 213 QDEETEGAVRRFIAEMRQRVQADRNVVN 240 ++EE E V+ + + QR + + VV+ Sbjct: 204 EEEEEEEKVQEAVRKRPQRTKTKKVVVS 231 Score = 35 (16.0 bits), Expect = 0.0011, Sum P(5) = 0.0011 Identities = 5/22 (22%), Positives = 12/22 (54%) Query: 651 HIFDVARVPDDQMYRLRDRLRL 672 HI+ +PD + ++L + + Sbjct: 390 HIYSYQFIPDTEDWQLEQNMEI 411 Score = 35 (16.0 bits), Expect = 0.0083, Sum P(6) = 0.0083 Identities = 10/30 (33%), Positives = 13/30 (43%) Query: 189 ENKNSRDAGKVVDSETASICDAIFQDEETE 218 E NS +V S DA ++EE E Sbjct: 179 EGGNSNKRKRVTRSTRQQAIDASEEEEEEE 208 >PD001891 p99.2 (39) GRPE(22) // HEAT SHOCK PROTEIN CHAPERONE GRPE HOMOLOG PRECURSOR MITOCHONDRION TRANSIT PEPTIDE Length = 189 Score = 81 (37.1 bits), Expect = 0.017, P = 0.017 Identities = 22/112 (19%), Positives = 52/112 (46%) Query: 16 NNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEV 75 N + ++E+++E+Q++ + Q ++V + EE+ + +E + +E+K + Sbjct: 4 NAENLEEENEEEQEEESEEQEEEEVQEETEELEEELEELEEELEELKDKYLRLQAEFENY 63 Query: 76 LKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTKLFRIFE 127 K + +E + +QK + P L++ PE A K ++ + E Sbjct: 64 RKRTQREMEEAKKYAVQKLLKDLLPVLDNLERALSAVPESASKNEEVKSLVE 115 >PD000023 p99.2 (401) TPM1(11) Q25893(7) TPM2(6) // PROTEIN REPEAT TROPOMYOSIN COILED COIL ALTERNATIVE SPLICING SIGNAL PRECURSOR CHAIN Length = 210 Score = 81 (37.1 bits), Expect = 0.018, P = 0.018 Identities = 22/104 (21%), Positives = 47/104 (45%) Query: 18 DRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLK 77 ++ +E ++E ++ +MQ +++ K EE ++E + +E K+ EE + + Sbjct: 37 EKKKEMEEELEEMQKKMQKTEEEKEKSEEEKKKEEQEKEEEEEAKEEEAEEEQAAKNRRE 96 Query: 78 TKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTK 121 E +KE + E + E E ++ E K E+ + K Sbjct: 97 QLAEEEKEKKEERQESAKQKAEEAEKAAEESERKKKEEESEAAK 140 Score = 79 (36.2 bits), Expect = 0.035, P = 0.035 Identities = 23/120 (19%), Positives = 55/120 (45%) Query: 2 AYRKRGATVEADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEV 61 A +R E + + QE +K ++ + + K+EE +EE K ++E Sbjct: 91 AKNRREQLAEEEKEKKEERQESAKQKAEEAEKAAEESERKKKEEESEAAKEEEKKAKEEE 150 Query: 62 KKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTK 121 K+ +EE ++ E + +++ +KE + + ++ + + K+ ++ E+ K+ K Sbjct: 151 KEKEEEEEEKAEEKKEAEKQAKKEAEEKAKEEAEAKKAEEAAKAKEEKESVAEKTKEAEK 210 Score = 76 (34.8 bits), Expect = 0.093, P = 0.089 Identities = 19/101 (18%), Positives = 53/101 (52%) Query: 21 QEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLKTKE 80 QEK++E++ + + +++E++ + +E+ + R E K EE+++ E + K+ Sbjct: 72 QEKEEEEEAKEEEAEEEQAAKNRREQLAEEEKEKKEERQESAKQKAEEAEKAAEESERKK 131 Query: 81 EHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTK 121 + ++ + +K E ++ ++ + + ++A+KQ K Sbjct: 132 KEEESEAAKEEEKKAKEEEKEKEEEEEEKAEEKKEAEKQAK 172 Score = 76 (34.8 bits), Expect = 0.093, P = 0.089 Identities = 18/111 (16%), Positives = 61/111 (54%) Query: 11 EADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESK 70 E + + ++ +E+ ++++++ + + +++ + K ++EE + ++E ++S K++++ Sbjct: 59 EKEKSEEEKKKEEQEKEEEEEAKEEEAEEEQAAKNRREQLAEEEKEKKEERQESAKQKAE 118 Query: 71 QLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTK 121 + + + E +KE + E ++ + +E ++ E+ K E+ K+ K Sbjct: 119 EAEKAAEESERKKKEEESEAAKEEEKKAKEEEKEKEEEEEEKAEEKKEAEK 169 >PD074905 p99.2 (1) O42263_XENLA // KINESINRELATED PROTEIN MOTOR PROTEIN MICROTUBULES ATPBINDING COILED COIL Length = 161 Score = 75 (34.3 bits), Expect = 0.019, Sum P(2) = 0.019 Identities = 16/46 (34%), Positives = 27/46 (58%) Query: 310 LHDNFESLWDTITTSNYILARSVVPDLKELVSTEAQIQKMSQDLQL 355 L D+ + +++ + N IL ++ LK T+AQ+QK Q+LQL Sbjct: 85 LKDDLQQKLESLLSENIILKENIDTTLKHHSDTQAQLQKTQQELQL 130 Score = 38 (17.4 bits), Expect = 0.019, Sum P(2) = 0.019 Identities = 7/41 (17%), Positives = 22/41 (53%) Query: 16 NNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIK 56 N ++ +EK + +N++++ K + + D Q++++ Sbjct: 54 NQYLLERLQEEKLELSNKLEILQKEMETSVLLKDDLQQKLE 94 >PD031168 p99.2 (3) O06969(1) P54(1) US45(1) // PROTEIN PRECURSOR SIGNAL P54 CELL WALL SECRETED Length = 148 Score = 64 (29.3 bits), Expect = 0.027, Sum P(2) = 0.027 Identities = 15/62 (24%), Positives = 30/62 (48%) Query: 20 MQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEVLKTK 79 ++ +D E + + K + + V D+ +++ + E TKEE K+L + +K Sbjct: 34 IEAQDKEITELQENQAKAQKQIKDLNDKVLDTSNKVEDKKEENDKTKEEIKKLKKEIKET 93 Query: 80 EE 81 EE Sbjct: 94 EE 95 Score = 47 (21.5 bits), Expect = 0.027, Sum P(2) = 0.027 Identities = 9/25 (36%), Positives = 18/25 (72%) Query: 337 KELVSTEAQIQKMSQDLQLEALTIQ 361 KE+ TE +I+K ++ L+ +A ++Q Sbjct: 88 KEIKETEERIEKRNETLKKQARSLQ 112 >PD107575 p99.2 (1) YN8V_YEAST // HYPOTHETICAL 36.4 KD PROTEIN IN POP2HOL1 INTERGENIC REGION Length = 80 Score = 74 (33.9 bits), Expect = 0.053, P = 0.051 Identities = 16/75 (21%), Positives = 42/75 (56%) Query: 16 NNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDEVKKSTKEESKQLLEV 75 N+D DE+ DQ+N + + K +S K+++ + E+I+ +E +++ ++ +V Sbjct: 6 NSDFEDFSSDEETDQHNVLIQTKKKISSKDDIFSKKVEDIESENESDIEEEQKQEEKEDV 65 Query: 76 LKTKEEHQKEIQYEI 90 + +E+ +++ E+ Sbjct: 66 EQPDKENGEKLDREV 80 Parameters: E=0.1 B=500 V=500 -ctxfactor=1.00 Query ----- As Used ----- ----- Computed ---- Frame MatID Matrix name Lambda K H Lambda K H +0 0 BLOSUM62 0.317 0.134 0.370 same same same Query Frame MatID Length Eff.Length E S W T X E2 S2 +0 0 881 881 0.10 77 3 11 22 0.20 34 Statistics: Query Expected Observed HSPs HSPs Frame MatID High Score High Score Reportable Reported +0 0 67 (30.7 bits) 1972 (903.1 bits) 46 46 Query Neighborhd Word Excluded Failed Successful Overlaps Frame MatID Words Hits Hits Extensions Extensions Excluded +0 0 17991 30225742 5859552 24306066 60098 1958 Database: prodom_99_2 Release date: unknown Posted date: 10:12 PM EDT Jul 29, 1999 # of letters in database: 18,560,502 # of sequences in database: 157,167 # of database sequences satisfying E: 9 No. of states in DFA: 569 (56 KB) Total size of DFA: 230 KB (256 KB) Time to generate neighborhood: 0.02u 0.00s 0.02t Real: 00:00:00 Time to search database: 40.91u 0.04s 40.95t Real: 00:00:41 Total cpu time: 40.95u 0.06s 41.01t Real: 00:00:42 --- END of BLASTP output --- ------------------------------------------------------------ --- --- Again: these results were obtained based on the domain data- --- base collected by Daniel Kahn and his coworkers in Toulouse. --- --- PLEASE quote: --- F Corpet, J Gouzy, D Kahn (1998). The ProDom database --- of protein domain families. Nucleic Ac Res 26:323-326. --- --- The general WWW page is on: ---- --------------------------------------- --- http://www.toulouse.inra.fr/prodom.html ---- --------------------------------------- --- --- For WWW graphic interfaces to PRODOM, in particular for your --- protein family, follow the following links (each line is ONE --- single link for your protein!!): --- http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD008866 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD008866 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD008866 ==> graphical output of all proteins having domain PD008866 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD000002 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD000002 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD000002 ==> graphical output of all proteins having domain PD000002 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD000422 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD000422 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD000422 ==> graphical output of all proteins having domain PD000422 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD140913 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD140913 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD140913 ==> graphical output of all proteins having domain PD140913 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD001891 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD001891 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD001891 ==> graphical output of all proteins having domain PD001891 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD000023 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD000023 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD000023 ==> graphical output of all proteins having domain PD000023 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD074905 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD074905 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD074905 ==> graphical output of all proteins having domain PD074905 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD031168 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD031168 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD031168 ==> graphical output of all proteins having domain PD031168 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD107575 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD107575 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD107575 ==> graphical output of all proteins having domain PD107575 --- --- NOTE: if you want to use the link, make sure the entire line --- is pasted as URL into your browser! --- --- END of PRODOM --- ------------------------------------------------------------ ________________________________________________________________________________ The alignment that has been used as input to the network is: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________________________________________________________ --- --- Version of database searched for alignment: --- SWISS-PROT release 38.0 (7/99) with 80000 proteins --- --- ------------------------------------------------------------ --- MAXHOM multiple sequence alignment --- ------------------------------------------------------------ --- --- MAXHOM ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY --- ID : identifier of aligned (homologous) protein --- STRID : PDB identifier (only for known structures) --- PIDE : percentage of pairwise sequence identity --- WSIM : percentage of weighted similarity --- LALI : number of residues aligned --- NGAP : number of insertions and deletions (indels) --- LGAP : number of residues in all indels --- LSEQ2 : length of aligned sequence --- ACCNUM : SwissProt accession number --- NAME : one-line description of aligned protein --- --- MAXHOM ALIGNMENT HEADER: SUMMARY ID STRID IDE WSIM LALI NGAP LGAP LEN2 ACCNUM NAME vp2_rotbu 100 100 881 0 0 881 P17462 RNA-BINDING PROTEIN VP2 ( vp2_rotbr 98 99 880 1 1 880 P12472 RNA-BINDING PROTEIN VP2 ( vp2_rots1 92 95 879 3 4 881 P22672 RNA-BINDING PROTEIN VP2 ( vp2_rothw 91 95 880 3 11 890 P11231 RNA-BINDING PROTEIN VP2 ( vp2_rotpc 46 66 863 7 25 872 P26191 RNA-BINDING PROTEIN VP2 ( --- --- MAXHOM ALIGNMENT: IN MSF FORMAT MSF of: /home/phd/server/work/predict_h11817647.hsspFilter from: 1 to: 881 /home/phd/server/work/predict_h11817647.msfRet MSF: 881 Type: P 23-Dec-99 04:36:5 Check: 448 .. Name: predict_h1180 Len: 881 Check: 1498 Weight: 1.00 Name: vp2_rotbu Len: 881 Check: 1498 Weight: 1.00 Name: vp2_rotbr Len: 881 Check: 440 Weight: 1.00 Name: vp2_rots1 Len: 881 Check: 8116 Weight: 1.00 Name: vp2_rothw Len: 881 Check: 9800 Weight: 1.00 Name: vp2_rotpc Len: 881 Check: 9096 Weight: 1.00 // 1 50 predict_h1180 MAYRKRGATV EADINNNDRM QEKDDEKQDQ NNRMQLSDKV LSKKEEVVTD vp2_rotbu MAYRKRGATV EADINNNDRM QEKDDEKQDQ NNRMQLSDKV LSKKEEVVTD vp2_rotbr MAYRKRGARR EANINNNDRM QEKDDEKQDQ NNRMQLSDKV LSKKEEVVTD vp2_rots1 MAYRKRGARR ETNLKQDERM QEKEDSKNIN NdkSQLSEKV LSKKEEIITD vp2_rothw MAYRKRGAKR ENLPQQNERL QEKEIEKDvn NRKQQLSDKV LSQKEEIITD vp2_rotpc MISRNRRRNT QQKDAEKEKQ TENVEEKEIK EAKEQVKDEK QVITEENVDS 51 100 predict_h1180 SQEEIKIRDE VKKSTKEESK QLLEVLKTKE EHQKEIQYEI LQKTIPTFEP vp2_rotbu SQEEIKIRDE VKKSTKEESK QLLEVLKTKE EHQKEIQYEI LQKTIPTFEP vp2_rotbr SQEEIKIADE VKKSTKEESK QLLEVLKTKE EHQKEIQYEI LQKTIPTFEP vp2_rots1 NQEEVKISDE VKKSNKEESK QLLEVLKTKE EHQKEVQYEI LQKTIPTFEP vp2_rothw AQDDIKIAGE IKKSSKEESK QLLEILKTKE DHQKEIQYEI LQKTIPTFES vp2_rotpc PKDVKEQSNT VNLQKNDLVK EVINilNTIV AENKVEIEEV VKKYIPSYST 101 150 predict_h1180 KESILKKLED IKPEQAKKQT KLFRIFEPRQ LPIYRANGEK ELRNRWYWKL vp2_rotbu KESILKKLED IKPEQAKKQT KLFRIFEPRQ LPIYRANGEK ELRNRWYWKL vp2_rotbr KESILKKLED IKPEQAKKQT KLFRIFEPRQ LPIYRANGEK ELRNRWYWKL vp2_rots1 KESILKKLED IKPEQAKKQT KLFRIFEPKQ LPIYRANGER ELRNRWYWKL vp2_rothw KESILKKLED IRPEQAKKQM KLFRIFEPKQ LPIYRANGEK ELRNRWYWKL vp2_rotpc DKLIVKNYRN SRIK.CQTYN KLFRLLHVKS Y.LYDVNGEK KLSTRWYWKL 151 200 predict_h1180 KKDTLPDGDY DVREYFLNLY DQVLTEMPDY LLLKDMAVEN KNSRDAGKVV vp2_rotbu KKDTLPDGDY DVREYFLNLY DQVLTEMPDY LLLKDMAVEN KNSRDAGKVV vp2_rotbr KKDTLPDGDY DVREYFLNLY DQVLTEMPDY LLLKDMAVEN KNSRDAGKVV vp2_rots1 KRDTLPDGDY DVREYFLNLY DQVLMEMPDY LLLKDMAVEN KNSRDAGKVV vp2_rothw KKDTLPDGDY DVREYFLNLY DQILIEMPDY LLLKDMAVEN KNSRDAGKVV vp2_rotpc LKDDLPAGDY SVRQFFLSLY LNVLDEMPDY VMLRDMAVDN PYSAEAGKIV 201 250 predict_h1180 DSETASICDA IFQDEETEGA VRRFIAEMRQ RVQADRNVVN YPSILHPIDY vp2_rotbu DSETASICDA IFQDEETEGA VRRFIAEMRQ RVQADRNVVN YPSILHPIDY vp2_rotbr DSETASICDA IFQDEETEGA VRRFIAEMRQ RVQADRNVVN YPSILHPIDY vp2_rots1 DSETAAICDA IFQDE.EPKA VRRFIAEMRQ RVQADRNVVN YPSILHPIDH vp2_rothw DSETANICDA IFQDEETEGV VRRFIADMRQ QVQADRNIVN YPSILHPIDH vp2_rotpc DEKSKEILVE IYQDQMTEGY IRRYMSDLRH RISGETNTAK YPAILHPVDE 251 300 predict_h1180 AFNEYFLQHQ LVEPLNNDII FNYIPERIRN DVNYILNMDR NLPSTARYIR vp2_rotbu AFNEYFLQHQ LVEPLNNDII FNYIPERIRN DVNYILNMDR NLPSTARYIR vp2_rotbr AFNEYFLQHQ LVEPLNNDII FNYIPERIRN DVNYILNMDR NLPSTARYIR vp2_rots1 AFNEYFLQHQ LVEPLNNVYI FNYIPERIRN DVNYILNMDR NLPSTARYIR vp2_rothw AFNEYFLNHQ LVEPLNNEII FNYIPERIRN DVNYILNMDM NLPSTARYIR vp2_rotpc ELNKYFLEHQ LIQPLTTRNI AELIPTQLYH DPNYVFNIDA AFLTNSRFVP 301 350 predict_h1180 PNLLQDRLNL HDNFESLWDT ITTSNYILAR SVVPDLKELV STEAQIQKMS vp2_rotbu PNLLQDRLNL HDNFESLWDT ITTSNYILAR SVVPDLKELV STEAQIQKMS vp2_rotbr PNLLQDRLNL HDNFESLWDT ITTSNYILAR SVVPDLKELV STEAQIQKMS vp2_rots1 PNLLQDRLNL HDNFESLWDT ITTSNYILAR SVVPDLKELV STEAQIQKMS vp2_rothw PNLLQDRLNL HDNFESLWDT ITTSNYILAR SVVPDLkeLV STEAQIQKMS vp2_rotpc PYLTQDRIGL HDGFESIWDA KTHADYVSAR RFVPDLTELV DAEKQMKEML 351 400 predict_h1180 QDLQLEALTI QSETQFLTGI NSQAANDCFK TLIAAMLSQR TMSLDFVTTN vp2_rotbu QDLQLEALTI QSETQFLTGI NSQAANDCFK TLIAAMLSQR TMSLDFVTTN vp2_rotbr QDLQLEALTI QSETQFLTGI NSQAANDCFK TLIAAMLSQR TMSLDFVTTN vp2_rots1 QDLQLEALTI QSETQFLTGI NSQAANDCFK TLIAAMLSQR TMSLDFVTTN vp2_rothw QDLQLEALTI QSETQFLAGI NSQAANDCFK TLIAAMLSQR TMSLDFVTTN vp2_rotpc QC....KLNH NSWQELVHGR .....NEAFK FIIGTVLSTR TIAVEFITSN 401 450 predict_h1180 YMSLISGMWL LTVVPNDMFI RESLVACQLA IVNTIIYPAF GMQRMHYRNG vp2_rotbu YMSLISGMWL LTVVPNDMFI RESLVACQLA IVNTIIYPAF GMQRMHYRNG vp2_rotbr YMSLISGMWL LTVVPNDMFI RESLVACQLA IVNTIIYPAF GMQRMHYRNG vp2_rots1 YMSLISGMWL LTVIPNDMFI RESLVACQLA IINTIVYPAF GMQRMHYRNG vp2_rothw YMSLISGMWL LTVIPNDMFL RESLVACELA IINTIVYPAF GMQRMHYRNG vp2_rotpc YMSLASCMYL MTIMPSEIFL RESLVAMQLA VINTLIYPAL GLAQMHYQAG 451 500 predict_h1180 DPQTPFQIAE QQIRKFSGSG IGWHFVNNNQ FRQVVIDGVL NQVLNDNIRN vp2_rotbu DPQTPFQIAE QQIRKFSGSG IGWHFVNNNQ FRQVVIDGVL NQVLNDNIRN vp2_rotbr DPQRPFQIAE QQIQNFQVAN W.LHFVNNNQ FRQVVIDGVL NQVLNDNIRN vp2_rots1 DPQTPFQIAE QQIQNFQVAN W.LHFVNYNQ FRQVVIDGVL NQVLNDNIRN vp2_rothw DPQTPFQIAE QQIQNFQVAN W.LHFINNNR FRQVVIDGVL NQTLNDNIRN vp2_rotpc EIRreMQVAN RPIRQWL... ...HHCNTLQ FGRQVTEGVT HLRFTNDIMT 501 550 predict_h1180 VHVIKQLMQA LMQLSRQQFP TMPVDYKRSI QRGILLLSNR LGQLVDLTRL vp2_rotbu VHVIKQLMQA LMQLSRQQFP TMPVDYKRSI QRGILLLSNR LGQLVDLTRL vp2_rotbr GHVINQLMEA LMQLSRQQFP TMPVDYKRSI QRGILLLSNR LGQLVDLTRL vp2_rots1 GHVVNQLMEA LMQLSRQQFP TMPVDYKRSI QRGIFLLSNR LGQLVDLTRL vp2_rothw GQVINQLMEA LMQLSRQQFP TMPVDYKRSI QRGILLLSNR LGQLVDLTRL vp2_rotpc GRIVNLFSTM LVALSSQPFA TYPLDYKRSV QRALQLLSNR TAQIADLTRL 551 600 predict_h1180 LAYNYETLMA CVTMNMQHVQ TLTTEKLQLT SVTSLCMLIG NATVIPSPQT vp2_rotbu LAYNYETLMA CVTMNMQHVQ TLTTEKLQLT SVTSLCMLIG NATVIPSPQT vp2_rotbr LAYNYETLMA CVTMNMQHVQ TLTTEKLQLT SVTSLCMLIG NATVIPSPQT vp2_rots1 LSYINETLMA CITMNMQHVQ TLTTEKLQLT SVTSLCMLIG NATVIPSPQT vp2_rothw VSYNYETLMA CVTMNMQHVQ TLTTEKLQLT SVTSLCMLIG NTTVIPSPQT vp2_rotpc IVYNYTTLSA CIVMNMHLVG TLTVERIQAT ALTSLIMLIS NKTVIPEPSS 601 650 predict_h1180 LFHYYNVNVN FHSNYNERIN DAVAIITAAN RLNLYQKKMK AIVEDFLKRL vp2_rotbu LFHYYNVNVN FHSNYNERIN DAVAIITAAN RLNLYQKKMK AIVEDFLKRL vp2_rotbr LFHYYNVNVN FHSNYNERIN DAVAIITGAN RLNLYQKKMK AIVEDFLKRL vp2_rots1 LFHYYNVNVN FHSNYNERIN DAVAIITAAN RLNLYQKKMK SIVEDFLKRL vp2_rothw LFHYYNINVN FHSNYNERIN DAVAIITAAN RLNLYQKKMK SIVEDFLKRL vp2_rotpc LFSYFSSNIN FLTNYNEQID NVVAEIMAAY RLDLYQQKML MLVTRFVSRL 651 700 predict_h1180 HIFDVARVPD DQMYRLRDRL RLLPVEVRRL DIFNLILMNM DQIERASDKI vp2_rotbu HIFDVARVPD DQMYRLRDRL RLLPVEVRRL DIFNLILMNM DQIERASDKI vp2_rotbr HIFDVARVPD DQMYRLRDRL RLLPVEVRRL DIFNLILMNM DQIERASDKI vp2_rots1 QIFDVARVPD DQMYRLRDRL RLLPVEIRRL DIFNLIAMNM EQIERASDKI vp2_rothw QIFDVPRVPD DQMYRLRDRL RLLPVERRRL DIFNLILMNM EQIERASDKI vp2_rotpc YIFDAPKIPP DQMYRLRNRL RNIPVERRRA DVFRIIMNNR DLIEKTSERI 701 750 predict_h1180 AQGVIIAYRD MQLERDEMYG YVNIARNLDG FQQINLEELM RTGDYAQITN vp2_rotbu AQGVIIAYRD MQLERDEMYG YVNIARNLDG FQQINLEELM RTGDYAQITN vp2_rotbr AQGVIIAYRD MQLERDEMYG YVNIARNLDG FQQINLEELM RTGDYAQITN vp2_rots1 AQGVIIAYRD MQLERDEMYG YVNIARNLDG FQQINLEELM RSGDYAQITN vp2_rothw AQGVIIAYRD MQLERDEMYG YVNIARNLDG YQQINLEELM RTGDYGQITN vp2_rotpc CQGVLLSYSP MPLTYVEDVG LTNVVNDTNG FQIINIEEIE KTGDYSAITN 751 800 predict_h1180 MLLNNQPVAL VGALPFVTDS SVISLIAKLD ATVFAQIVKL RKVDTLKPIL vp2_rotbu MLLNNQPVAL VGALPFVTDS SVISLIAKLD ATVFAQIVKL RKVDTLKPIL vp2_rotbr MLLNNQPVAL VGALPFVTDS SVISLIANVD ATVFAQIVKL RKVDTLKPIL vp2_rots1 MLLNNQPVAL VGALPFITDS SVISLIAKLD ATVFAQIVKL RKVDTLKPIL vp2_rothw MLLNNQPVAL VGALPFVTDS SVISLIAKLD ATVFAQIVKL RKVDTLKPIL vp2_rotpc ALLRDTPIIL KGAIPYVTNS SVIDVLSKID TTVFASIVKD RDISKLKPIK 801 850 predict_h1180 YKINSDSNDF YLVANYDWVP TSTTKVYKQV PQQFDFRNSM HMLTSNLTFT vp2_rotbu YKINSDSNDF YLVANYDWVP TSTTKVYKQV PQQFDFRNSM HMLTSNLTFT vp2_rotbr YKINSDSNDF YLVANYDWVP TSTTKVYKQV PQQFDFRNSM HMLTSNLTFT vp2_rots1 YKINSDSNDF YLVANYDWIP TSTTKVYKQV PQQFDFRASM HMLTSNLTFT vp2_rothw YKINSDSNDF YLVANYDWIP TSTTKVYKQV PQPFDFRASM HMLTSNLTFT vp2_rotpc FTINSDSSEY YLVHNNKWTP TTTTAVYKAR SQQFNIQHSV SMLESNLFFV 851 881 predict_h1180 VYSDLLAFVS ADTVEPINAV AFDNMRIMNE L vp2_rotbu VYSDLLAFVS ADTVEPINAV AFDNMRIMNE L vp2_rotbr VYSDLLAFVS ADTVEPINAV AFDNMRIMNE L vp2_rots1 VYSDLLAFVS ADTVEPINAV AFDNMRIMNE L vp2_rothw VYSDLLSFVS ADTVEPINAV AFDNMRIMNE L vp2_rotpc VYNDLFKYIK TTTVLPINAV SYDGARIMQE . ________________________________________________________________________________ Result of COILS prediction (Andrei Lupas): ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A Lupas: Methods in Enzymology, 1996, 266, 513-525. version 2.2: Rob B. Russell & Andrei N. Lupas, 1999 ________________________________________________________________________________ --- COILS HEADER: SUMMARY COILS version 2.2: R.B. Russell, A.N. Lupas, 1999 using MTK matrix. weights: a,d=2.5 and b,c,e,f,g=1.0 For the threshold of 5 ( probability > 0.5): window size = 14 0 residues in coiled coil domain window size = 21 0 residues in coiled coil domain window size = 28 28 residues in coiled coil domain . : . : . : . : . 5 seq MAYRKRGATVEADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTD frame-14 aaaaabcdeabcdefgabcabcdefgabcdefgbcdefggabcdefgabc frame-21 aaabcdefgabcdefgabcdefgabcdefgefgabcdefgabcabcdefg frame-28 aaababcdeabcdefgabcabcdefgabcdefgabcdefgabcdefgabc prob-14 ---------111111111111111111111111----------------- prob-21 -------------------------------------------------- prob-28 --------------------------111111111111111111111111 . : . : . : . : . 10 seq SQEEIKIRDEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPTFEP frame-14 defgefabcdeabcdabcdefgabcdefgbcdefggbcdefgfgabcabc frame-21 abcdefgabcdabcabcdefgabcdefgabcdefggbcdefgggefgabc frame-28 defgefgabcdefgabcdefgabcdefgabcdefgdefgefggdefgfgc prob-14 ---------------33333333333333111111--------------- prob-21 -----------1111111111111111111111111-------------- prob-28 1111---55555555555555555555555555551111----------- . : . : . : . : . 15 seq KESILKKLEDIKPEQAKKQTKLFRIFEPRQLPIYRANGEKELRNRWYWKL frame-14 abcdefgabcdefgdefggfggabcdefgbabcdefgabcdefgcdefge frame-21 abcdefgabcdefgabcdefgdefggfgefgbabcdefgabcdefgabcd frame-28 defgabcdefgabcdefgabcdefgefgefggdefgabcdefggcdeaab prob-14 -------------------------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 20 seq KKDTLPDGDYDVREYFLNLYDQVLTEMPDYLLLKDMAVENKNSRDAGKVV frame-14 fgggabcdefgaabcdefgabcdefgabcabcabcdefgabcdefgefga frame-21 efggaabcdefgabcdefgabcdefgabcdefabcabcdefgabcdefga frame-28 cdefgabcdefgabcdefgabcdefgababcdabcabcdefgabcdefga prob-14 -------------------------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 25 seq DSETASICDAIFQDEETEGAVRRFIAEMRQRVQADRNVVNYPSILHPIDY frame-14 bcdefgcdefgababcdefgabcdabcdefgabcdefgbcdefggbcabc frame-21 bcdefgabcdabcdefabcdefgabcdefgabcdefggabcdefgbcabc frame-28 bcdefgabcdefgabcdefgabcdefgdefgabcdefgbcdefggbcdef prob-14 -------------------------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 30 seq AFNEYFLQHQLVEPLNNDIIFNYIPERIRNDVNYILNMDRNLPSTARYIR frame-14 defabcdefgabcdefggdefgababcabcdefgabcdefggbcdefgda frame-21 defgabcdefgabcdefgdefgcdefgabcdefgabcdefgabcdefgga frame-28 gabcdefgabcdefgabcdeabcdefgaabcdefgabcdefgabcdefga prob-14 -------------------------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 35 seq PNLLQDRLNLHDNFESLWDTITTSNYILARSVVPDLKELVSTEAQIQKMS frame-14 bcdabcdefgabcdefgabcdefgeabcabcabcdabcabcdefgabcde frame-21 bcdabcdefgabcdefgabcdefgabcdabcabcdabcdefgabcdefga frame-28 bcdabcdefgabcdefgabcdefgabcdabcdefgabcdefgabcdefga prob-14 --------------------------------------111111111111 prob-21 -----------------------------------111111111111111 prob-28 -----------------------------------222222222222222 . : . : . : . : . 40 seq QDLQLEALTIQSETQFLTGINSQAANDCFKTLIAAMLSQRTMSLDFVTTN frame-14 fgdefgabcdefgcdefgcdeabcdabcdefgabcdefgefggabcdefg frame-21 bcdefgabcdefgabcdefgabcdefggabcdefgabcdefggabcdefg frame-28 bcdefgabcdefgabcdefgabcdefgabcdefggabcdefgabcdefgg prob-14 11------------------------------------------------ prob-21 111111-------------------------------------------- prob-28 2222222222222------------------------------------- . : . : . : . : . 45 seq YMSLISGMWLLTVVPNDMFIRESLVACQLAIVNTIIYPAFGMQRMHYRNG frame-14 abcdefgabcdefgeabcdabcdefgabcdefgdefgbcdefgabcdeab frame-21 abcdefgabcdefgababcdefgabcdefgabcdefggabcabcdefgab frame-28 abcdefgabcdefgabcdefgfgabcdefgabcdefggabcabcdefgab prob-14 -------------------------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 50 seq DPQTPFQIAEQQIRKFSGSGIGWHFVNNNQFRQVVIDGVLNQVLNDNIRN frame-14 cdefgabcdefgabcdefgfggcabcaaabcdefgabcdeabcdefgaba frame-21 cdefgabcabcdefgabcdefgabcdabcdefgababcdeabcdefgabc frame-28 cdefgabcdefgabcdefgabcdefgababcdeababcdeabcdefgabc prob-14 -------------------------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 55 seq VHVIKQLMQALMQLSRQQFPTMPVDYKRSIQRGILLLSNRLGQLVDLTRL frame-14 bcdabcdefgabcdefggfgggabcaabcdefgabcdefgabcdefgefg frame-21 defgabcdefgabcdefgfggdeabaabcdefgabcdefgabcdefgdef frame-28 defgabcdefgabcdefgfggdabcdabcdefgabcdabcdefgabcdef prob-14 ---33333333333333--------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 60 seq LAYNYETLMACVTMNMQHVQTLTTEKLQLTSVTSLCMLIGNATVIPSPQT frame-14 gabcdefgabcdefgabcabcdefgabcdefgefgefgabcdefgbcdef frame-21 gabcdefgabcdefgabcdefgbcdefgabcdefgabcdefgefgfgdef frame-28 gabcdefgabcdefgabcdefgabcdefgefgefgabcdefgefgbcdef prob-14 -------------------------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 65 seq LFHYYNVNVNFHSNYNERINDAVAIITAANRLNLYQKKMKAIVEDFLKRL frame-14 abcdefgaabcabcdefgabcdefabcdefgabcdefgabcdefgdefga frame-21 aabcdefgabcabcdefgabcdefabcdefgabcdefgabcdefgdefga frame-28 aabcabcdefgabcdefgabcabcdefgabcdefgabcdefgabcdefga prob-14 -------------------------------11111111111111----- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 70 seq HIFDVARVPDDQMYRLRDRLRLLPVEVRRLDIFNLILMNMDQIERASDKI frame-14 bcdefgbcdefgabcdefgabcdefgdefabcabcdefgabcdefgabcd frame-21 bcdefgbcdefgabcdefgabcdeaabcabcdabcdefgabcdefgabcd frame-28 bcdefgefgdefabcdefgababcabcdaabcabcdabcabcdefgabcd prob-14 -------------------------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 75 seq AQGVIIAYRDMQLERDEMYGYVNIARNLDGFQQINLEELMRTGDYAQITN frame-14 efgdefgabcdefgabcdefabcdefgabcdefgabcdefggabcdefga frame-21 efgabcdabcdefgabcdefgabcdefgbcdefgaabcdefgabcdefga frame-28 efgabcdefgabcdefgdefgabcdefgbcdefgabcdefgabcdefgab prob-14 -------------------------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 80 seq MLLNNQPVALVGALPFVTDSSVISLIAKLDATVFAQIVKLRKVDTLKPIL frame-14 bcdefgabcdefgaaaababcabcdabcdefgabcdefgdefgbcdefga frame-21 bcdefgefgdefgabcababcdabcabcdefgabcdefgabcdefgefga frame-28 cdefggabcdefgababcabcdefgabcdefgabcdefgabcdefgabcd prob-14 -------------------------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 85 seq YKINSDSNDFYLVANYDWVPTSTTKVYKQVPQQFDFRNSMHMLTSNLTFT frame-14 bcdefgabcdefggfggfgabcdabcabcdefabcdefgabcdefgabab frame-21 bcdefgabcdefgefggfgabcdabaabcdefabcdefgababcdefgab frame-28 efgefgefgdefgdefgfabcdefgabcdefgabcdabcdeabcdefgab prob-14 -------------------------------------------------- prob-21 -------------------------------------------------- prob-28 -------------------------------------------------- . : . : . : . : . 90 seq VYSDLLAFVSADTVEPINAVAFDNMRIMNEL frame-14 cdefgabcdefgcdefaabcdefgabcdefg frame-21 cdefgabcdeabcdefgabcdefgabcdefg frame-28 cdefgabcdefgabcdefgabcdefgcdefg prob-14 ------------------------------- prob-21 ------------------------------- prob-28 ------------------------------- ________________________________________________________________________________ Prediction of: - secondary structure, by PHDsec - solvent accessibility, by PHDacc PHD: Profile fed neural network systems from HeiDelberg ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Author: Burkhard Rost EMBL, Heidelberg, FRG Meyerhofstrasse 1, 69 117 Heidelberg Internet: Predict-Help@EMBL-Heidelberg.DE All rights reserved. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Secondary structure prediction by PHDsec: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Author: Burkhard Rost EMBL, Heidelberg, FRG Meyerhofstrasse 1, 69 117 Heidelberg Internet: Rost@EMBL-Heidelberg.DE All rights reserved. About the network method ~~~~~~~~~~~~~~~~~~~~~~~ The network procedure is described in detail in: 1) Rost, Burkhard; Sander, Chris: Prediction of protein structure at better than 70% accuracy. J. Mol. Biol., 1993, 232, 584-599. A brief description is given in: Rost, Burkhard; Sander, Chris: Improved prediction of protein secondary structure by use of se- quence profiles and neural networks. Proc. Natl. Acad. Sci. U.S.A., 1993, 90, 7558-7562. The PHD mail server is described in: 2) Rost, Burkhard; Sander, Chris; Schneider, Reinhard: PHD - an automatic mail server for protein secondary structure prediction. CABIOS, 1994, 10, 53-60. The latest improvement steps (up to 72%) are explained in: 3) Rost, Burkhard; Sander, Chris: Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 1994, 19, 55-72. To be quoted for publications of PHD output: Papers 1-3 for the prediction of secondary structure and the pre- diction server. About the input to the network ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The prediction is performed by a system of neural networks. The input is a multiple sequence alignment. It is taken from an HSSP file (produced by the program MaxHom: Sander, Chris & Schneider, Reinhard: Database of Homology-Derived Structures and the Structural Meaning of Sequence Alignment. Proteins, 1991, 9, 56-68. For optimal results the alignment should contain sequences with varying degrees of sequence similarity relative to the input protein. The following is an ideal situation: +-----------------+----------------------+ | sequence: | sequence identity | +-----------------+----------------------+ | target sequence | 100 % | | aligned seq. 1 | 90 % | | aligned seq. 2 | 80 % | | ... | ... | | aligned seq. 7 | 30 % | +-----------------+----------------------+ Estimated Accuracy of Prediction ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A careful cross validation test on some 250 protein chains (in total about 55,000 residues) with less than 25% pairwise sequence identity gave the following results: ++================++-----------------------------------------+ || Qtotal = 72.1% || ("overall three state accuracy") | ++================++-----------------------------------------+ +----------------------------+-----------------------------+ | Qhelix (% of observed)=70% | Qhelix (% of predicted)=77% | | Qstrand(% of observed)=62% | Qstrand(% of predicted)=64% | | Qloop (% of observed)=79% | Qloop (% of predicted)=72% | +----------------------------+-----------------------------+ .......................................................................... These percentages are defined by: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | number of correctly predicted residues |Qtotal = --------------------------------------- (*100) | number of all residues | | no of res correctly predicted to be in helix |Qhelix (% of obs) = -------------------------------------------- (*100) | no of all res observed to be in helix | | | no of res correctly predicted to be in helix |Qhelix (% of pred)= -------------------------------------------- (*100) | no of all residues predicted to be in helix .......................................................................... Averaging over single chains ~~~~~~~~~~~~~~~~~~~~~~~~~~~ The most reasonable way to compute the overall accuracies is the above quoted percentage of correctly predicted residues. However, since the user is mainly interested in the expected performance of the prediction for a particular protein, the mean value when averaging over protein chains might be of help as well. Computing first the three state accuracy for each protein chain, and then averaging over 250 chains yields the following average: +-------------------------------====--+ | Qtotal/averaged over chains = 72.2% | +-------------------------------====--+ | standard deviation = 9.3% | +-------------------------------------+ .......................................................................... Further measures of performance ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Matthews correlation coefficient: +---------------------------------------------+ | Chelix = 0.63, Cstrand = 0.53, Cloop = 0.52 | +---------------------------------------------+ .......................................................................... Average length of predicted secondary structure segments: . +------------+----------+ . | predicted | observed | +-----------+------------+----------+ | Lhelix = | 10.3 | 9.3 | | Lstrand = | 5.0 | 5.3 | | Lloop = | 7.2 | 5.9 | +-----------+------------+----------+ .......................................................................... The accuracy matrix in detail: +---------------------------------------+ | number of residues with H, E, L | +---------+------+------+------+--------+ | |net H |net E |net L |sum obs | +---------+------+------+------+--------+ | obs H |12447 | 1255 | 3990 | 17692 | | obs E | 949 | 7493 | 3750 | 12192 | | obs L | 2604 | 2875 |19962 | 25441 | +---------+------+------+------+--------+ | sum Net |16000 |11623 |27702 | 55325 | +---------+------+------+------+--------+ Note: This table is to be read in the following manner: 12447 of all residues predicted to be in helix, were observed to be in helix, 949 however belong to observed strands, 2604 to observed loop regions. The term "observed" refers to the DSSP assignment of secondary structure calculated from 3D coordinates of experimentally determined structures (Dictionary of Secondary Structure of Proteins: Kabsch & Sander (1983) Biopolymers, 22, 2577-2637). Position-specific reliability index ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The network predicts the three secondary structure types using real numbers from the output units. The prediction is assigned by choosing the maximal unit ("winner takes all"). However, the real numbers contain additional information. E.g. the difference between the maximal and the second largest output unit can be used to derive a "reliability index". This index is given for each residue along with the prediction. The index is scaled to have values between 0 (lowest reliability), and 9 (highest). The accuracies (Qtot) to be expected for residues with values above a particular value of the index are given below as well as the fraction of such residues (%res).: +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | index| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | | %res |100.0| 99.2| 90.4| 80.9| 71.6| 62.5| 52.8| 42.3| 29.8| 14.1| +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | | | | | | | | | | | | | Qtot | 72.1| 72.3| 74.8| 77.7| 80.3| 82.9| 85.7| 88.5| 91.1| 94.2| | | | | | | | | | | | | +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | H%obs| 70.4| 70.6| 73.7| 77.1| 80.1| 83.1| 86.0| 89.3| 92.5| 96.4| | E%obs| 61.5| 61.7| 63.7| 66.6| 69.1| 71.7| 74.6| 77.0| 77.8| 68.1| | | | | | | | | | | | | | H%prd| 77.8| 78.0| 80.0| 82.6| 84.7| 86.9| 89.2| 91.3| 93.1| 95.4| | E%prd| 64.5| 64.7| 67.8| 71.0| 74.2| 77.6| 81.4| 85.1| 89.8| 93.5| +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ The above table gives the cumulative results, e.g. 62.5% of all residues have a reliability of at least 5. The overall three-state accuracy for this subset of almost two thirds of all residues is 82.9%. For this subset, e.g., 83.1% of the observed helices are correctly predicted, and 86.9% of all residues predicted to be in helix are correct. .......................................................................... The following table gives the non-cumulative quantities, i.e. the values per reliability index range. These numbers answer the question: how reliable is the prediction for all residues labeled with the particular index i. +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | index| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | | %res | 8.8| 9.5| 9.3| 9.1| 9.7| 10.5| 12.5| 15.7| 14.1| +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | | | | | | | | | | | | Qtot | 46.6| 50.6| 57.7| 62.6| 67.9| 74.2| 82.2| 88.3| 94.2| | | | | | | | | | | | +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | H%obs| 36.8| 42.3| 49.5| 55.2| 61.7| 69.9| 78.8| 87.4| 96.4| | E%obs| 44.7| 44.5| 52.1| 55.4| 60.9| 68.0| 75.9| 81.0| 68.1| | | | | | | | | | | | | H%prd| 49.9| 52.5| 60.3| 64.2| 69.2| 77.5| 85.4| 89.9| 95.4| | E%prd| 41.7| 47.1| 53.6| 57.0| 64.0| 71.6| 78.8| 88.8| 93.5| +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ For example, for residues with Relindex = 5 64% of all predicted betha- strand residues are correctly identified. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Solvent accessibility prediction by PHDacc: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Author: Burkhard Rost EMBL, Heidelberg, FRG Meyerhofstrasse 1, 69 117 Heidelberg Internet: Rost@EMBL-Heidelberg.DE All rights reserved. About the network method ~~~~~~~~~~~~~~~~~~~~~~~ The network for prediction of secondary structure is described in detail in: Rost, Burkhard; Sander, Chris: Prediction of protein structure at better than 70% accuracy. J. Mol. Biol., 1993, 232, 584-599. The analysis of the prediction of solvent exposure is given in: Rost, Burkhard; Sander, Chris: Conservation and prediction of solvent accessibility in protein families. Proteins, 1994, 20, 216-226. To be quoted for publications of PHD exposure prediction: Both papers quoted above. Definition of accessibility ~~~~~~~~~~~~~~~~~~~~~~~~~~ For training the residue solvent accessibility the DSSP (Dictionary of Secondary Structure of Proteins; Kabsch & Sander (1983) Biopolymers, 22, 2577-2637) values of accessible surface area have been used. The prediction provides values for the relative solvent accessibility. The normalisation is the following: | ACCESSIBILITY (from DSSP in Angstrom) |RELATIVE_ACCESSIBILITY = ------------------------------------- * 100 | MAXIMAL_ACC (amino acid type i) where MAXIMAL_ACC (i) is the maximal accessibility of amino acid type i. The maximal values are: +----+----+----+----+----+----+----+----+----+----+----+----+ | A | B | C | D | E | F | G | H | I | K | L | M | | 106| 160| 135| 163| 194| 197| 84| 184| 169| 205| 164| 188| +----+----+----+----+----+----+----+----+----+----+----+----+ | N | P | Q | R | S | T | V | W | X | Y | Z | | 157| 136| 198| 248| 130| 142| 142| 227| 180| 222| 196| +----+----+----+----+----+----+----+----+----+----+----+ Notation: one letter code for amino acid, B stands for D or N; Z stands for E or Q; and X stands for undetermined. The relative solvent accessibility can be used to estimate the number of water molecules (W) in contact with the residue: W = ACCESSIBILITY /10 The prediction is given in 10 states for relative accessibility, with RELATIVE_ACCESSIBILITY = (PREDICTED_ACC * PREDICTED_ACC) where PREDICTED_ACC = 0 - 9. Estimated Accuracy of Prediction ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A careful cross validation test on some 238 protein chains (in total about 62,000 residues) with less than 25% pairwise sequence identity gave the following results: Correlation ........... The correlation between observed and predicted solvent accessibility is: ----------- corr = 0.53 ----------- This value ought to be compared to the worst and best case prediction scenario: random prediction (corr = 0.0) and homology modelling (corr = 0.66). (Note: homology modelling yields a relative accurate prediction in 3D if, and only if, a significantly identical sequence has a known 3D structure.) 3-state accuracy ................ Often the relative accessibility is projected onto, e.g., 3 states: b = buried (here defined as < 9% relative accessibility), i = intermediate ( 9% <= rel. acc. < 36% ), e = exposed ( rel. acc. >= 36% ). A projection onto 3 states or 2 states (buried/exposed) enables the compilation of a 3- and 2-state prediction accuracy. PHD reaches an overall 3-state accuracy of: Q3 = 57.5% (compared to 35% for random prediction and 70% for homology modelling). In detail: +-----------------------------------+-------------------------+ | Qburied (% of observed)=77% | Qb (% of predicted)=60% | | Qintermediate (% of observed)= 9% | Qi (% of predicted)=44% | | Qexposed (% of observed)=78% | Qe (% of predicted)=56% | +-----------------------------------+-------------------------+ 10-state accuracy ................. The network predicts relative solvent accessibility in 10 states, with state i (i = 0-9) corresponding to a relative solvent accessibility of i*i %. The 10-state accuracy of the network is: Q10 = 24.5% .......................................................................... These percentages are defined by: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | number of correctly predicted residues |Q3 = --------------------------------------- (*100) | number of all residues | | no of res. correctly predicted to be buried |Qburied (% of obs) = ------------------------------------------- (*100) | no of all res. observed to be buried | | | no of res. correctly predicted to be buried |Qburied (% of pred)= ------------------------------------------- (*100) | no of all residues predicted to be buried .......................................................................... Averaging over single chains ~~~~~~~~~~~~~~~~~~~~~~~~~~~ The most reasonable way to compute the overall accuracies is the above quoted percentage of correctly predicted residues. However, since the user is mainly interested in the expected performance of the prediction for a particular protein, the mean value when averaging over protein chains might be of help as well. Computing first the correlation between observed and predicted accessibility for each protein chan, and then averaging over all 238 chains yields the following average: +-------------------------------====--+ | corr/averaged over chains = 0.53 | +-------------------------------====--+ | standard deviation = 0.11 | +-------------------------------------+ .......................................................................... Further details of performance accuracy ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The accuracy matrix in detail: .............................. -------+----------------------------------------------------+----------- \ PHD | 0 1 2 3 4 5 6 7 8 9 | SUM %obs -------+----------------------------------------------------+----------- OBS 0 | 8611 140 8 44 82 169 772 334 27 0 | 10187 16.6 OBS 1 | 4367 164 0 50 106 231 738 346 44 3 | 6049 9.8 OBS 2 | 3194 168 1 68 125 303 951 513 42 7 | 5372 8.7 OBS 3 | 2760 159 8 80 136 327 1246 746 58 19 | 5539 9.0 OBS 4 | 2312 144 2 72 166 396 1615 1245 124 19 | 6095 9.9 OBS 5 | 1873 96 3 84 138 425 1979 1834 187 27 | 6646 10.8 OBS 6 | 1387 67 1 60 80 278 2237 2627 231 51 | 7019 11.4 OBS 7 | 1082 35 0 32 56 225 1871 3107 302 60 | 6770 11.0 OBS 8 | 660 25 0 27 43 136 1206 2374 325 87 | 4883 7.9 OBS 9 | 325 20 2 27 29 74 648 1159 366 214 | 2864 4.7 -------+----------------------------------------------------+----------- SUM |26571 1018 25 544 961 2564 13263 14285 1706 487 | %pred | 43.3 1.7 0.0 0.9 1.6 4.2 21.6 23.3 2.8 0.8 | -------+----------------------------------------------------+----------- Note: This table is to be read in the following manner: 8611 of all residues predicted to be in exposed by 0%, were observed with 0% relative accessibility. However, 325 of all residues predicted to have 0% are observed as completely exposed (obs = 9 -> rel. acc. >= 81%). The term "observed" refers to the DSSP compilation of area of solvent accessibility calculated from 3D coordinates of experimentally determined structures (Diction- ary of Secondary Structure of Proteins: Kabsch & Sander (1983) Biopolymers, 22, 2577-2637). Accuracy for each amino acid: ............................. +---+------------------------------+-----+-------+------+ |AA | Q3 b%o b%p i%o i%p e%o e%p | Q10 | corr | N | +---+------------------------------+-----+-------+------+ | A | 59.0 87 60 2 38 66 57 | 31 | 0.530 | 5054 | | C | 62.0 91 67 5 39 25 21 | 34 | 0.244 | 893 | | D | 56.5 21 45 6 49 94 57 | 20 | 0.321 | 3536 | | E | 60.8 9 40 3 41 98 61 | 21 | 0.347 | 3743 | | F | 63.3 94 67 9 46 29 37 | 27 | 0.366 | 2436 | | G | 52.1 75 51 1 31 67 53 | 22 | 0.405 | 4787 | | H | 50.9 63 53 23 45 71 50 | 18 | 0.442 | 1366 | | I | 64.9 95 68 6 41 30 38 | 34 | 0.360 | 3437 | | K | 66.6 2 11 2 37 98 67 | 23 | 0.267 | 3652 | | L | 61.6 93 65 8 44 31 40 | 31 | 0.368 | 5016 | | M | 60.1 92 64 5 39 45 44 | 29 | 0.452 | 1371 | | N | 55.5 45 45 8 38 87 59 | 17 | 0.410 | 2923 | | P | 53.0 48 48 9 39 83 56 | 18 | 0.364 | 2920 | | Q | 54.3 27 44 7 44 92 56 | 20 | 0.344 | 2225 | | R | 49.9 15 47 36 47 76 51 | 18 | 0.372 | 2765 | | S | 55.6 69 53 3 51 81 56 | 22 | 0.464 | 3981 | | T | 51.8 61 51 8 38 78 53 | 21 | 0.432 | 3740 | | V | 61.1 93 65 5 40 39 42 | 34 | 0.418 | 4156 | | W | 56.2 85 62 20 49 29 27 | 21 | 0.318 | 891 | | Y | 49.7 73 52 33 49 36 38 | 19 | 0.359 | 2301 | +---+------------------------------+-----+-------+------+ Abbreviations: AA: amino acid in one-letter code b%o, i%o, e%o: = Qburied, Qintermediate, Qexposed (% of observed), i.e. percentage of correct prediction in each state, see above b%p, i%p, e%p: = Qburied, Qintermediate, Qexposed (% of predicted), i.e. probability of correct prediction in each state, see above b%o: = Qburied (% of observed), see above Q10: percentage of correctly predicted residues in each of the 10 states of predicted relative accessibility. corr: correlation between predicted and observed rel. acc. N: number of residues in data set Accuracy for different secondary structure: ........................................... +--------+------------------------------+----+-------+-------+ | type | Q3 b%o b%p i%o i%p e%o e%p |Q10 | corr | N | +--------+------------------------------+----+-------+-------+ | helix | 59.5 79 64 8 44 80 56 | 27 | 0.574 | 20100 | | strand | 61.3 84 73 9 46 69 37 | 35 | 0.524 | 13356 | | loop | 54.4 64 43 11 44 78 61 | 18 | 0.442 | 27968 | +--------+------------------------------+----+-------+-------+ Abbreviations as before. Position-specific reliability index ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The network predicts the 10 states for relative accessibility using real numbers from the output units. The prediction is assigned by choosing the maximal unit ("winner takes all"). However, the real numbers contain additional information. E.g. the difference between the maximal and the second largest output unit (with the constraint that the second largest output is compiled among all units at least 2 positions off the maximal unit) can be used to derive a "reliability index". This index is given for each residue along with the prediction. The index is scaled to have values between 0 (lowest reliability), and 9 (highest). The accuracies (Q3, corr, asf.) to be expected for residues with values above a particular value of the index are given below as well as the fraction of such residues (%res).: +---+------------------------------+----+-------+-------+ |RI | Q3 b%o b%p i%o i%p e%o e%p |Q10 | corr | %res | +---+------------------------------+----+-------+-------+ | 0 | 57.5 77 60 9 44 78 56 | 24 | 0.535 | 100.0 | | 1 | 59.1 76 63 9 45 82 57 | 25 | 0.560 | 91.2 | | 2 | 61.7 79 66 4 47 87 58 | 27 | 0.594 | 77.1 | | 3 | 66.6 87 70 1 51 89 63 | 30 | 0.650 | 57.1 | | 4 | 70.0 89 72 0 83 91 67 | 32 | 0.686 | 45.8 | | 5 | 72.9 92 75 0 0 93 70 | 34 | 0.722 | 35.6 | | 6 | 76.3 95 77 0 0 93 75 | 36 | 0.769 | 24.7 | | 7 | 79.0 97 79 0 0 93 78 | 39 | 0.803 | 16.0 | | 8 | 80.9 98 80 0 0 91 81 | 43 | 0.824 | 9.6 | | 9 | 81.2 99 80 0 0 88 83 | 45 | 0.828 | 5.9 | +---+------------------------------+----+-------+-------+ Abbreviations as before. The above table gives the cumulative results, e.g. 45.8% of all residues have a reliability of at least 4. The correlation for this most reliably predicted half of the residues is 0.686, i.e. a value comparable to what could be expected if homology modelling were possible. For this subset of 45.8% of all residues, 89% of the buried residues are correctly predicted, and 72% of all residues predicted to be buried are correct. .......................................................................... The following table gives the non-cumulative quantities, i.e. the values per reliability index range. These numbers answer the question: how reliable is the prediction for all residues labeled with the particular index i. +---+------------------------------+----+-------+-------+ |RI | Q3 b%o b%p i%o i%p e%o e%p |Q10 | corr | %res | +---+------------------------------+----+-------+-------+ | 0 | 40.9 79 40 16 41 21 40 | 14 | 0.175 | 8.8 | | 1 | 45.4 61 46 28 44 48 44 | 17 | 0.278 | 14.1 | | 2 | 47.4 53 52 10 46 80 44 | 19 | 0.343 | 19.9 | | 3 | 52.9 75 59 4 50 77 47 | 23 | 0.439 | 11.4 | | 4 | 60.0 81 63 0 83 84 56 | 25 | 0.547 | 10.1 | | 5 | 65.2 82 70 0 0 93 62 | 28 | 0.607 | 10.9 | | 6 | 71.3 90 72 0 0 94 70 | 31 | 0.692 | 8.8 | | 7 | 76.0 94 76 0 0 95 75 | 34 | 0.762 | 6.3 | | 8 | 80.5 97 81 0 0 94 79 | 39 | 0.808 | 3.8 | | 9 | 81.2 99 80 0 0 88 83 | 45 | 0.828 | 5.9 | +---+------------------------------+----+-------+-------+ For example, for residues with RI = 4 83% of all predicted intermediate residues are correctly predicted as such. The resulting network (PHD) prediction is: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________________________________________________________ PHD: Profile fed neural network systems from HeiDelberg ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Prediction of: secondary structure, by PHDsec solvent accessibility, by PHDacc and helical transmembrane regions, by PHDhtm Author: Burkhard Rost EMBL, 69012 Heidelberg, Germany Internet: Rost@EMBL-Heidelberg.DE All rights reserved. The network systems are described in: PHDsec: B Rost & C Sander: JMB, 1993, 232, 584-599. B Rost & C Sander: Proteins, 1994, 19, 55-72. PHDacc: B Rost & C Sander: Proteins, 1994, 20, 216-226. PHDhtm: B Rost et al.: Prot. Science, 1995, 4, 521-533. Some statistics ~~~~~~~~~~~~~~~ Percentage of amino acids: +--------------+--------+--------+--------+--------+--------+ | AA: | L | N | V | I | D | | % of AA: | 10.8 | 7.4 | 7.2 | 7.2 | 6.9 | +--------------+--------+--------+--------+--------+--------+ | AA: | Q | R | E | T | A | | % of AA: | 6.8 | 6.1 | 5.9 | 5.7 | 5.7 | +--------------+--------+--------+--------+--------+--------+ | AA: | K | S | Y | M | F | | % of AA: | 5.4 | 4.9 | 4.0 | 3.9 | 3.9 | +--------------+--------+--------+--------+--------+--------+ | AA: | P | G | H | W | C | | % of AA: | 3.4 | 2.4 | 1.4 | 0.7 | 0.6 | +--------------+--------+--------+--------+--------+--------+ Percentage of secondary structure predicted: +--------------+--------+--------+--------+ | SecStr: | H | E | L | | % Predicted: | 61.4 | 8.6 | 30.0 | +--------------+--------+--------+--------+ According to the following classes: all-alpha: %H>45 and %E< 5; all-beta : %H<5 and %E>45 alpha-beta : %H>30 and %E>20; mixed: rest, this means that the predicted class is: mixed class PHD output for your protein ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Thu Dec 23 04:37:09 1999 Jury on: 10 different architectures (version 5.94_317 ). Note: differently trained architectures, i.e., different versions can result in different predictions. About the protein ~~~~~~~~~~~~~~~~~ HEADER /home/phd/server/work/predict_h11817647. COMPND SOURCE AUTHOR SEQLENGTH 881 NCHAIN 1 chain(s) in predict_h11817647 data set NALIGN 1 (=number of aligned sequences in HSSP file) WARNING ~~~~~~~ Expected accuracy is about 72% if, and only if, the alignment contain sufficient information. For your sequence there was no homologue in the current version of Swissprot detected. This implies that the expected accuracy is about 6-10 percentage points lower ! Abbreviations: PHDsec ~~~~~~~~~~~~~~~~~~~~~ sequence: AA : amino acid sequence secondary structure: HEL: H=helix, E=extended (sheet), blank=other (loop) PHD: Profile network prediction HeiDelberg Rel: Reliability index of prediction (0-9) detail: prH: 'probability' for assigning helix prE: 'probability' for assigning strand prL: 'probability' for assigning loop note: the 'probabilites' are scaled to the interval 0-9, e.g., prH=5 means, that the first output node is 0.5-0.6 subset: SUB: a subset of the prediction, for all residues with an expected average accuracy > 82% (tables in header) note: for this subset the following symbols are used: L: is loop (for which above " " is used) ".": means that no prediction is made for this residue, as the reliability is: Rel < 5 Abbreviations: PHDacc ~~~~~~~~~~~~~~~~~~~~~ SS : secondary structure HEL: H=helix, E=extended (sheet), blank=other (loop) solvent accessibility: 3st: relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%. PHD: Profile network prediction HeiDelberg Rel: Reliability index of prediction (0-9) O_3: observed relative acc. in 3 states: B, I, E note: for convenience a blank is used intermediate (i). P_3: predicted relative accessibility in 3 states 10st:relative accessibility in 10 states: = n corresponds to a relative acc. of n*n % subset: SUB: a subset of the prediction, for all residues with an expected average correlation > 0.69 (tables in header) note: for this subset the following symbols are used: "I": is intermediate (for which above " " is used) ".": means that no prediction is made for this residue, as the reliability is: Rel < 4 protein: predict length 881 ....,....1....,....2....,....3....,....4....,....5....,....6 AA |MAYRKRGATVEADINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIRDE| PHD sec | HHHHHHHHHHHHH HHHHHHHHHHHHH EEEEE HHHHHHHHHH| Rel sec |999657872136854543433314699667556443241344122122890435556724| detail: prH sec |000000013567876765656546799778777665324222110100004666767856| prE sec |000121000000000000000000000000000000101111445454100000010000| prL sec |988778875432123233333353200221222223564556333435894232221133| subset: SUB sec |LLLLLLLL...HHH.H........HHHHHHHHH...............LL...HHHHH..| accessibility 3st: P_3 acc |eee eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeebeeeeeeeeeeebeeeeeeeeeeee| 10st: PHD acc |996576877778777787777777777777777760777777777860777877777787| Rel acc |001141233141423453334242413325613312425411351101532451271234| subset: SUB acc |....e.....e.e..ee...e.e.e....ee.....e.ee...e....e..ee..e...e| ....,....7....,....8....,....9....,....10...,....11...,....12 AA |VKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQT| PHD sec |H HHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHH HHHHHHHH| Rel sec |305543588999999928999627899999999547978637999866615388876778| detail: prH sec |542233688999999958899758889999999731010167998877742388887888| prE sec |110000000000000000000000000000000000000000000000000000000000| prL sec |346665211000000041000241100000000268988731000122257511112111| subset: SUB sec |..LL..HHHHHHHHHH.HHHHH.HHHHHHHHHHH.LLLLL.HHHHHHHH.L.HHHHHHHH| accessibility 3st: P_3 acc |beeeeeeebeebbebbebeeeeeeeebeebbee bbe eeeeebbee eeeeeeebeeee| 10st: PHD acc |077779780770070070677777760770077500747777700773787777707777| Rel acc |433343510235434431132314312224733040302145064240430336205610| subset: SUB acc |b...e.e....bb.bb.......e.....bb...b.....ee.bb.e.e....e..ee..| ....,....13...,....14...,....15...,....16...,....17...,....18 AA |KLFRIFEPRQLPIYRANGEKELRNRWYWKLKKDTLPDGDYDVREYFLNLYDQVLTEMPDY| PHD sec |HHHHHH HHHHHHHHHHHH HHHHHHHHHHHHHHHHH H| Rel sec |876643258998556688511467777668827997877158999999999999982236| detail: prH sec |877655211000000001234677777778851001011578999999999999984437| prE sec |011121210000221100011100000110000000000000000000000000000000| prL sec |111122468898667788643221111110137997887421000000000000015551| subset: SUB sec |HHHH...LLLLLLLLLLLL...HHHHHHHHH.LLLLLLL.HHHHHHHHHHHHHHHH...H| accessibility 3st: P_3 acc |ebbbbbeeee ebbe ebeeebee bbbeb eeebeebe ebbebbbebbeebbeebbeb| 10st: PHD acc |600000777747006570777077500060577707706370060006007600770070| Rel acc |157043201311212013233222152424023310400128117961810286414200| subset: SUB acc |.bb.b....................b.b.b......e....b..bbb.b...bbe.b...| ....,....19...,....20...,....21...,....22...,....23...,....24 AA |LLLKDMAVENKNSRDAGKVVDSETASICDAIFQDEETEGAVRRFIAEMRQRVQADRNVVN| PHD sec |HHHHH HHHHHHHHHHHH HHHHHHHHHHHHHHHHHHH | Rel sec |775351136999724477760679999999950415688999999999998626567434| detail: prH sec |776563431000143311114789999999864347788999999999998751111233| prE sec |112311011000000001100000000000010000000000000000000010001100| prL sec |001114557998856677774210000000024642211000000000001137777656| subset: SUB sec |HHH.H...LLLLL...LLLL.HHHHHHHHHHH...HHHHHHHHHHHHHHHHH.LLLL...| accessibility 3st: P_3 acc |bbbeebbbebeebeebbebbeeeeeebbebbbeeeebeb bbbbbbeb e beeeebeee| 10st: PHD acc |000660007077079007007776770070006677070400000070574077770677| Rel acc |779106541052122652251541455500930022211080166017101430210013| subset: SUB acc |bbb..bbb..e....bb..b.ee.eebb..b.........b..bb..b...b........| ....,....25...,....26...,....27...,....28...,....29...,....30 AA |YPSILHPIDYAFNEYFLQHQLVEPLNNDIIFNYIPERIRNDVNYILNMDRNLPSTARYIR| PHD sec | HHHHHHHHHHHHHH HHHHHHHHHHHH EEEE | Rel sec |633466134799999998775443885999998389752698724411111333685357| detail: prH sec |233111436899999998876633116899998688863100110123444333200000| prE sec |001211000000000000000000000000000000001000056641100000002321| prL sec |755567563100000000112366882100000310124798733234345656786578| subset: SUB sec |L...LL...HHHHHHHHHHHH...LLHHHHHHH.HHHH.LLLL...........LLL.LL| accessibility 3st: P_3 acc |bbbbbbbbbeebbebbbebbbbebbeee bbebbbeebee bbbbbbbbeebeeeb bbe| 10st: PHD acc |000000000770070006000060067750070008607750000000077077705006| Rel acc |233860340225351791227520112308341713141100139544011112121251| subset: SUB acc |...bb..b...b.e.bb...bb.......b.e.b...b......bbbb..........b.| ....,....31...,....32...,....33...,....34...,....35...,....36 AA |PNLLQDRLNLHDNFESLWDTITTSNYILARSVVPDLKELVSTEAQIQKMSQDLQLEALTI| PHD sec | HHHHH E HHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHHHHHHH| Rel sec |824214666169822020232244344556616459999999999999988994598735| detail: prH sec |033356777420033323223566555667741679999999999999988996688866| prE sec |000000000000011342211000011111110000000000000000000001000000| prL sec |856543222579855333455433322121147320000000000000011002201132| subset: SUB sec |L.....HHH.LLL..............HHHH.L.HHHHHHHHHHHHHHHHHHH.HHHH.H| accessibility 3st: P_3 acc |bebeeb beb eebebbbebebeeebbbb ebbeebeebbeeeeebeebbeebebeebee| 10st: PHD acc |070670306047606000607067700003700670770077776077006606077067| Rel acc |114000031401171523111001123190115017324440141357700111521722| subset: SUB acc |..b......b...b.b............b...b..b..bbe..e..eeb.....b..b..| ....,....37...,....38...,....39...,....40...,....41...,....42 AA |QSETQFLTGINSQAANDCFKTLIAAMLSQRTMSLDFVTTNYMSLISGMWLLTVVPNDMFI| PHD sec |HHHHHHHE HHHHHHHHHHHHHHHHHH EEEEE HHHHHHHHH EEEEE HHH| Rel sec |226786106671166999999999998761526451122235576331336645762123| detail: prH sec |557787431115577899999999998774201114354456677534231100013345| prE sec |000001430000000000000000000000157664211110111112557762101222| prL sec |342100137784422000000000001124631211333322211353110126874332| subset: SUB sec |..HHHH..LLL..HHHHHHHHHHHHHHHH.L.E.E......HHHH.....EE.LLL....| accessibility 3st: P_3 acc |ebeeebbebeebebbbebbeebbbbbbbe bbbbebbbbbbbbbbbbbbbbbbbbeebbb| 10st: PHD acc |707760070660700070066000000074000060000000000000000000076000| Rel acc |341315232110146036910696156430151516760438585758398542410147| subset: SUB acc |.b...b.......bb..bb..bbb.bbb...b.b.bbb.b.bbbbbbb.bbbb.b...bb| ....,....43...,....44...,....45...,....46...,....47...,....48 AA |RESLVACQLAIVNTIIYPAFGMQRMHYRNGDPQTPFQIAEQQIRKFSGSGIGWHFVNNNQ| PHD sec |HHHHHHHHHHHHHHHE HHHHHHHHHH HHHHHHHHHH HHHHHHHHH| Rel sec |458899999876451134234899997449987711259999999729994225522386| detail: prH sec |568889998887663112566899988630000143578999998740003456754587| prE sec |210000000000113421000000000000001011000000000000000101111100| prL sec |121100000011212455433100001368988844420000000159996342133311| subset: SUB sec |.HHHHHHHHHHH.H.......HHHHHH..LLLLL...HHHHHHHHH.LLL...HH...HH| accessibility 3st: P_3 acc |bbbbbbbbbbbbbbbbbbbbbbbebbbeeeeeeeebebbeeeb ebeeeebbbbbbbeee| 10st: PHD acc |000000000000000000000006000679777770600767057069790000000676| Rel acc |008788749869677957765430721110332241056121604300102543253010| subset: SUB acc |..bbbbbbbbbbbbbbbbbbbb..b.........e..bb...b.e......bb..b....| ....,....49...,....50...,....51...,....52...,....53...,....54 AA |FRQVVIDGVLNQVLNDNIRNVHVIKQLMQALMQLSRQQFPTMPVDYKRSIQRGILLLSNR| PHD sec |HHHHHHH EE HHH HHHHHHHHHHHHHHHHH HHHHHHHHHHHHHH| Rel sec |546544413211111121115899999999999865378889983217888999999742| detail: prH sec |666666643223334454336899999999999877510000013458888999999865| prE sec |001222011334320111221100000000000000000000000000000000000000| prL sec |221111245442234433331000000000000122388889986541111000000134| subset: SUB sec |H.HH................HHHHHHHHHHHHHHHH.LLLLLLL...HHHHHHHHHHH..| accessibility 3st: P_3 acc |beebbbebbeeeebeeeb eb bbebbbebbbebbeeebeb bebe bbebbbbbbbe | 10st: PHD acc |076000700666606770570500700070007007760704526075006000000065| Rel acc |612070246000041214011088307246741553114010000110540075056400| subset: SUB acc |b...b..bb....b...b....bb..b.ebbb.bb...b.........bb..bb.bbb..| ....,....55...,....56...,....57...,....58...,....59...,....60 AA |LGQLVDLTRLLAYNYETLMACVTMNMQHVQTLTTEKLQLTSVTSLCMLIGNATVIPSPQT| PHD sec |HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEE EE | Rel sec |899999999999969988887898668876221367655342332111215751259812| detail: prH sec |899999999999979988887898778887544577666554555444312100000053| prE sec |000000000000000000011000100000112200111111123444431024520000| prL sec |100000000000020001000000110111333211122223221111246864479845| subset: SUB sec |HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHH...........LLL..LLL..| accessibility 3st: P_3 acc |ebbbbbbb bbbbbbebbbbbbbbbbebbebbbeeebebbbbbbbbbbbbbebbbeebee| 10st: PHD acc |600000005000000700000000006007000666060000000000000700077077| Rel acc |030510860764142257289939550280232011311124489796711026301121| subset: SUB acc |...b..bb.bbb.b..bb.bbb.bbb..b............bbbbbbbb....b......| ....,....61...,....62...,....63...,....64...,....65...,....66 AA |LFHYYNVNVNFHSNYNERINDAVAIITAANRLNLYQKKMKAIVEDFLKRLHIFDVARVPD| PHD sec | EEEEEEEE HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEE H| Rel sec |114322214315632688999999999999999999999999999988642462576994| detail: prH sec |332112221001135788989999999999999999999999999988763101212006| prE sec |235544445542000000000000000000000000000000000000014673000000| prL sec |421232332346764201000000000000000000000000000010122215787993| subset: SUB sec |...........LL..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...E.LLLLL.| accessibility 3st: P_3 acc |bbebbbbbbbbbebbbeebeebbbbbbbbbbbebbbeebebbbeebbe bbbbbbbebbe| 10st: PHD acc |007000000000600066077000000000007000760700077007400000007009| Rel acc |551231126162100011612599393861072420317105931643090830103102| subset: SUB acc |bb......b.b.......b..bbb.b.bb..b.b....b..bb..bb..b.b........| ....,....67...,....68...,....69...,....70...,....71...,....72 AA |DQMYRLRDRLRLLPVEVRRLDIFNLILMNMDQIERASDKIAQGVIIAYRDMQLERDEMYG| PHD sec |HHHHHHHHHHHH HHHHHHHHHHH HHHHHHHHHHHHHHHEEEEE EEE E| Rel sec |899999999852988225799999998132999954599951112686189742216451| detail: prH sec |899999999875000246789999998435898876799864443100000000000101| prE sec |000000000000000121000000000000000000000000125787410125541224| prL sec |100000000124988532100000001464000023200024431001488764447664| subset: SUB sec |HHHHHHHHHHH.LLL..HHHHHHHHHH...HHHHH.HHHHH....EEE.LLL....L.L.| accessibility 3st: P_3 acc |ebbb b e b ebbbebb bebbebbbeb eebeebbeebbbbbbbbbeebebeeeee b| 10st: PHD acc |700050474057000700506006000604660670077000000000670707676750| Rel acc |107008111611233100000780987140119130342651894751122212110204| subset: SUB acc |..b..b...b...........bb.bbb.b...b....e.bb.bbbbb............b| ....,....73...,....74...,....75...,....76...,....77...,....78 AA |YVNIARNLDGFQQINLEELMRTGDYAQITNMLLNNQPVALVGALPFVTDSSVISLIAKLD| PHD sec |EEEEE EEEHHHHHH HHHHHHHHHH EEE EE HHHHHHHHHHH| Rel sec |265524688611211578985586699999996449927524551047378999999993| detail: prH sec |111010001111110688987212799999997630000100012211388899999986| prE sec |576653100033544000000000000000000000037652214421000000000000| prL sec |312236788744344210012787100000002369951136763357611000000013| subset: SUB sec |.EEE..LLLL.....HHHHHHLLLHHHHHHHHH..LL.EE..LL...L.HHHHHHHHHH.| accessibility 3st: P_3 acc |bbbbbeeeebbbbbbbeebeeebebbebbbbbbeeebbbbebbbbbbbebbbbebbbebe| 10st: PHD acc |000007697000000066067606006000000786000070000000700007000706| Rel acc |012522004240263710512011131953245330233814732163045880872220| subset: SUB acc |...b....e.b..b.b..b........bb..bb......b.bb...b..bbbb.bb....| ....,....79...,....80...,....81...,....82...,....83...,....84 AA |ATVFAQIVKLRKVDTLKPILYKINSDSNDFYLVANYDWVPTSTTKVYKQVPQQFDFRNSM| PHD sec |HHHHHHHHHHHHH EEEEEE EEEEE HHHHHHHHHH E HHHH| Rel sec |399999996442435893377783899647887478898862254653323211516799| detail: prH sec |699999987665632000000000000100000000000013566765555432147899| prE sec |000000000000000003588786100127888610001110001100111123100000| prL sec |300000002224357896311113898761111378898875322123233343651100| subset: SUB sec |.HHHHHHHH.....LLL..EEEE.LLLL.EEEE.LLLLLLL..H.HH.......L.HHHH| accessibility 3st: P_3 acc |bbbbbbbbee ebeebebbebeb bebeebbbbbb ebbeeebbebbee eeebebebbb| 10st: PHD acc |000000007747077060060604060770000005700777007007757660607000| Rel acc |228880852113034410414170212015776010500010113712301103132153| subset: SUB acc |..bbb.bb......eb..b.b.b......bbbb...e........b............b.| ....,....85...,....86...,....87...,....88...,....89...,....90 AA |HMLTSNLTFTVYSDLLAFVSADTVEPINAVAFDNMRIMNEL| PHD sec |HHHHH EEHHHHHHHHHH HHHHHH | Rel sec |99852651325998999982167412455455558899339| detail: prH sec |99875112226888999985410001122221268888530| prE sec |00000013551000000000001343211111000000000| prL sec |00124764221000000013578644666666621000369| subset: SUB sec |HHHH.LL...HHHHHHHHH..LL....LL.LLLHHHHH..L| accessibility 3st: P_3 acc |ebbebbb bbbbbbbbebbeeebbebbbbbbbbbb bbeee| 10st: PHD acc |70060005000000007007770060000000000400779| Rel acc |25714070929301843353212415638852002076310| subset: SUB acc |.bb.b.b.b.b...bb..b....b.bb.bbb.....bb...| ________________________________________________________________________________ The resulting prediction of globularity is: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________________________________________________________ --- --- GLOBE: prediction of protein globularity --- --- nexp = 402 (number of predicted exposed residues) --- nfit = 307 (number of expected exposed residues --- diff = 95.00 (difference nexp-nfit) --- =====> your protein appears as compact, as a globular domain --- --- --- GLOBE: further explanations preliminaryily in: --- http://www.columbia.edu/~rost/Papers/98globe.html --- --- END of GLOBE ________________________________________________________________________________ ----------------------------------------------------------------------------- - PredictProtein (PP): News 1999 - ----------------------------------------------------------------------------- - - - PP home: - New York http://dodo.cpmc.columbia.edu/predictprotein - - - PP mirrors: - Australia (ANGIS) http://molmod.angis.org.au//predictprotein England (EBI) http://www.ebi.ac.uk/~rost/predictprotein Germany (EMBL) http://www.embl-heidelberg.de/predictprotein India (CDFC) http://iris.cdfd.org.in/~www/pp/predictprotein India (Pune) http://202.41.70.33/predictprotein Israel (Beer-Sheva) http://www.cs.bgu.ac.il/~dfischer/predictprotein Italy (Rome) http://obelix.bio.uniroma2.it/www/predictprotein Singapore (BIC) http://embl.bic.nus.edu.sg/predictprotein Spain (CNB) http://www.es.embnet.org/Services/MolBio/PredictProtein Switzerland (Glaxo) http://www.gwer.ch/tools/predictprotein - - - Tools to post-process PP results: - - - - Generate a PostScript (or GIF, or TIFF): - ESPript (New York) http://dodo.cpmc.columbia.edu/cgi/pp/ESPript ESPript (Toulouse) http://www-pgm1.ipbs.fr:8080/ESPript - - -----------------------------------------------------------------------------