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Query: 5xon_W mol:protein length:612 Protein that forms a complex with Spt4p, from PDB1018

Results of FFAS03 search in PDB1018
Master-slave alignment(slide right to see more) does not show gaps in the query sequence, use ali links to display alignment between query and templates.
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# Score Template Links and tools%idFirst GPGSASTTAPQRLLIPTVDDPGIWGVKVRLGKEKDVVRQILKKKLAREGTKNPLEIYSAFQRDSFKGHVYIEARKAEAINDALKGNVNVFSNNSKFLVGIVEYKDLLRPVKSSDVKLTRGSYVRVKNGKFKGDLAQVDEVLENGLEARLKLVPRLDYGKDLSHLSTSSSVDSTKNRRKFYTSKFRPAQRLFSEAEARVHEPTIRRDRDGFVTYGGEEYYEGFLYKTFRLQNLIVNSINPTLNELSLFQSNEESTTIDLSTIADSLKETAKNLVSFQPGDNVEIINGELNHLTGTVSSVNQSTIVSVRLHSDDDTINSETVEIPTSDLRKIFNVGDHVRVIHGKHTDDTGLIVEVNGDKVEFISNQTKRTVIVFSNYLIKSTDSTVSINESGRFELHDLVQVNSDLVGIVIRAQKDSFDVLCSDGKLLSLPPVSIYSKLNLNPNQQIAIDSNGVEVKVGDTVREFTGERRQGTILHVYRNFLFLRSREIVENQGVFVTSSNRVKTITSKSNGTGGQISGPDLSRMNPSRVIPPPSIPVANQRMTGRDPTLNKTVKIRQGGYKGKIGIVKEANGDRFRVELHNPNKTIPIPCSFLLIESTHGWVPYEDFVASDRLast
1 -156.0005xon_W mol:protein length:612 Protein that forms a complex with Spt4p  ali model  100  1GPGSASTTAPQRLLIPTVDDPGIWGVKVRLGKEKDVVRQILKKKLAREGTKNPLEIYSAFQRDSFKGHVYIEARKAEAINDALKGNVNVFSNNSKFLVGIVEYKDLLRPVKSSDVKLTRGSYVRVKNGKFKGDLAQVDEVLENGLEARLKLVPRLDYGKDLSHLSTSSSVDSTKNRRKFYTSKFRPAQRLFSEAEARVHEPTIRRDRDGFVTYGGEEYYEGFLYKTFRLQNLIVNSINPTLNELSLFQSNEESTTIDLSTIADSLKETAKNLVSFQPGDNVEIINGELNHLTGTVSSVNQSTIVSVRLHSDDDTINSETVEIPTSDLRKIFNVGDHVRVIHGKHTDDTGLIVEVNGDKVEFISNQTKRTVIVFSNYLIKSTDSTVSINESGRFELHDLVQVNSDLVGIVIRAQKDSFDVLCSDGKLLSLPPVSIYSKLNLNPNQQIAIDSNGVEVKVGDTVREFTGERRQGTILHVYRNFLFLRSREIVENQGVFVTSSNRVKTITSKSNGTGGQISGPDLSRMNPSRVIPPPSIPVANQRMTGRDPTLNKTVKIRQGGYKGKIGIVKEANGDRFRVELHNPNKTIPIPCSFLLIESTHGWVPYEDFVASDR 612
2 -120.0005oik_Z mol:protein length:1087 Transcription elongation factor SPT5  ali model follow..  28  157GSDELSDDITQQQLLPGVKDPNLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGYNQQMVPIKEMTDVLKV-VKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDYDRIKARMSLKDWFAKR-------KKFKRPPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFEDQPEG----IDLEVVTESTGKEREHNFQPGDNVEVCEGELINLQGKILSVDGNKITIMP----KHEDLKDMLEFPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSETASGVDVGGQHEWGELVQLDPQTVGVIVRLERETFQVLNMYGKVVTVRHQAVTRKKDNRFAVALDSEQNNIHVKDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGGMFVCKTRHLVLAGGSKPRDVTNFTPSAGGQRGGFGSPGGGSGGMSRGRGRRDNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLTTVGSRRPGGMTSTYGR.. 767
3 -46.3004ytk_A mol:protein length:130 Transcription elongation factor SPT5  ali model follow..  42  1....................................................................................................................LEEGSYVRIKRGIYKGDLAMVDQISENNLEVMLKIVPRLDYGKFDEIDPTTQQRKSR-----RPTFAHRAPPQLFNPTMALRLQANLYKRDDRHFTYKNEDYIDGYLYKSFRIQHVETKNIQPTVEELARFGS........................................................................................................................................................................................................................................................................................................................................................................... 129
4 -45.5003qqc_D mol:protein length:163 Transcription antitermination protein nusG  ali model follow..  20  2...................AGKIFAVRVTHGQEETTAKLIYSKVRT-----YNLPIYAILAPSRVKGYIFVEAPNKGVVDEAIRGIRHARGV-LPGEVPFKEIEHFLE-EKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAIVPIPVTIKGDYVRLISKLQKEEAAALE.............................................................................................................................................................................................................................................................................................................................................................................................................................................. 157
5 -40.7004zn1_A mol:protein length:147 Transcription elongation factor Spt5  ali model follow..  25  2......................IFAVRTMVGQEKNIAGLMASRA-----EKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGI-VPGTIAIEEIEPLLT-PKKIIENIEKGDVVEIIAGPFKGERAKVIRVDKHKEEVTLELENAAVPIPITLPVEGVKIVSKHKD..................................................................................................................................................................................................................................................................................................................................................................................................................................................... 147
6 -37.0004ytl_A mol:protein length:99 Transcription elongation factor SPT5  ali model follow..  41  1..................................................................................................................................................................................................................................................................................FQPGDRIEVLNGEQRGSKGIVTRTTKDIATIKL------NGFTTPLEFPISTLRKIFEPGDHVTVINGEHQGDAGLVLMVEQGQVTFMSTQTSREVTITANNLSK......................................................................................................................................................................................................................................... 99
7 -36.5003h7h_B mol:protein length:106 Transcription elongation factor SPT5  ali model follow..  29  2................SHMDPNLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRGYWNQQMVPIKEMTDVLK-VVKEVANLGSGC........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... 106
8 -35.2005xog_W mol:protein length:83 Spt4/5 complex component  ali model follow..  98  3...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GPSIPVANQRMTGRDPTLNKTVKIRQGGYKGKIGIVKEANGDRFRVELHNPNKTIPIPCSFLLIESTHGWVPYEDFVASDR 83
9 -34.9002exu_A mol:protein length:200 Transcription initiation protein SPT4/SPT5  ali model follow..  34  83.PAEVVELLPHYKPRDGSGSATIWGVRCRPGKEKELIRKLLKKKFNLDRGKKKLKILSIFQRDNYTGRIYIEAPKQSVIEKFCNGVPDIYISQ-KLLIPVQELPLLLKPNLE.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... 194
10 -34.0003lpe_A mol:protein length:92 Putative transcription antitermination protein nusG  ali model follow..  25  2............SRRASVGAHMIFAVRTMVGQEKNIAGLMASRA-----EKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIV-PGTIAIEEIEPLLT........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ 91
11 -28.7002e70_A mol:protein length:71 Transcription elongation factor SPT5  ali model follow..  32  1.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GSSGSSGMSRGRGRRDNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLTTVGSRR............ 71
12 -28.2003ewg_A mol:protein length:91 Putative transcription antitermination protein nusG  ali model follow..  27  2......................IFAVRTMVGQEKNIAGLMASRA-----EKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIV-PGTIAIEEIEPLLTPKLE.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... 85
13 -26.3002do3_A mol:protein length:69 Transcription elongation factor SPT5  ali model follow..  37  4............................................................................................................................................................................................................................................................................................................................GSSGEFPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSE...................................................................................................................................................................................................................................... 69
14 -26.2005oho_A mol:protein length:113 Transcription elongation factor SPT5  ali model follow..  26  2.........................................................................................................................................................................................................................................................................................................................................................................................................PWGELVQLDPQTVGVIVRLERETFQVLNMYGKVVTVRHQAVTRKKDNRFAVALDSEQNNIHVKDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGGMFVCKTRHLVLA........................................................................................................... 113
15 -20.2005ohq_A mol:protein length:111 Transcription elongation factor SPT5  ali model follow..  17  4..................................................................................................................................................................................................................................................................................VTTDIQVKVRDTQVVGQTGVIRSVTGGMCSVYL------KDSEKVVSISSEHLEPITTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKLLEA..................................................................................................................................................................................................................................... 111
16 -17.1005ms0_F mol:protein length:183 Transcription termination/antitermination protein NusG  ali model follow..  15  3..............MSEAPKKRWYVVQAFSGFEGRVATSLREHIKLHNMEDLFGEVRRKSERKFFPGYVLVQMVMNDASWHLVRSVPRVMTSDRPAPISDKEVDAIMNRLQQVKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSV............................................................................................................................................................................................................................................................................................................................................................................................................................................................................. 164
17 -16.9002lq8_A mol:protein length:177 Transcription antitermination protein nusG  ali model follow..  17  1................GAMKKKWYIVLTMSGYEEKVKENIEKKVEATRIVIPIRGGQRRKSEKLFPGYVFVEMIMNDEAYNFVRSVPYVMSGGQPVPVKDREMRPILRLAGLEELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNV............................................................................................................................................................................................................................................................................................................................................................................................................................................................................. 157
18 -16.6002xhc_A mol:protein length:352 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  12  6.......................YIVLTMSGYEEKVKENIEKKVEATGIKNLVGRIERLILSPKAKLHVNNGKNKGDLIAEEPPIYARRSGVIVDVKNVRKIVVETIDRKYTKGTKVKQGLPLSKNEEYICELDGKIVEIERMKKVVVQTPDGEQDVYYIPLDVFDRDRIKKGKEVKQGEMLAEARKFFAKVSGRVEVVDYSTRKEIRIYKTKRRKLF--GYVFVEMIMNDEAYNFVRSVPYVMGFVSSGGQPVPVKDREMRPILRLPVKVELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVT----GRETPVVLHVSEVEKI.......................................................................................................................................................................................................................................................................................... 352
19 -15.8002e6z_A mol:protein length:59 Transcription elongation factor SPT5  ali model follow..  39  2............................................................................................................................................................................................................................................................................SSGSSGFQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHED----LKDMLEFPAQELRKY.......................................................................................................................................................................................................................................................................................... 59
20 -15.0001m1g_A mol:protein length:248 Transcription antitermination protein nusG  ali model follow..  19  76................SVLGKKGVTTFRIENGEVKVVESVEGDTCVITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRGGKPVPLKEEEVQNILNQIKRGKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMI............................................................................................................................................................................................................................................................................................................................................................................................................................................................................. 229
21 -14.4002oug_A mol:protein length:162 Transcriptional activator rfaH  ali model follow..  13  5.......................YLLYCKRGQLQRAQEHLERQAVNITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHGASPAIVPSAVIHQLSVYKPKDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARMLLLNLINK.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................... 148
22 -12.8002ckk_A mol:protein length:127 KIN17  ali model follow..  14  15..................................................................................................................................................................................................................................................................................LQPEIIVKIITEKYHKKKAIVKEVIDKYTAVVKM-----IDSGDKLKLDQTHLETVIAPGKRILVLNGGYRGNEGTLESINEKTFSATIVIETGPLK................................................................................................................................................................................................................................................. 111
23 -11.6002kvq_G mol:protein length:63 Transcription antitermination protein nusG  ali model follow..  14  12....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................PGEMVRVNDGPFADFNGVVEEVDYEKVSVSIFGRATPVELDFSQVEKA................ 63
24 -11.6002lcl_A mol:protein length:66 Transcriptional activator rfaH  ali model follow..  18  16....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................PGDKVIITEGAFEGFQAIFTEPDGEALLLNLINKEIKHSVKNTEFRKL................ 66
25 -11.2003h8z_A mol:protein length:128 Fragile X mental retardation syndrome-related protein 2  ali model follow..  16  1.................................................................................................................................................................................................................................................................................AYFQGLPVEVRGSNGAFYKGFVKDVHEDSVTIFFENNWQSER-----QIPFGDVRKEITEGDEVEVYSRANEQELARVRMMKGDFYVIEYAACDATYNEIVTLERLRPVNPNPLATKGSF........................................................................................................................................................................................................................... 128
26 -11.0002mi6_A mol:protein length:62 Transcription termination/antitermination protein NusG  ali model follow..  10  11....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................VGESVTVMDGPFATLPATISEVNAEQVLVSIFGRETPVELTFGQVSKI................ 62
27 -11.0006duq_M mol:protein length:60 Transcription termination/antitermination protein NusG  ali model follow..  14  9....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................PGEMVRVNDGPFADFNGVVEEVDYEKVSVSIFGRATPVELDFSQVEKA................ 60
28 -10.8004tse_A mol:protein length:174 E3 ubiquitin-protein ligase MIB1  ali model follow..  20  7..............................................................................................................................................................................................................................................................................NPGGLQIGDLVNIDLDETLTTTGTVCGIDEDHDIVVQYPSGNRIVRSGDAAQGAEGGTSQFQVGDLVQVCYDLERGKVGRVQQIYSD--DLKVEVCGTSWTYNPAAVSKVASAGSAISN............................................................................................................................................................................................................................... 174
29 -10.4001nz9_A mol:protein length:58 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  19  7....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................EGDQVRVVSGPFADFTGTVTEINPERVMVTIFGRETPVELDFSQVV.................. 56
30 -10.2003j7z_U mol:protein length:104 50S ribosomal protein L24  ali model follow..  18  1......................................................................................................................................................................................................................................................................................................................................MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEG........................................................................................................................................................................................................................................................ 38
31 -10.0001s72_T mol:protein length:120 50S ribosomal protein L24P  ali model follow..  18  46.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GDTVEVLRGDFAGEEGEVINVDLDKAVIHVEDEEVPRPLDTSNVRVTDLD............. 103
32 -9.9605mmi_V mol:protein length:192 plastid ribosomal protein uL24c  ali model follow..  23  66..............................................................................................................................................................................................................................................................................HKMHVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDLNLKTKIKIEAAIHSSNVMKILEDGRKVRYLIK-----TGEIV.................................................................................................................................................................................................................................................................... 169
33 -9.7804fib_A mol:protein length:129 Uncharacterized protein ydhK  ali model follow..  15  1..................................................................................................................................................................................................................................................................................MKVGSQVIINTSHMKGMKGAEATVTGAYDTTAYVVSYTPTNGGQRVDVIQEEIKKTLQPGDQVILEASHMKGMKGEIDSAEKTTVYMVDYTSTT.................................................................................................................................................................................................................................................... 105
34 -9.6305mlc_W mol:protein length:191 50S ribosomal protein L24, chloroplastic  ali model follow..  21  65..............................................................................................................................................................................................................................................................................HKRHVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDLNFKTKIKIEAAIHSSNVMKILEDVRKVRYLIK-----TGEIV.................................................................................................................................................................................................................................................................... 168
35 -9.5601nkw_S mol:protein length:115 50S ribosomal protein L24  ali model follow..  29  16..........................................................................................................................................................................................................................................................................................................................................FKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVE........................................................................................................................................................................................................................................................ 49
36 -9.4402ky9_A mol:protein length:132 Uncharacterized protein ydhK  ali model follow..  16  1..................................................................................................................................................................................................................................................................................MKVGSQVIINTSHMKGMKGAEATVTGAYDTTAYVVSYTPTNGGQRVDVIQEEIKKTLQPGDQVILEASHMKGMKGEIDSAEKTTVYMVD......................................................................................................................................................................................................................................................... 100
37 -9.3404v4i_S mol:protein length:110 50S ribosomal protein L24  ali model follow..  28  2.....................................................................................................................................................................................................................................................................................................................................RVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVE........................................................................................................................................................................................................................................................ 40
38 -9.3305v7q_U mol:protein length:105 50S ribosomal protein L24  ali model follow..  25  2.........................................................................................................................................................................................................................................................................................................................................KVHKGDTVLVISGKDKGAKGKVLQAYPDRNRVLVE........................................................................................................................................................................................................................................................ 36
39 -9.2805o60_V mol:protein length:105 50S ribosomal protein L24  ali model follow..  25  2.........................................................................................................................................................................................................................................................................................................................................KVHKGDTVLVISGKDKGAKGKVLVAYPDRNKVLVE........................................................................................................................................................................................................................................................ 36
40 -9.2703j3v_U mol:protein length:103 50S ribosomal protein L24  ali model follow..  28  2.........................................................................................................................................................................................................................................................................................................................................HVKKGDKVMVISGKDKGKQGTILAAFPKKDRVLVE........................................................................................................................................................................................................................................................ 36
41 -9.2704wce_R mol:protein length:105 50S ribosomal protein L24  ali model follow..  25  2.........................................................................................................................................................................................................................................................................................................................................HIKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVE........................................................................................................................................................................................................................................................ 36
42 -9.1904uc4_A mol:protein length:119 Lysine-specific demethylase 4B  ali model follow..  10  1............................................................................................................................................................................................................................................................................GSHMRAVSLGQVVITKNRNGLYYRCRVIGAASQTCYEVNFDDGSYSDNLYPESITSRDQLGPPSEGELVELRWTDGNLYKAKFISSVTSHIYQVEFEDGSQLTVKRGDIFTLEEE..................................................................................................................................................................................................................................... 117
43 -9.1603j7y_V mol:protein length:216 uL24  ali model follow..  19  52..............................................................................................................................................................................................................................................................................EDWYLFCGDTVEILEGKDAGKQGKVVQVIRQRNWVVVGGLNTHYRIPSEAPLLHRQVKRFTEAGERVRVSTR-----SGRII.................................................................................................................................................................................................................................................................... 154
44 -9.1304mdw_A mol:protein length:166 Uncharacterized protein YdhK  ali model follow..  15  35..........................................................................................................................................................................................................................................................................LQESKNPKYKVGSQVIINTSHMKGMKGAEATVTGAYDTTAYVVSYTPTNGGQRVDVIQEEIKKTLQPGDQVILEASHMKGMKGEIDSAEKTTVYMVD......................................................................................................................................................................................................................................................... 142
45 -9.1205d6w_A mol:protein length:121 Lysine-specific demethylase 4A  ali model follow..  12  2...........................................................................................................................................................................................................................................................................SHMALQSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDE...................................................................................................................................................................................................................................... 118
46 -9.1004ce4_Y mol:protein length:216 MRPL24  ali model follow..  19  52..............................................................................................................................................................................................................................................................................EDWHLFCGDKVEILEGKDAGKQGKVVQVIRQRNWVVVEGLNTHYRIPSEAPLLHNQVKRFTEAGERVRVSTR-----SGRII.................................................................................................................................................................................................................................................................... 154
47 -9.0602xdp_A mol:protein length:123 LYSINE-SPECIFIC DEMETHYLASE 4C  ali model follow..  11  1............................................................................................................................................................................................................................................................................SMCEKVISVGQTVITKHRNTRYYSCRVMAVTSQTFYEVMFDDGSFSRDTFPEDIVSRDCLKLPAEGEVVQVKWPDGKLYGAKYFGSNIAHMYQVEFEDGSQIAMKREDIYTLDEE..................................................................................................................................................................................................................................... 117
48 -9.0402gf7_A mol:protein length:119 Jumonji domain-containing protein 2A  ali model follow..  11  7..................................................................................................................................................................................................................................................................................ITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEE..................................................................................................................................................................................................................................... 117
FFAS is supported by the NIH grant R01-GM087218-01
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Selected papers from Godzik Lab
Ying Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley Deacon, John Wooley, Scott Lesley, Ian Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik. Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima. Science. 2009 Sep 18;325(5947):1544-9.

Mayya Sedova, Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Kai W Post, Thomas Hrabe, Eduard Porta-Pardo, Adam Godzik Cancer3D 2.0:: interactive analysis of 3D patterns of cancer mutations in cancer subsets. Nucleic Acids Research, gky1098 2018; Published on November 8 2018.

Plewczynski D, Tkacz A, Godzik A., Rychlewski L. A support vector machine approach to the identification of phosphorylation sites. Cell Mol Biol Lett. 2005;10(1):73-89.