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Query: 5ohq_A mol:protein length:111 Transcription elongation factor SPT5, 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.
    .   10    .   20    .   30    .   40    .   50    .   60    .   70    .   80    .   90    .  100    .  110
# Score Template Links and tools%idFirst GPWVTTDIQVKVRDTYLDTQVVGQTGVIRSVTGGMCSVYLKDSEKVVSISSEHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKLLEALast
1 -56.2005ohq_A mol:protein length:111 Transcription elongation factor SPT5  ali model  100  1GPWVTTDIQVKVRDTYLDTQVVGQTGVIRSVTGGMCSVYLKDSEKVVSISSEHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKLLEA 111
2 -47.0002ckk_A mol:protein length:127 KIN17  ali model follow..  20  12DYWLQPEIIVKIITKKLGEKYHKKKAIVKEVIDKTAVVKMIDSGDKLKLDQTHLETVIPAPGKRILVLNGGYRGNEGTLESINEKTFSATIVKGRRVEGIQYEDISKLA.. 127
3 -33.9005oik_Z mol:protein length:1087 Transcription elongation factor SPT5  ali model follow..  98  977SDWVTTDIQVKVRDTYLDTQVVGQTGVIRSVTGGMCSVYLKDSEKVVSISSEHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKLLEA 1087
4 -26.7004ytl_A mol:protein length:99 Transcription elongation factor SPT5  ali model follow..  16  1...FQPGDRIEVLN----GEQRGSKGIVTRTTKDIATIKLNGFTTPLEFPISTLRKIF-EPGDHVTVINGEHQGDAGLVLMVEQGQVTFMSTQTSREVTITANNLSK.... 99
5 -20.2005xon_W mol:protein length:612 Protein that forms a complex with Spt4p  ali model follow..  17  275...FQPGDNVEIIN----GELNHLTGTVSSVNQSTIVSVRTINSETVEIPTSDLRKIF-NVGDHVRVIHGKHTDDTGLIVEVNGDKVEFISNQTKRTVIVFSNYLIKSTDS 383
6 -15.6005xog_W mol:protein length:83 Spt4/5 complex component  ali model follow..  18  21.............................................................NKTVKIRQGGYKGKIGIVKEANGDRFRVELHNPNKTIPIPCSFLLIESTH 70
7 -15.3002do3_A mol:protein length:69 Transcription elongation factor SPT5  ali model follow..  22  3..........................................SGSSGEFPAQELRKYF-KMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSE. 69
8 -14.8002e70_A mol:protein length:71 Transcription elongation factor SPT5  ali model follow..  14  21.............................................................GQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLTTV... 67
9 -12.6001s72_T mol:protein length:120 50S ribosomal protein L24P  ali model follow..  12  38.....................................................QRNVRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVE................... 76
10 -12.5002e6z_A mol:protein length:59 Transcription elongation factor SPT5  ali model follow..  22  9...........................................................QPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDDMLEFPAQELRKY... 59
11 -12.0005xy3_Y mol:protein length:138 Ribosomal protein L24, putative  ali model follow..  12  45.....................................................IKRLPIRRDDEVMIFSGRMQNRTGKVTAVKLSEMRIYVD................... 83
12 -11.6001nkw_S mol:protein length:115 50S ribosomal protein L24  ali model follow..  27  17...........................................................KKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVE................... 49
13 -11.6003jcs_W mol:protein length:143 ribosomal protein L24  ali model follow..  15  42.....................................................VRAMPVRKDDEVIVKRGTFKGREGKVTACYRLKWVILID................... 80
14 -11.5005t2a_X mol:protein length:143 uL24  ali model follow..  15  42.....................................................VRAMPVRKDDEVIVKRGAFKGREGKVTACYRLKWVIHID................... 80
15 -11.4002ww9_L mol:protein length:127 60S RIBOSOMAL PROTEIN L26-A  ali model follow..  17  45.....................................................IKALPIRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVD................... 83
16 -11.4003j6b_Q mol:protein length:297 54S ribosomal protein L40, mitochondrial  ali model follow..  20  64...........................................................IPGDRVVVMSGASKGNIAVIKSFDKRTNSFILDE.................. 97
17 -11.3005v7q_U mol:protein length:105 50S ribosomal protein L24  ali model follow..  30  4...........................................................HKGDTVLVISGKDKGAKGKVLQAYPDRNRVLVE................... 36
18 -11.2005o60_V mol:protein length:105 50S ribosomal protein L24  ali model follow..  30  4...........................................................HKGDTVLVISGKDKGAKGKVLVAYPDRNKVLVE................... 36
19 -11.2004v4i_S mol:protein length:110 50S ribosomal protein L24  ali model follow..  18  8...........................................................KKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVE................... 40
20 -11.2002gf7_A mol:protein length:119 Jumonji domain-containing protein 2A  ali model follow..  11  12..........KVISKHKNGRFY--QCEVVRLTTEFYEVNFDDGSFSDNLYPEDIVSQPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEE 117
21 -11.1004wce_R mol:protein length:105 50S ribosomal protein L24  ali model follow..  27  4...........................................................KKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVE................... 36
22 -11.1003j3v_U mol:protein length:103 50S ribosomal protein L24  ali model follow..  30  4...........................................................KKGDKVMVISGKDKGKQGTILAAFPKKDRVLVE................... 36
23 -11.1005xxb_X mol:protein length:141 Ribosomal protein uL24  ali model follow..  12  44.....................................................VRSLPIRKDDEVMVVRGHHHDREGKVTKVYRKKWVIHIE................... 82
24 -11.1005t5h_Z mol:protein length:113 60S ribosomal protein L26  ali model follow..  15  36.....................................................VRAMPVRKDDEVRVKRGAYKGREGKVTACYRLRWVIHID................... 74
25 -11.0003j7z_U mol:protein length:104 50S ribosomal protein L24  ali model follow..  15  6...........................................................RRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEG................... 38
26 -11.0003j79_Z mol:protein length:126 60S ribosomal protein uL24  ali model follow..  12  44.....................................................TRSLPVRKDDEVLICRGHNHGREGKVVKINRKRYKIYVE................... 82
27 -10.9005d6w_A mol:protein length:121 Lysine-specific demethylase 4A  ali model follow..  11  14..........KVISKHKNGRFY--QCEVVRLTTEFYEVNFDDGSFSDNLYPEDIVSQPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEE 119
28 -10.9002oug_A mol:protein length:162 Transcriptional activator rfaH  ali model follow..  18  55.......LFVEFPEVIHTTTINATRGVSHFVRFGASPAIVPSAQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEALLLNLINKEIKHSVKNTEFRKL... 162
29 -10.9004qvz_A mol:protein length:214 Fragile X mental retardation protein 1  ali model follow..  13  2....MEELVVEVRGS--NGAFY--KAFVKDVHEDSITVAFENNQPDRQIPFHDVRFPPPNESDEVEVYSRANEKELAKVRMIKGEFYVIEYAACDATEIVTIERL...... 113
30 -10.8004uc4_A mol:protein length:119 Lysine-specific demethylase 4B  ali model follow..  9  12..........VVITKNRNGLYY--RCRVIGAASQCYEVNFDDGSYSDNLYPESITSRPPSEGELVELRWTDGNLYKAKFISSVTSHIYQVEFEDGSQLTVKRGDIFTLEEE 117
31 -10.7005mlc_W mol:protein length:191 50S ribosomal protein L24, chloroplastic  ali model follow..  24  70...........................................................KVGDTVKVISGGEKGKIGEISKIHKHNSTVIIK................... 102
32 -10.6004ce4_Y mol:protein length:216 MRPL24  ali model follow..  17  57...........................................................FCGDKVEILEGKDAGKQGKVVQVIRQRNWVVVEG.................. 90
33 -10.5003j7y_V mol:protein length:216 uL24  ali model follow..  14  57...........................................................FCGDTVEILEGKDAGKQGKVVQVIRQRNWVVVGG.................. 90
34 -10.5001m1g_A mol:protein length:248 Transcription antitermination protein nusG  ali model follow..  20  139.......ILIKAMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSEKGDQVRVIEGPFMNFTGTVEEVHPEKVMISIFGRMTPVELDFDQVEKI... 248
35 -10.5003h8z_A mol:protein length:128 Fragile X mental retardation syndrome-related protein 2  ali model follow..  12  2...YFQGLPVEVRGS--NGAFY--KGFVKDVHEDSVTIFFENNWQSERIPFGDVRLPPPTEGDEVEVYSRANEQELARVRMMKGDFYVIEYAACDATYNVTLERL...... 114
36 -10.4002xdp_A mol:protein length:123 LYSINE-SPECIFIC DEMETHYLASE 4C  ali model follow..  12  12..........TVITKHRNTRYY--SCRVMAVTSQFYEVMFDDGSFSRDTFPEDIVSRPPAEGEVVQVKWPDGKLYGAKYFGSNIAHMYQVEFEDGSQIAMKREDIYTLDEE 117
37 -10.4005mmi_V mol:protein length:192 plastid ribosomal protein uL24c  ali model follow..  23  71...........................................................KVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKD.................. 104
38 -10.3002lq8_A mol:protein length:177 Transcription antitermination protein nusG  ali model follow..  26  124...........................................................KVGDMVKIISGPFEDFAGVIKEIDPERVNVTIFGRETPVVLHVSEVEKI... 176
39 -10.2003qqc_D mol:protein length:163 Transcription antitermination protein nusG  ali model follow..  16  46.......IFVEAPNKGVVDEAIRGIRHARGVLPGEVPF-----KEIEHFLEEKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQ................... 125
40 -9.8402xhc_A mol:protein length:352 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  16  236.......VFVEMIMNDEAYNFVRSVPYVMGF--------VSSGGQPVPVKDREMRPIL-KVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTETPVVLHVSEVEKI... 352
41 -9.7604zn1_A mol:protein length:147 Transcription elongation factor Spt5  ali model follow..  13  74...........................................EEIEPLLTPKKIIENIEKGDVVEIIAGPFKGERAKVIRVDKHKEEVTLELENAAVPIPIT........ 133
42 -9.6705ms0_F mol:protein length:183 Transcription termination/antitermination protein NusG  ali model follow..  16  87...................SVPRVMGFIGGTSDRPAPISDKEVDAIMNRLQQVGDKPRPEPGEMVRVNDGPFADFNGVVEEVDYEKVSVSIFGRATPVELDFSQVEKA... 183
43 -9.6102lcl_A mol:protein length:66 Transcriptional activator rfaH  ali model follow..  18  15...........................................................YPGDKVIITEGAFEGFQAIFTEPDGEALLLNLINKEIKHSVKNTEFRKL... 66
44 -9.4903lgf_A mol:protein length:125 Tumor suppressor p53-binding protein 1  ali model follow..  11  12..........RVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKGHESGELYYSIEKEGQRKWYKRMAVI..... 109
45 -9.3005oho_A mol:protein length:113 Transcription elongation factor SPT5  ali model follow..  18  12......................QTVGVIVRLERETFQV-LNMYGKVVTVRHQAVTRKK-HVKDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVE............... 98
46 -9.2104ytk_A mol:protein length:130 Transcription elongation factor SPT5  ali model follow..  12  2...........................................................EEGSYVRIKRGIYKGDLAMVDQISENNLEVML.................... 33
47 -9.2002g3r_A mol:protein length:123 Tumor suppressor p53-binding protein 1  ali model follow..  11  10..........RVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKGHESGELYYSIEKEGQRKWYKRMAVI..... 107
48 -9.1503j7o_Y mol:protein length:145 Ribosomal protein uL24  ali model follow..  12  44.....................................................VRSMPIRKDDEVQVVRGHYKGQIGKVVQVYRKKYVIYIE................... 83
49 -9.1402kvq_G mol:protein length:63 Transcription antitermination protein nusG  ali model follow..  20  11...........................................................EPGEMVRVNDGPFADFNGVVEEVDYEKVSVSIFGRATPVELDFSQVEKA... 63
50 -9.1005zcj_C mol:protein length:180 TP53-binding protein 1  ali model follow..  11  36..........RVVAKWSSNGYF--SGKITRDGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKGHESGELYYSIEKEGQRKWYKRMAV...... 132
51 -9.0702mi6_A mol:protein length:62 Transcription termination/antitermination protein NusG  ali model follow..  16  10...........................................................EVGESVTVMDGPFATLPATISEVNAEQVLVSIFGRETPVELTFGQVSKI... 62
52 -9.0201ssf_A mol:protein length:156 Transformation related protein 53 binding protein 1  ali model follow..  11  14..........RVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKRKESGELYYSIEKEGQRKWYKRMAV...... 110
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.

Rychlewski L, Zhang B, Godzik A. Functional insights from structural predictions: analysis of the Escherichia coli genome. Protein Sci. 1999 Mar;8(3):614-24.