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Query: 3dm3_A mol:protein length:105 Replication factor A, 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 EIKDTYNIGELSPGMTATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETGSIRVTLWDNLTDIDVGRGDYVRVRGYIREGYYGGLECTANYVEILKKGEKIESLast
1 -54.2003dm3_A mol:protein length:105 Replication factor A  ali model  100  1EIKDTYNIGELSPGMTATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETGSIRVTLWDNLTDIDVGRGDYVRVRGYIREGYYGGLECTANYVEILKKGEKIES 105
2 -46.1002k5v_A mol:protein length:104 Replication protein A  ali model follow..  43  3.....YKISELMPNLSGTINAEVVAAYPKKEFSRKDGTKGQLKSLFLKDDTGSIRGTLWNELADFEVKKGDIAEVSG-YVKQGYSGLEISVDNIGIIEKSLE... 98
3 -44.7003e0e_A mol:protein length:97 Replication protein A  ali model follow..  44  2....NYKISELMPNLSGTINAEVVTAYPKKEFSRKDGTKGQLKSLFLKDDTGSIRGTLWNELADFEVKKGDIAEVSG-YVKQGYSGLEISVDNIGIIEKS..... 96
4 -44.6002k50_A mol:protein length:115 Replication factor A related protein  ali model follow..  22  6...RMDTISKLEEGAETPVTGRVMKISSPRTFTTRKGREGKLANVIIADDTGELRAVFWTENIKLKFREGDVIRIKDVNIRGFGGRKEAHLMPRSTVEVLDPLE. 109
5 -39.0002mna_A mol:protein length:117 Single-stranded DNA binding protein (SSB)  ali model follow..  20  3.....EKVGNLKPNMEVNVTVRVLEASEARQIQTKNG-VRTISEAIVGDETGRVKLTLWGKHAGS-IKEGQVVKIENAWTTAFKGQVQLNAGSKTKIAEASE... 98
6 -38.9001wjj_A mol:protein length:145 hypothetical protein F20O9.120  ali model follow..  20  14..PVFVKVEQLKPGTTHTLTVKVIEANIVVPVTRRPSQPSRIVECLIGDETGCILFTARNDQVDL-MKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGA... 122
7 -38.6001o7i_A mol:protein length:119 SINGLE STRANDED DNA BINDING PROTEIN  ali model follow..  20  3.....EKVGNLKPNMEVNVTVRVLEASEARQIQTKNG-VRTISEAIVGDETGRVKLTLWGKHAGS-IKEGQVVKIENAWTTAFKGQVQLNAGSKTKIAEASEDG. 100
8 -37.7005d8e_A mol:protein length:115 SOSS complex subunit B1  ali model follow..  18  1.MTTETFVKDIKPGLKLNLIFIVLETGRVTKT----KDGHEVRTCKVADKTGSINISVWDDVGNL-IQPGDIIRMTKGYASVFKGCLTLYTGRGGDLQKIGE... 97
9 -37.4002kbn_A mol:protein length:109 Conserved protein  ali model follow..  18  3..PQLTKIVDIVENGQANLKAKVIQLWENTH-------ESISQVGLLGDETGIIKFTIWKNAELPLLEQGESYLLRSVVVGEYNDRFQVQVNKNSSIEKLSE... 96
10 -36.6002k75_A mol:protein length:106 uncharacterized protein Ta0387  ali model follow..  15  1..SDLVKIRDVSLSTPVSVIGKITGIHKKE--YESDGTTKSVYQGYIEDDTARIRISSFGKQ----LQDSDVVRIDNARVAQFNGYLSLSVGDSSRIESVNV... 95
11 -30.4004jbm_A mol:protein length:193 Interferon-inducible protein AIM2  ali model follow..  12  96ETPRISKLKIQPCGTIVNGLFKV----------QKITEEKDRVLYGIHDKTGTMEVLVLGNPSKTKCEEGDKIRLTFFEVSKNGVKIQLKSGPCSFFKVIKAAKP 190
12 -30.3002oq0_A mol:protein length:206 Gamma-interferon-inducible protein Ifi-16  ali model follow..  2...SHMQVTPRRNVQKRPVIVKVLSTTKPFEYETPEMEKKIMFHATVATQTQFFHVKVLNTSLKEKFNGKKIIIISDYLEYD-----LLEVNEESTVSEAGPNQT 100
13 -29.2003rn2_A mol:protein length:208 Interferon-inducible protein AIM2  ali model follow..  18  106KAGETPKINTLQTQPLGTIVNGLFVV-------QKVTEKKKNILFDLSDNTGKMEVLGVRNEDTMKCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTIKVIKAKKK 203
14 -27.7004owt_B mol:protein length:211 SOSS complex subunit B1  ali model follow..  18  1.MTTETFVKDIKPGLKLNLIFIVLETGRVTKT----KDGHEVRTCKVADKTGSINISVWDDVGNL-IQPGDIIRLTKGYASVFKGCLTLYTGRGGDLQKIGE... 97
15 -27.0004l5t_A mol:protein length:203 Interferon-activable protein 202  ali model follow..  11  107RPIEHLKICDLHLQTEERLVDGEFKVYRKSS-------GNNCICYGIWDDTGAMKVVVSGQLTSVNCEIGNTIRLVCFELTSNADEWFLRATRYSYMEVIMPEK. 203
16 -24.2004jbj_A mol:protein length:198 Interferon-activable protein 202  ali model follow..  18  110ETLKISKIKELDSGTLIYGVFAVEKKK----------VNDKSITFKIKDNEDNIKVVWDKEQHNINYEKGDKLQLFSFHLRKGNGKPILHSGNHSFIK....... 197
17 -23.3001jmc_A mol:protein length:246 PROTEIN (REPLICATION PROTEIN A (RPA))  ali model follow..  13  125DFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRNNREVAKRNIYLMDTSGVVTATLWGEDADKDGSRQPVLAIKGARVSDFGGR-SLSVLSSSTIIANPDIPE 231
18 -23.2004l5q_A mol:protein length:199 Interferon-activable protein 202  ali model follow..  16  82EINETATVSEAAPNQMFEVPKNIIRSAKEVFAVEKKKVNDKSITFKIKDNEDNIKVVWDKEQHNINYEKGDKLQLFSFHLRKGNGKPILHSGNHSFIKG...... 198
19 -22.7004lnq_A mol:protein length:197 Interferon-activable protein 202  ali model follow..  18  78EINETATVSEAAPNQMFEVPKNIIKISKIKELDSGTKVNDKSITFKIKDNEDNIKVVWDKEQHNINYEKGDKLQLFSFHLRKGNGKPILHSGNHSFIKGEK.... 196
20 -21.4001fgu_A mol:protein length:252 REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT  ali model follow..  14  121DFTGIDDLENKSKDSLVDIIGICKSYEDATKITRSNNREVAKRNIYLMDTSGVVTATLWGEDADKDGSRQPVLAIKGARVSDFGGR-SLSVLSSSTIIANPDIPE 227
21 -20.7001ynx_A mol:protein length:114 Replication factor-A protein 1  ali model follow..  19  1.TRPIFAIEQLSPYQVWTIKARVSYKGEIKTWHNQRG-DGKLFNVNFLDTSGEIRATAFNDFATKILQEGKVYYVSKAKLQPAKPPYELNLDRDTVIEECFDESN 114
22 -17.7003kjo_A mol:protein length:299 Protection of telomeres protein 1  ali model follow..  15  10...IYTPLNQLKGGTIVNVYGVVKFFKPPYLSKGTD-----CSVVTIVDQTNVLTCLLFSGNYEA-YKNGDIVRFHRLKIQVYKKETQGITSSGFASLTFEGTLG 111
23 -16.9004gnx_C mol:protein length:444 Putative uncharacterized protein  ali model follow..  12  120EFVRINELESVEANQQCDVIGILDSYGELSEIVSKSQRPVQKRELTLVDQGNSVKLTLWGKTAETGVDEKPVLAFKGVKVGDFGGR-SLSMFSSSTMLINPDITE 230
24 -16.6006d6v_D mol:protein length:701 Telomerase-associated protein 82  ali model follow..  358NGQKNNKYRQNNNNSKSEVLKTSKQYLSVLAVVDIQSSDKNIRLKICDNSCNELKVVIFPDLCYEKFSINKWYYFNEFVRQIYNDEVQLKNNIHSSIKESDDQRK 472
25 -15.6001qzg_A mol:protein length:187 Protection of telomeres protein 1  ali model follow..  10  40...........KKNTIVNLFGIVKDFTPSRQ--SLHGTKDWVTTVYLWDPT-GLQIHLFSKQGND-KQVGQPLLLHQITLRSYRDRTQGLSKDQFR......... 130
26 -14.3001jb7_A mol:protein length:495 telomere-binding protein alpha subunit  ali model follow..  18  37...EYVELAKASLAQPQHFYAVVIDATFPYKTNQER-----ICSLKIVDPTDYATLVLYAKRFED-HRAGDIIRVHRATLRLYNGQRQFNANVFYS......... 143
27 -14.1003nbh_B mol:protein length:147 RecQ-mediated genome instability protein 2  ali model follow..  20  56..............AAVWMQGRVVMADR--------------GEARLRDPSGDFSVRGLERVPRPCLVPGKYVMVMG-VVQACSPEPCLQAVKMTDLSDNPIHES 133
28 -13.8003mxn_B mol:protein length:150 RecQ-mediated genome instability protein 2  ali model follow..  20  59..............AAVWMQGRVVMADR--------------GEARLRDPSGDFSVRGLERVPRPCLVPGKYVMVMG-VVQACSPEPCLQAVKMTDLSDNPIHES 136
29 -13.6004gnx_B mol:protein length:136 Putative uncharacterized protein  ali model follow..  18  14.IRQILNAEQPHPDAEFILDGAELGQLTFVAVVRNISRNATNVAYSVEDGTGQIEVRQWLDSSSDDIRNNVYVRVLG-TLKSFQNRRSISSGHMRPVIDYNEV.. 120
30 -13.5004joi_A mol:protein length:166 CST complex subunit STN1  ali model follow..  23  37..............KQVDVLGTVIGVRERDAFYS----------YGVDDSTGVINCICWKKLNTESIEIGDTIRVRG-SIRTYREEREIHATTYYKVD....... 138
31 -12.9001nnx_A mol:protein length:109 Protein ygiW  ali model follow..  14  24SVTTVESAKSLRDDTWVTLRGNIVERISDDLY-------------VFKDASGTINVDIDHKR-GVTVTPKDTVEIQG-EVDKDWNSVEIDVKQIRKVN....... 108
32 -12.6004hid_A mol:protein length:143 Protection of telomeres protein 1  ali model follow..  21  3..DSFSLLSQITPHQRCSFYAQVIKTWY----------SDKNFTLYVTDYTENIRCILWDEHDFNYIKEGDYVVMKNVRTKIDHLG................... 102
33 -12.6002pi2_A mol:protein length:270 Replication protein A 32 kDa subunit  ali model follow..  16  49.....CTISQLLSATQVTIVGIIRHAEK----------APTNIVYKIDDMTAAPMDVRQWVDTDDTVPPETYVKVAG-HLRSFQNKKSLVAFKIMPLEDMNEF.. 155
34 -12.5003kf6_A mol:protein length:159 Protein stn1  ali model follow..  15  48..............RWIQIVGYIAAIDIYEG----------KHVLTVDDCSGMVLRVVFIIQDDFSMSPGNVVCVFG-KINSFRSEVELIAQSFEELRDPNDE.. 132
35 -12.5003kf8_A mol:protein length:220 Protein stn1  ali model follow..  11  84............PVNQINIFGKIVYEQYKEKEFNGVEESYVI--LVISDFIGIDSKIRVRLSQEQKKNYGKIVELEG-EIYNWYDSINVSKKPDRELKVSK.... 178
36 -12.3003rln_A mol:protein length:200 Gamma-interferon-inducible protein 16  ali model follow..  14  77EVYPFTLVADVNADRNMEIPAGLIASASVTPEVHKKNVRGEFTYYEIQDATGKMEVVVHGRLTTINCEEGDKLKLTCFELAPKSGNGELRSVIHSHIKVIKTRKN 200
37 -11.8003rlo_A mol:protein length:204 Gamma-interferon-inducible protein 16  ali model follow..  14  77EVYPFTLVADVNADRNMEIPKGLIRSASVTPEVHKKNVRGEFTYYEIQDNTGKMEVVVHGRLTTINCEEGDKLKLTCFELAPKSGNGELRSVIHSHIKVIKTRKN 200
38 -10.9004gla_C mol:protein length:109 OBody NL8  ali model follow..  20  7KTHWTAEITPNLHGTEVVVAGWVASLGDY----------GRVKIVKVSDREGGAAVPVYLEAGKAELSREDVVVIKGIVEAS-GRGVEIFPSEIWILNKAKA... 109
39 -10.4001x54_A mol:protein length:434 Asparaginyl-tRNA synthetase  ali model follow..  19  3EKVYCQEVKPELDGKKVRLAGWVYTNM----------RVGKKIFLWIRDSTGIVQAVVAKNVVGEELGRESSVIVEGIVKAD-PGGAEVHVEKLEVIQAVSE... 103
40 -10.3004gn5_A mol:protein length:113 OBody AM3L15  ali model follow..  20  5KTHWTAEITPNLHGSEVVVAGWVAHLGD----------YGRVKIVKVSDREGGAAVPVYLERGKAELSREDVVVIKGIVEAGWPTGVEIFPSEIWILNKAKPLP. 111
41 -10.0001b8a_A mol:protein length:438 PROTEIN (ASPARTYL-TRNA SYNTHETASE)  ali model follow..  19  3RTHYSSEITEELNGQKVKVAGWVWEVK----------DLGGIKFLWIRDRDGIVQITAPKKKVDPELRSEDVVAVEGVVNFTPKAGFEILPEKIVVLNRAET... 103
42 -9.7106bwy_A mol:protein length:361 Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion  ali model follow..  29.....SSQELQKKNTIVNLFGIVKDFTPSR--QSLHGTKDWVTTVYLWDPTIGLQIHLFSKQGND-KQVGQPLLLHQITLRSYRDRTQGLSKDQFR......... 125
43 -9.4004gn4_B mol:protein length:108 OBody AM2EP06  ali model follow..  20  6KTHWTAEITPNLHGSEVVVAGWVAHLGD----------YGRVKIVKVSDREGGAAVPVYLERGKAELSREDVVVIKGIVEASEQTGVEIFPSEIWILNKA..... 108
44 -9.3701wyd_A mol:protein length:429 hypothetical aspartyl-tRNA synthetase  ali model follow..  20  3RSHFIADVTPEYDGKEVIWAGWVHLLR----------DLGGKKFIILRDKTGLGQVVVDKNSSAQELTQESVIQVRGIVKAD-PRGIELHAEEITLLSKAKA... 100
45 -9.3604glv_B mol:protein length:107 OBody AM3L09  ali model follow..  20  5KTHWTAEITPNLHGSEVVVAGWVAHLGD----------YGRVKIVKVSDREGGAAVPVYLERGKAELSREDVVVIKGIVEATTVTGVEIFPSEIWILNKA..... 107
46 -9.3603au7_A mol:protein length:402 Putative uncharacterized protein  ali model follow..  12  265HLIGEEEVHRLENYRSYRLRGRVTLEPYDI--------EGGHVFFEIDTKFGSVKCAAFEPTKQRLLRKGDVVEVYGSMKKDTINLEKIQIVELAE......... 357
47 -9.0704j15_A mol:protein length:521 Aspartate--tRNA ligase, cytoplasmic  ali model follow..  58VLVRVRDLTIQKADEVVWVRARVHTSR----------AKGKQCFLVLRQQQFNVQALVAVGDHAANINKESIVDVEGVVRKVNQQDVELHVQKIYVISLAEP... 164

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.

Ye Y, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics. 2003 Oct;19 Suppl 2:II246-II255.