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Query: 1rio_A mol:protein length:98 Repressor protein CI, 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 MSTKKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEFSPSIAREIYEMYEAVLast
1 -48.5001rio_A mol:protein length:98 Repressor protein CI  ali model  100  1MSTKKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEFSPSIAREIYEMYEAV 92
2 -46.4001lli_A mol:protein length:92 PROTEIN (LAMBDA REPRESSOR)  ali model follow..  96  1.STKKKPLTQEQLEDARRLKAIYEKKKNELGLSQESLADKLGMGQSGIGALFNGINALNAYNAALLAKILKVSVEEFSPSIAREIYEMYEAV 91
3 -40.9003kz3_A mol:protein length:80 Repressor protein CI  ali model follow..  92  1......SLTQEQLEDARRLKAIWEKKKNELGLSYESVADKMGMGQSAVAALFNGINALNAYNAALLAKILKVSVEEFSPSIAREIR...... 80
4 -30.5002wiu_B mol:protein length:88 HTH-TYPE TRANSCRIPTIONAL REGULATOR HIPB  ali model follow..  12  2.......MSFQKIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAKNASPESTEQQNL 86
5 -30.3002ef8_A mol:protein length:84 Putative transcription factor  ali model follow..  21  9................RCLVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVASRLGLPMDILLKDTYESISK. 83
6 -29.7003bdn_A mol:protein length:236 Lambda Repressor  ali model follow..  100  1.STKKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEFSPSIAREIYEMYEAV 91
7 -29.5003f6w_A mol:protein length:83 XRE-family like protein  ali model follow..  14  13................QALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYALLSKLEAMTPS..... 83
8 -29.5001adr_A mol:protein length:76 P22 C2 REPRESSOR  ali model follow..  14  2..............NTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLL.............. 65
9 -29.4005k98_B mol:protein length:91 Antitoxin HipB  ali model follow..  12  5.......MSFQKIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDTKNASPESTEQQDL 89
10 -29.1004z5h_A mol:protein length:72 Antitoxin HipB  ali model follow..  14  3..........QKIYSPTQLANAMKLVRQQNGWTQAELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAK............ 72
11 -28.9003g5g_A mol:protein length:99 Regulatory protein  ali model follow..  20  1MGSSSSGLVPRESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK..... 91
12 -28.9002mez_A mol:protein length:106 Multiprotein Bridging Factor (MBP-like)  ali model follow..  20  1........ENAELEIVTDYYKIIKTAREQLGISQQQLAQKLKVSENIVKRFESGKLKPTISQARQLEKILGIKLVTPLENNEESEKEFDDT. 83
13 -28.7004ia8_A mol:protein length:82 Regulatory protein  ali model follow..  20  2........SHMESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTAISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK..... 80
14 -28.6004i6t_A mol:protein length:82 Regulatory protein  ali model follow..  20  2........SHMESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRAYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK..... 80
15 -28.6004i6u_A mol:protein length:82 Regulatory protein  ali model follow..  20  2........SHMESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTFISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK..... 80
16 -28.5003fya_A mol:protein length:99 Regulatory protein  ali model follow..  20  13........SHMESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDATYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK..... 91
17 -28.5003mlf_A mol:protein length:111 transcriptional regulator  ali model follow..  10  10..........ENLYFQSNAMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNVKYDDIF.............. 77
18 -28.4004fn3_A mol:protein length:82 Regulatory protein  ali model follow..  20  2........SHMESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKALELIMKGLEVSDVVFFEMLIKEILK..... 80
19 -28.4004f8d_A mol:protein length:82 Regulatory protein  ali model follow..  20  2........SHMESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSANLTIKSLELIMKGLEVSDVVFFEMLIKEILK..... 80
20 -28.3002b5a_A mol:protein length:77 C.BclI  ali model follow..  20  3..........NEIEIKRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPASTFFRKMEEE........ 76
21 -28.3002k9q_A mol:protein length:77 uncharacterized protein  ali model follow..  17  2.................ELSNELKVERIRLSLTAKSVAEEMGISRQQLCNIEQSETAPVVVKYIAFLRSKGVDLNALFDRIIVNKLE..... 71
22 -28.2001x57_A mol:protein length:91 Endothelial differentiation-related factor 1  ali model follow..  10  9.............RVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGKD.............. 73
23 -28.1003ivp_A mol:protein length:126 Putative transposon-related DNA-binding protein  ali model follow..  22  3........KKEDKYDFRALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSVDEFF.............. 72
24 -28.0003bs3_A mol:protein length:76 Putative DNA-binding protein  ali model follow..  10  7..............NQQMMLNRIKVVLAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELLNVDPRQLING............ 72
25 -27.9003lfp_A mol:protein length:98 Csp231I C protein  ali model follow..  25  2..................LIRRLKDARLRAGISQEKLGVLAGIDEASMNQYEKGKHAPDFEMANRLAKVLKIPVSYLY.............. 65
26 -27.8003omt_A mol:protein length:73 uncharacterized protein  ali model follow..  14  5..............TERKIFNRLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVRELI.............. 68
27 -27.5002xiu_A mol:protein length:66 CYLR2  ali model follow..  10  2..................IINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNCPLEDIFQWQPE......... 66
28 -27.4001utx_A mol:protein length:66 CYLR2  ali model follow..  10  2..................IINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIFQWQPE......... 66
29 -27.4001y7y_A mol:protein length:74 C.AhdI  ali model follow..  24  4........HHDHYADLVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPRELF.............. 73
30 -27.3002kpj_A mol:protein length:94 SOS-response transcriptional repressor, LexA  ali model follow..  10  10..................FSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNINKSDLIEDKKLNIDTVPIE. 82
31 -27.2004o8b_A mol:protein length:122 Uncharacterized protein  ali model follow..  18  2..................LGTRLKAARIRAGYSQKQLGMLVGMDSARMNQYERERHSPNMRTSEQLAMVLQVPMAYLY.............. 65
32 -27.2003op9_A mol:protein length:114 Pli0006 protein  ali model follow..  15  3...........AMTIQHQFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHLSIDELVGYVQED........ 75
33 -27.1005uk3_A mol:protein length:176 Uncharacterized protein  ali model follow..  15  1MRIYSRLFQSSANYARQIMSNQFIKAKESKGLTYQQMAQLLSVNKVWLTSVLHGQNCCDIQLAHRICDTLGISHEYAN.............. 79
34 -27.1003vk0_A mol:protein length:114 Transcriptional regulator  ali model follow..  15  5.KLTLPAELPDEQDLRAVLAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVERKRWNIALSNIEKMAAALGVAAYQLLLPPQERLKLMTNS. 94
35 -27.1003kxa_A mol:protein length:141 Putative uncharacterized protein  ali model follow..  20  56...........DKIALKAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLEVRAAFERRYEYMEQA. 135
36 -26.8005j2y_A mol:protein length:80 Regulatory protein  ali model follow..  13  1.......MASHERTQPQNMAFRAKATRTARRESQETFWSRFGISQSCGSRFENGENLPFIYLLLHFYIEGQITDRQLAD............. 73
37 -26.4002l49_A mol:protein length:99 C protein  ali model follow..  9  2...............SNTISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQTPQFTKYTLW.............. 64
38 -26.4001b0n_A mol:protein length:111 PROTEIN (SINR PROTEIN)  ali model follow..  16  2..................IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNQTNPSIQFLEKVSAVLDVSVHTLLDEKHET........ 68
39 -26.3003eus_A mol:protein length:86 DNA-binding protein  ali model follow..  14  1....QAMTKTLRTPEHVYLCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAACEG.................... 68
40 -26.3002ewt_A mol:protein length:71 putative DNA-binding protein  ali model follow..  29  2...........SSEYAKQLGAKLRAIRTQQGLSLHGVEEKSQWKAVVVGSYERGDRAVTVQRLAELADFYGVPVQELLP............. 71
41 -26.2001per_L mol:protein length:69 PROTEIN (434 REPRESSOR)  ali model follow..  27  1.................SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK-RPRFLPELASALGVSVDWLLNGTSDS........ 66
42 -26.0002ofy_A mol:protein length:86 Putative XRE-family transcriptional regulator  ali model follow..  19  1..MVRVPLTAEELERGQRLGELLRSARG--DMSMVTVAFDAGISVETLRKIETGRATPAFFTIAAVARVLDLSLDDVAAVVTFGPVSTS... 86
43 -25.8002p5t_A mol:protein length:158 Putative transcriptional regulator PezA  ali model follow..  12  2..................IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYVDIVGE............ 63
44 -25.7003f51_A mol:protein length:117 Clp gene regulator (ClgR)  ali model follow..  14  12.ISESAPRKAPEPLLREALGAALRSFRADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHALGASVADVLIEAAGS........ 94
45 -25.5004ghj_A mol:protein length:101 Probable transcriptional regulator  ali model follow..  21  24...........AAALAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAEKGKVQLDIMIAILMALDLTEQIDLFIPK............ 92
46 -25.5001zug_A mol:protein length:71 PHAGE 434 CRO PROTEIN  ali model follow..  18  2................QTLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTK-RPRFLFEIAMALNCDPVWLQ.............. 62
47 -25.3005woq_A mol:protein length:120 Transcriptional regulator ClgR  ali model follow..  7  9................EVIGDVLRNARTDQGRTLREVSDAARVSLGYLSEVERGRKEASSELLSAICDALDVPLSRVLTDAGESMARREHDA 84
48 -25.2001sq8_A mol:protein length:64 dh434  ali model follow..  27  3..................MGERIRARRIQLGLNQAELAQKVGVDQQAIEQLENGKAK-RPRFLPELARALGVAVDWLL.............. 61
49 -25.2002jvl_A mol:protein length:107 TrMBF1  ali model follow..  12  30.............TVGKEVGKAIEQGRQEPTMTQAELGKEIGETAATVASYERGTATPDQNILSKMERVLNVKLRGAN.............. 96
50 -25.2002r63_A mol:protein length:63 REPRESSOR PROTEIN FROM BACTERIOPHAGE 434  ali model follow..  30  1.................SISSRVKSKMIQLGLNQAELAQKVGTTQQSIEQLENGKTK-RPRFLPELASALGVSVDWLL.............. 60
51 -25.1005a7l_A mol:protein length:80 CI  ali model follow..  19  3................TDTSNRLKQIMAERNLKQVDILNLIKLSKSTLSQYVNSVQSPDQNRIYLLAKTLGVSEAWLM.............. 73
52 -25.1004pu3_D mol:protein length:118 Toxin-antitoxin system antidote transcriptional repressor Xre family  ali model follow..  9  26YEDTLLETIMASPLNQQSLGLLIKERRKSAALTQDVAAMLCGVTKKTLIRVEKGED-VYISTVFKILDGLGIDIVSAQTSDTET........ 108
53 -24.8006b9s_A mol:protein length:457 Methylphosphonate synthase  ali model follow..  11  2....EKKIDFKPDSYLIRSGNNFLGILNDIKRRPEDAANELGVSIEEINSIISGKQKISPSLIEKAVNIWPVNERDFYIVSDDCSSGIL... 86
54 -24.7003zhi_A mol:protein length:83 CI  ali model follow..  19  4................TDTSNRLKQIMAERNLKQVDILNLIKLSKSTLSAYVASVQSPDQNRIYLLAKTLGVSEAWLM.............. 74
55 -24.6004y42_A mol:protein length:156 Cyanate hydratase  ali model follow..  17  4........SLHYSSPRETLTDTIMMAKIRKNLTFEAINQGTGLSLAFVTAALLGQHPLPEQAARVVAEKLDLDEDAIR.............. 73
56 -24.4003zhm_A mol:protein length:79 CI  ali model follow..  19  2................TDTSNRLKQIMAERNLKQVDILNLIKLSKSTLSQYVNSVQSPDQNRIYLLAKTLGVSEAWLM.............. 72
57 -23.8003qq6_A mol:protein length:78 HTH-type transcriptional regulator sinR  ali model follow..  15  2...............SSMIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNQTNPSIQFLEKVSAVLDVSVHTLLDEKHET........ 71
58 -23.6001dw9_A mol:protein length:156 CYANATE LYASE  ali model follow..  24  4........SQINRNIRLDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSIL.............. 73
59 -23.5001y9q_A mol:protein length:192 transcriptional regulator, HTH_3 family  ali model follow..  15  1.......MSLTDVMFKSQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFSAFFAN............ 73
60 -23.4001zz6_A mol:protein length:198 Hydroxypropylphosphonic Acid Epoxidase  ali model follow..  14  2.........SNTKTASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGELTLTQLGRIAHVLGTSIGALTPPAGNDLDD..... 80
61 -23.1006b9r_A mol:protein length:450 Hydroxyethylphosphonate dioxygenase  ali model follow..  11  1..MSTPDALGSDAARAARAAALLRAAANDLKRNDRAAEADLGLPPGSFGDYVSGRLPITWDLISRAAQAWPLNERDLLPIHNDTPQGLR... 87
62 -22.7003b7h_A mol:protein length:78 Prophage Lp1 protein 11  ali model follow..  22  3.............TDGEFVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFEGRSKPTITTIRKVCGTLGISVHDFFD............. 69
63 -22.5002qfc_A mol:protein length:293 PlcR protein  ali model follow..  17  4................EKLGSEIKKIRVLRGLTQKQLSENI-CHQSEVSRIESGAVYPSMDILQGIAAKLQIPIIHFYEVLIYSDIERKKQF 78
64 -21.3005fd4_A mol:protein length:324 ComR  ali model follow..  10  1MGSSSSGLVPR-FMNDKEFGQRVRQLRESASMTREQFCDELELSVRQLTRIEAGASKPTFSKIQYIATRLGMGLYELMPDYVSLPERYSK.. 97
65 -21.3002aw6_A mol:protein length:317 PrgX  ali model follow..  12  2................FKIGSVLKQIRQELNYHQIDLYSGI-MSKSVYIKVEADSRPISVEELSKFSERLGVNFFEILNRAGMNTKSVNETG 76
66 -21.1004yv6_A mol:protein length:284 Transcriptional regulator  ali model follow..  18  3................KELGKTLRRLRQGKQVSISSLADEH-LSKSQISRFERGESEISCSRLLNLLDKLNITIDEFV.............. 63
67 -20.8005jub_A mol:protein length:310 Transcriptional regulator  ali model follow..  12  1............MNLKDSIGLRIKTERERQQMSREVLCLDGELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTELLDQDNITIPDEYYEM 81
68 -20.8003rzz_A mol:protein length:446 Hydroxyethylphoshphonate Dioxygenase (PhpD)  ali model follow..  11  216WSTGAFEEALKALSGKVSAGSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSASETGLTVLRTLGRALGFDYRVLLPADDQH........ 300
69 -20.7004ryk_A mol:protein length:306 Lmo0325 protein  ali model follow..  13  2................GSYGELIREIRLSKGLTQKEVYTGI-ISRSYAIGFEKGKHEITLSLFEEILKRIMVPLDEFFFIYRDFSSTEDDSF 76
70 -20.4005v5t_A mol:protein length:306 Conserved domain protein  ali model follow..  17  1.........QKEYMEYRPLGEEIERIRKGKNIPLRVFDEN-GVSSRSYQRFVQGNSELRISDLAIIVEILSISPMEMT.............. 68
71 -20.3002mqk_A mol:protein length:65 ATP-dependent target DNA activator B  ali model follow..  7  4..............NISDIRAGLRTLVENEETTFKQIALESGLSTGTISSFINDKYNGDNERVSQTLQRW...................... 59
72 -20.0002a6c_A mol:protein length:83 Helix-turn-helix motif  ali model follow..  17  3........SDKIMKMRSQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKDLFSLESLIDMITSIGLKVE................. 70
73 -19.1002o38_A mol:protein length:120 Hypothetical protein  ali model follow..  25  31........DAEERQTKLRLAYALNAVIDRARLSQAAAAARLGINQPKVSALRNYKEGFSVERLMTLLNALDQDVE................. 98
74 -19.0001s4k_A mol:protein length:120 putative cytoplasmic protein ydil  ali model follow..  8  1...............AMMNALELQALRRIFDMTIEECTIYITNNSATWQRWEAGDIPISPEIIARLKEMKARRQRRI............... 64
75 -18.7005y69_A mol:protein length:151 chain A  ali model follow..  11  2................SMTIKLLDEFLKKHDLTRYQLSKLTGISQNTLKDQNEKPNKYTVSILRSLSMISGLSVSDVLFELED......... 69
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.

Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics. 2002 Jan;18(1):77-82.