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anford Burnham Prebys Medical Discovery Institute

Query: d1i6aa_ c.94.1.1 (A:) Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain {Escherichia coli [TaxId: 562]}, from SCOP206

Results of FFAS03 search in SCOP206
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 ETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALVKESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGITLLPALAVPPERKRDGVVYLPAIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDGHFDLast
1 -111.000d1i6aa_ c.94.1.1 (A:) Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors  100  1ETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALVKESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGITLLPALAVPPERKRDGVVYLPAIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDGHFD 212
2 -101.000d3jv9a_ c.94.1.0 (A:) automated matches {Neisseria meningitidis [TaxId: 122586]}  ali model 3D-neighbors follow..  32  1...EGAFKLGLIFTVAPYLLPKLIVSLRRTAPKMPLMLEENYTHTLTESLKRGDVDAIIVAEPFQEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRMLGEEQVLLLTEGNCMRDQVLSSCSELAAKQRITLQGSSINTIRHMVASGLAISVLPATALT-ENDHMLFSIIPFEGTPPSRRVVLAYRRNFVRPKALSAMKAAIMQSQLHGVS 213
3 -98.900d3ho7a1 c.94.1.0 (A:90-308) automated matches {Porphyromonas gingivalis [TaxId: 837]}  ali model 3D-neighbors follow..  30  1...TGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGEIDMAIIASKAETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDEGHCFRDQLVRFCQMKGLHERQAYSGGSMEAFMRLVESGQGITFIPQLTVEQLSPSQKELVRPFGMPRPVREVRLAVRQDYSRRKLREQLIGLLRSAVPSDMH 210
4 -51.500d1ixca2 c.94.1.1 (A:90-294) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}  ali model 3D-neighbors follow..  14  2....GELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASV--AAIRWPDIAFARIVGTRVKVPISCIFRKEKQ-PPILARFVEHVRRSAKD... 205
5 -51.400d2fyia1 c.94.1.1 (A:88-307) LysR-type regulatory protein Cbl {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  20  2NDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASRLSNDPQLVAFPWFRWHHSLLVPHDHPLTQISPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAEQSSG-EQEEENLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSV... 210
6 -50.100d1al3a_ c.94.1.1 (A:) Cofactor-binding fragment of LysR-type protein CysB {Klebsiella aerogenes [TaxId: 28451]}  ali model 3D-neighbors follow..  19  2WPDKGSLYVATTHTQARYALPGVIKGFIERYPRVSLHMHQGSPTQIAEAVSKGNADFAIATALHLYDDLVMLPCYHWNRSIVVTPEHPLATKGSVSIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGVGVIASMAVD-PVSDPDLVKLDANGIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTR... 210
7 -33.200d3oxna_ c.94.1.0 (A:) automated matches {Vibrio parahaemolyticus [TaxId: 670]}  ali model 3D-neighbors follow..  18  7.....TFTIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVEPLRSEILGRVGVLCLLSKQHPLANQEMSLDDYLSHPHAMIAISDKALIEQALI----DKPQRKMVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTPFDYSMIWHARCEHSPAQEWLRSVVREECSRLIA 211
8 -32.800d2y7pa1 c.94.1.1 (A:90-301) automated matches {Burkholderia sp. [TaxId: 233098]}  ali model 3D-neighbors follow..  14  2DPFASTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNHGEVDGLLE---RAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSE... 211
9 -32.000d4rpoa_ c.94.1.0 (A:) automated matches {Sphingobium chlorophenolicum [TaxId: 46429]}  ali model 3D-neighbors follow..  14  3DPGTSNFRIAASDFGQALMLPRLYATLEETAPQVRVTGVNLRHGPLVEELESGSIDIAFGGFPTLSAGIKTQTLFREEYVCVMRQSHPALTHGLDLEAFRQCRHIIVTAHEHEQVEARLL---ELLPPESIRFTTENFLVSAVIAEETDVILTIPSRLARWFANRGGLTIFPVPIELPSIEVKQYWHERYDKDPGNIWLRRVIAKIGFQ... 214
10 -30.200d2esna2 c.94.1.1 (A:92-303) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]}  ali model 3D-neighbors follow..  13  2VPGQSQFVFAATDYTAFALLPPLMNRLQHSAPGVRLRLVNAERKLSVEALASGRIDFALGYDEEHEEGIQAHDWFADRYVVVARRDHPRLAGAPTLEGYLAERHAVVTPWNSGVIDRLLA---RSGLRREVAVQLPTVLAALFLAGSTDFLLTAPRHAARALAEAAGLALYPAPFDIPPYVLRLYSHVQHVGRDAHAWMIGQLKGL...... 211
11 -13.200d4io2a1 c.94.1.0 (A:3-248) automated matches {Adineta vaga [TaxId: 104782]}  ali model 3D-neighbors follow..  11  5...GITLRIGVIESVPFTIV-DLIEYLRDKM-DVQLAPPNTSYTGLVLALANGDYDIAIGDITVTSARREIVSISDNSMRILMRKGTLIDGMDDLKNGKIPYNRI--IRIGTAGEDYYLREISGGSRNFYP---KSRQEMYDSLLAGIIDVSFMDIGTAEYVTNNIYCNLTLVGEDFDKSTFGIVTPKEWLYAKDLDVNILSLRE....... 228
12 -13.100d4gvoa_ c.94.1.0 (A:) automated matches {Listeria monocytogenes [TaxId: 169963]}  ali model 3D-neighbors follow..  11  1...VQTITVGTGTQFPNVCF-ELVKEIDKRLPGYKFKFKTMDFSNLLVSLGAGKVDIVAHQMEKSKEREKKFLFNDVAYNNFPLQLTVLDSNNSINSTKDLAGKRVITSATSNGALVLKKINEEQGNNFEIAYEGQGSNDTANQLKTGADATISTPFAVDFQNKTSAIKEKVVGDVLSNAKVYFMLGKDE------TKLSKKVDEALQSIID 215
13 -12.900d4dz1a_ c.94.1.0 (A:) automated matches {Salmonella enterica [TaxId: 28901]}  ali model 3D-neighbors follow..  12  4...GRTLNVAVSPASPPMLF-ELFSSYCQSR-HCKLNITEYAWDGMLGAVASGQADVAFSGISITDKRKKVIPYYINSFYLVSMANHKITLN---NLNELNKYSI--YPRGMAYSDLIKNDLEPKGYYSLSKVKPTYNETMADLKNGNLDLAFIEEPVYFTFKNKKKMPIESRYVFKNVDQLGIAFKKGSPVRDDFNLWLKEQGP....... 217
14 -10.900d2ylna_ c.94.1.0 (A:) automated matches {Neisseria gonorrhoeae [TaxId: 485]}  ali model 3D-neighbors follow..  15  13...KGTVTVGTEGTYAPFTY-EVTRAVAEKL-GVKVEFKETQWDSMMAGLKAGRFDVVANQVGLTSPERQATFDKSEPYSWSGAVLVAHNDSNIKSIADIKGVKT-----AQSLTSNYGEKAKAAGAQLVPVDGLA--QSLTLIEQKRADATLNDELAV-KKNPNAGVKIVWSAPADEKVGSGLIVNKGND------EAVAKFSTAINELKA 221
15 -10.700d3kzga_ c.94.1.0 (A:) automated matches {Legionella pneumophila [TaxId: 272624]}  ali model 3D-neighbors follow..  14  1...SLNLTIGTSKFNPPFLMQEICRRL-----HATCTFEAYIFDDLFPALKNREVDLVIASMIITDERKKSLPYMESNSQYITTVDSKISTFDDLHGKKIIQDMLLGLSNNQSLMDYEAAKYWMASEPYAYKLIGKKYKLIGKKISIGEGYSIMANPDQFVLIKKINKILLEMEADGTYLRLYSEY.......................... 227
16 -10.300d2q88a1 c.94.1.0 (A:1-256) automated matches {Rhizobium meliloti (Sinorhizobium meliloti) [TaxId: 382]}  ali model 3D-neighbors follow..  15  11...QGFARIA-IANEPPFTAPDVAREIFKRLGVADVVASISEYGAMIPGLQAGRHDAITAGLFMKPERCAAVA-YSQPILFALKKGNPLGLKSYKDIADNPDAKI--APGGGTEEKLALEAGVPRDRVIVVPDGQSGLKMLQDGRIDVYSLPVLSINDLVSKANDPNVEVLAPVEGAPVYCDGAAFRKGDE------ALRDAFDVELAKLKE 226
17 -10.100d4eq9a_ c.94.1.0 (A:) automated matches {Streptococcus pneumoniae [TaxId: 637987]}  ali model 3D-neighbors follow..  1...KKEIIVATNGSPRPFIY-EVVRAIFKDSDKYDVKFEKTEWSGVFAGLDADRYNMAVNNLSYTKERLYAAPIAQNPNVLVVKKDD----SSIKSLDDIGGKSTEVVQATTSAKQLEAYNAEHTDNPTILNYTKADFQQIMVRLSDGFDYKIFDKIGVETVIKNQGLDNLKVIELPSDQQPYVYPLLAQGQDELKSFVDKRIKELYKD... 217
18 -9.850d3k4ua1 c.94.1.0 (A:2-233) automated matches {Wolinella succinogenes [TaxId: 844]}  ali model 3D-neighbors follow..  14  2....GELRVGLEPGYLPFEM-DLAREMAKAM-GVKLKLVPTSWDGLIPGLVTEKFDIIISGMTISQERNLRVN-FVEPYILLVKKGL---EKGVKSYKDLDKPELTLTKFGVSAEYAAKRLFKNAKLKTYDTEAEAVQEVLNGKADMFIFDLPFNVAFM---AQKGQGYLVHLDTSLTYEPLGWAIKKGDP--DFLNWLNHFLAQIKHD... 213
19 -9.700d3vvfa1 c.94.1.0 (A:1-236) automated matches {Thermus thermophilus [TaxId: 262724]}  ali model 3D-neighbors follow..  14  11...SGEIRIGTEGAFPPFNY-DLGNAIAERL-GLKPRWIAQSFDTLLIQLNQGRFDFVIASHGITEERARAVD-FTNPHYCTGGV---SRKGGPRTAKDLQGKVV-----GVQVGTTYMEAAQKIPGIKEVRTYQRDPDALQDLLAGRIDTWITDRFVAKEAIKERKLENTLQVGEL-QERVAMAVAKGNK------SLLDALNRALAELMQ 217
20 -9.590d2pvua_ c.94.1.0 (A:) automated matches {Geobacillus stearothermophilus [TaxId: 1422]}  ali model 3D-neighbors follow..  11  4...KKKVVVGTDAAFAPFEYMQLLDAVMKAA-GLDYELKNIGWDPLFASLQSKEVDMGISGITITDERKQSYPYFEATQVILVKQGSPVKNALDLKGKTIG------VQNATTGQEAAEKL---FGKGPHIKKFETTVVAIMELLNGGVDAVITDNAVANKNNPNKKLQVIEDPKNFASEYYGMIFPKNSELKAKVDEALKNVIN....... 212
21 -9.290d3mpka_ c.94.1.0 (A:) automated matches {Bordetella pertussis [TaxId: 257313]}  ali model 3D-neighbors follow..  17.....VVKVAVLNLFAPFISAAVLQLLQLRTGLDFEIIGVDTVEELIAKLRSGEADMAGALFVNSARESFSRPYVRNGMVIVTRQDPDAPV----DADHLDGRTVALVRN-----SAAIPLLQRRYPQAKVVTADNPSEAMLMVANGQADAVVQTQISASYYVNRYFAGKLRIASALDLPPAEIALATTRGQTELMSILNKALYSISNDELA 228

FFAS is supported by the NIH grant R01-GM087218-01
9 6 8 0 0   jobs submitted since Jan 1, 2011
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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.

Alexey M. Eroshkin, Andrew LeBlanc, Dana Weekes, Kai Post, Zhanwen Li, Akhil Rajput, Sal T. Butera, Dennis R. Burton, Adam Godzik. bNAber: database of broadly neutralizing HIV antibodies. Nucl. Acids Res. 2013; published on November 7, 2013.

Friedberg I, Jambon M, Godzik A. New avenues in protein function prediction. Protein Sci. 2006 Jun;15(6):1527-9.