current user: public

anford Burnham Prebys Medical Discovery Institute

Query: d1ixca2 c.94.1.1 (A:90-294) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}, 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.
    .   10    .   20    .   30    .   40    .   50    .   60    .   70    .   80    .   90    .  100    .  110    .  120    .  130    .  140    .  150    .  160    .  170    .  180    .  190    .  200    .
# Score Template Links and tools%idFirst VGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSAKDLast
1 -106.000d1ixca2 c.94.1.1 (A:90-294) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}  ali model 3D-neighbors  100  1VGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSAKD 205
2 -51.500d1i6aa_ c.94.1.1 (A:) Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  14  5.GPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALVKESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLML--EDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGITLLPALAPERKRDGVVYLPAIKPEPRRTIGLVYRPGSPRSRYEQLAEAIRARMDG 209
3 -50.500d2fyia1 c.94.1.1 (A:88-307) LysR-type regulatory protein Cbl {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  15  6.GVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSDPQLVAFPWFRWHHSLLVPHDHPLTQISPLTLESIAKWPLITYRQG---TGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAESSGEQEEENLIRLDTRHLFDANTVWLGLKRGQ-RNYVWRFLELCNAGLSV 210
4 -49.500d3jv9a_ c.94.1.0 (A:) automated matches {Neisseria meningitidis [TaxId: 122586]}  ali model 3D-neighbors follow..  16  2.GAFKLGLIFTVAPYLLPKLIVSLRRTAPKMPLMLEENYTHTLTESLKRGDVDAIIVAEPFQEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRMLGEEQVLLL--TEGNCMRDQVLSSCSELAAKQRIQGQGSSINTIRHMVASGLAISVLPAALTENDHMLFSIIPFEGTPPSRRVVLAYRRNFRPKALSAMKAAIMQSQLH 210
5 -49.100d1al3a_ c.94.1.1 (A:) Cofactor-binding fragment of LysR-type protein CysB {Klebsiella aerogenes [TaxId: 28451]}  ali model 3D-neighbors follow..  15  6.GSLYVATTHTQARYALPGVIKGFIERYPRVSLHMHQGSPTQIAEAVSKGNADFAIATEALHLDDLVMLPCYHWNRSIVVTPEHPLATKGSVSIEELAQYPLVTYTFG---TGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGVGVIASAVDPVSDPDLVKLDANGIFSHSTTKIGFRRST-RSYMYDFIQRFAPHLTR 210
6 -47.500d3ho7a1 c.94.1.0 (A:90-308) automated matches {Porphyromonas gingivalis [TaxId: 837]}  ali model 3D-neighbors follow..  14  2.GRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGEIDMAIIASKAETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDE--GHCFRDQLVRFCQMKGLHEQTAYSGGSMEAFMRLVESGQGITFIPQLTQLSPSQKELVRPFGMPRPVREVRLAVRQD-RRKLREQLIGLLRSAVPS 207
7 -30.400d4rpoa_ c.94.1.0 (A:) automated matches {Sphingobium chlorophenolicum [TaxId: 46429]}  ali model 3D-neighbors follow..  12  10..NFRIAASDFGQALMLPRLYATLEETAPQVRVTGVNLRHGPLVEELESGSIDIAFGGFPTLSAGIKTQTLFREEYVCVMRQSHPAL-THGLDLEAFRQCRHIIVTAHEFNHVHEQVEARLLELLPPESIRFTTENFLVSAVIAEETDVILTIPSRLARANRGGLTIFPVPIELPSIEVKQYWHERDKDPGNIWLRRVIAKIGFQ 214
8 -29.500d3oxna_ c.94.1.0 (A:) automated matches {Vibrio parahaemolyticus [TaxId: 670]}  ali model 3D-neighbors follow..  11  7..TFTIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVEPLRSEILGRVGVLCLLSKQHPLANQEMSLDDYLSHPHAMIAISDGVKALIEQALIDKPQR----KMVLRAYHLEAALAIVDTLPIIITVPADLAYLERYDLVVKPLPFQFTPFDYSMIWHRCEHSPAQEWLRSVVREECSR 208
9 -29.100d2y7pa1 c.94.1.1 (A:90-301) automated matches {Burkholderia sp. [TaxId: 233098]}  ali model 3D-neighbors follow..  11  9..TFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLE---RAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRVPFGLTTSPHPAKLPDIAINLFWAKYNRDPGNMWLRQLFVELFSE 211
10 -27.600d2esna2 c.94.1.1 (A:92-303) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]}  ali model 3D-neighbors follow..  14  9..TFVFAATDYTAFALLPPLMNRLQHSAPGVRLRLVNAERKLSVEALASGRIDFALGYDEEHPEGIQAHDWFADRYVVVARRDHPRLAGAPTLEGYLAERHAVVTPWNEDSGVIDRLLA---RSGLRREVAVQLPTVLAALFLAGSTDFLLTAPRHAARAEAAGLALYPAPFDIPPYVLRLYSHVQHVGRDAHAWMI........ 205
11 -14.500d1twya_ c.94.1.1 (A:) ABC transporter, periplasmic substrate-binding protein VCA0807 {Vibrio cholerae [TaxId: 666]}  ali model 3D-neighbors follow..  10  1.SEITIS--STSVARIMDVLAEKYNQQHPETYVAVQGVGSTAGISLLKKGVADIAYLTESEAQNTLHTFTLAFDGLAIVVNQANPVTNLTREQLYGINDQKIAVVTREASSGTRYSFESLMSDVAPTALVVNSNSMMKTLVNHNTQAVGIGSVDKSVKAIQFEKADPTSDNIAKHTYQLSILHYSDNADEQTKEFIAFLKS.... 234
12 -13.800d4n13a_ c.94.1.0 (A:) automated matches {Borrelia burgdorferi [TaxId: 224326]}  ali model 3D-neighbors follow..  9.........STTVSPILDEMILRYDKINNNTKVTYDAQGSSVGINGLFNKIYKIAILTKEEIEQGAKETVFAYDALIFITSPEIKITNITEENLAKIPDAKINFINRDSSSGSYSSIKDLLLNKIFKTHVIEKTSLTPHSIGYIGLGYAKNSIEKGLNILSVNSTYPTKETINSNKYTIKIVTNNKYEDKSVTQFIDFMTS.... 238
13 -12.400d4ecfa_ c.94.1.0 (A:) automated matches {Lactobacillus brevis [TaxId: 387344]}  ali model 3D-neighbors follow..  12  10.........STALQPLVEAAGEQYTGEHLGTFINVQGGGTGTGLSQIQEGAVQIGNSDLFAGEQKLVDHRVAVVGITPIVNKKVGVKNLSTNQLIKIADQSIVLINRAQGSGTRATFEQFGLA-NHRSKTAQEQDSSGMVRSIVATTVAFSYVNKTVQALSLNHVAPTEVNVTTNDWRIWHLYTKGHPTGLTKAFITYVQS.... 228
14 -10.800d4gvoa_ c.94.1.0 (A:) automated matches {Listeria monocytogenes [TaxId: 169963]}  ali model 3D-neighbors follow..  10  1VQTITVGTGTQKLTGYDVELVKEIDKRLPGYKFKFKTMDFSNLLVSLGAGKVDIVAHQMEKSKEREKKFLFNDVAYNNFPLQLTVLDSNNSISTKDLAGKRVIT---SATSNGALVLKKINEEQGNNFEIAYEGQGSNDTANQLKTGRADATISTPFAQNKTSAIKEKVVGDVLSNAKVYFMLGKDETK-LSKKVDEALQSIIDD 216
15 -9.890d4kd5a_ c.94.1.0 (A:) automated matches {Clostridium difficile [TaxId: 272563]}  ali model 3D-neighbors follow..  7.......SAAASLKEAMAKIEEEYKKVDSNVKLTVNYGASGSLQQQIEQGACDLFISAGQKQMKVLTMKDLVKNDLVLISSADSSVSGMKDLTTDKVKKIAVGEAESVPAGKYADEVLTNLNLKDKLKDKLVFAKDVKEVLAWVQSGVGFVYFSDTVNNDKIKVVEKTDEKTHSPITYPVSVIKASKNVDAAKKFEEFLLS.... 213

FFAS is supported by the NIH grant R01-GM087218-01
9 6 8 0 0   jobs submitted since Jan 1, 2011
Comments and questions to: webmaster

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.