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Query: d3ho7a1 c.94.1.0 (A:90-308) automated matches {Porphyromonas gingivalis [TaxId: 837]}, 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 TGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGEIDMAIIASKAETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDEGHCFRDQLVRFCQMKGLHERQTAYSGGSMEAFMRLVESGQGITFIPQLTVEQLSPSQKELVRPFGMPRPVREVRLAVRQDYSRRKLREQLIGLLRSAVPSDMHKLQTGQHLALast
1 -110.000d3ho7a1 c.94.1.0 (A:90-308) automated matches {Porphyromonas gingivalis [TaxId: 837]}  ali model 3D-neighbors  100  1TGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGEIDMAIIASKAETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDEGHCFRDQLVRFCQMKGLHERQTAYSGGSMEAFMRLVESGQGITFIPQLTVEQLSPSQKELVRPFGMPRPVREVRLAVRQDYSRRKLREQLIGLLRSAVPSDMHKLQTGQHLA 219
2 -101.000d3jv9a_ c.94.1.0 (A:) automated matches {Neisseria meningitidis [TaxId: 122586]}  ali model 3D-neighbors follow..  24  1EGAFKLGLIFTVAPYLLPKLIVSLRRTAPKMPLMLEENYTHTLTESLKRGDVDAIIVAEPFQEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRMLGEEQVLLLTEGNCMRDQVLSSCSELAAKQRTNTLQGSSINTIRHMVASGLAISVLPATALTE-NDHMLFSIIPFEGTPPSRRVVLAYRRNFVRPKALSAMKAAIMQSQLHGVSFI....... 215
3 -98.800d1i6aa_ c.94.1.1 (A:) Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  30  4SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALVKESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDT-HFRATSLETLRNMVAAGSGITLLPALAVPPERKRDGVVYLPAIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDGHFD......... 212
4 -48.100d2fyia1 c.94.1.1 (A:88-307) LysR-type regulatory protein Cbl {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  16  5SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASRLSNDPQLVAFPWFRWHHSLLVPHDHPLTQISPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLA-DIVLSAQDSDVIKTYVALGLGIGLVAEQSSGEQEEENLIRL-DTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIK........ 214
5 -47.500d1ixca2 c.94.1.1 (A:90-294) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}  ali model 3D-neighbors follow..  14  2.GELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRRPSFADEVIGLFKHAGIEP-RIARVVEDATAALALTMAGAASSIVPASV--AAIRWPDIAFARIVGTRVKVPISCIFRKE--QPPILARFVEHVRRSAKD............ 205
6 -46.400d1al3a_ c.94.1.1 (A:) Cofactor-binding fragment of LysR-type protein CysB {Klebsiella aerogenes [TaxId: 28451]}  ali model 3D-neighbors follow..  17  5KGSLYVATTHTQARYALPGVIKGFIERYPRVSLHMHQGSPTQIAEAVSKGNADFAIATALHLYDDLVMLPCYHWNRSIVVTPEHPLATKGSVSIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTP-RIVFTATDADVIKTYVRLGLGVGVIASMAVDPVSDPDLVKL-DANGIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVVD........ 214
7 -33.100d3oxna_ c.94.1.0 (A:) automated matches {Vibrio parahaemolyticus [TaxId: 670]}  ali model 3D-neighbors follow..  16  7..TFTIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVEPLRSEILGRVGVLCLLSKQHPLANQEMSLDDYLSHPHAMIAISDKALIEQAL-----IDKPQRKMVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTPFDYSMIWHARCEHSPAQEWLRSVVREECSRLIAK........ 212
8 -32.500d4rpoa_ c.94.1.0 (A:) automated matches {Sphingobium chlorophenolicum [TaxId: 46429]}  ali model 3D-neighbors follow..  13  10..NFRIAASDFGQALMLPRLYATLEETAPQVRVTGVNLRHGPLVEELESGSIDIAFGGFPTLSAGIKTQTLFREEYVCVMRQSHPALTHGLDLEAFRQCRHIIVTAHEFNHVHEQVEARLLELLPPESIRFTTENFLVSAVIAEETDVILTIPSRLARWFANRGGLTIFPVPIELPSIEVKQYWHERYDKDPGNIWLRRVIAKIGFQ............ 214
9 -31.700d2y7pa1 c.94.1.1 (A:90-301) automated matches {Burkholderia sp. [TaxId: 233098]}  ali model 3D-neighbors follow..  13  9..TFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNHGEVDGLLE----RAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA........... 212
10 -29.800d2esna2 c.94.1.1 (A:92-303) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]}  ali model 3D-neighbors follow..  15  9..TFVFAATDYTAFALLPPLMNRLQHSAPGVRLRLVNAERKLSVEALASGRIDFALGYDEEHEEGIQAHDWFADRYVVVARRDHPRLAGAPTLEGYLAERHAVVTPWNE--DSGVIDRLLARSGLRREVAVQLPTVLAALFLAGSTDFLLTAPRHAARALAEAAGLALYPAPFDIPPYVLRLYSHVQHVGRDAHAWMIGQLKGL............... 211
11 -14.200d4gvoa_ c.94.1.0 (A:) automated matches {Listeria monocytogenes [TaxId: 169963]}  ali model 3D-neighbors follow..  13  1VQTITVGTGTQFPNVCF-ELVKEIDKRLPGYKFKFKTMDFSNLLVSLGAGKVDIVAHQMEKSKER-EKKFLFNDVAYNNFPLQLTVLDSNN-STKDLAGKRV--TSATSNGALVLKKINEEQGNNFEIAYEGQGSNDTANQLKTGRADATISTPFAVDFQNKTSAIKEKVVGDVLSNAKVYFMLGKD--ETKLSKKVDEALQSIIDDGTLKKLSEK... 225
12 -12.700d4io2a1 c.94.1.0 (A:3-248) automated matches {Adineta vaga [TaxId: 104782]}  ali model 3D-neighbors follow..  12  5GITLRIGVIESVPFT-LIEYLRDKMGFVADVQLAPPNTSYTGLVLALANGDYDIAIGDITVTSARRESNSISDNSMRILMRKGTLIDGMDDLKNGKIPYNRI--IRIGTAGEDYYLREISGGSRNFYPLK---SRQEMYDSLLAGIIDVSFMDIGTAEYVTNNIYCNLTLVGEDFDKSTFGIVTPKEWLYAKDLDVNILSLRE................ 228
13 -11.700d4dz1a_ c.94.1.0 (A:) automated matches {Salmonella enterica [TaxId: 28901]}  ali model 3D-neighbors follow..  13  4GRTLNVAVSPASPPM-IDLELFSSYCQSRHCKLNITEYAWDGMLGAVASGQADVAFSGISITDKRKKVIPYYINSFYLVSMANHKI---TLNNLNELNKYSI--YPRGMAYSDLIKNDLEPKGYSLSKVKLYPTYNETMADLKNGNLDLAFIEEPVYFTFKNKKKMPIESRYVFKNVDQLGIAFKKGSPVRDDFNLWLKEQGPQKISGIVDS....... 226
14 -11.300d4eq9a_ c.94.1.0 (A:) automated matches {Streptococcus pneumoniae [TaxId: 637987]}  ali model 3D-neighbors follow..  10  2.KEIIVATNGSPRPFIY-EVVRAIFKDSDKYDVKFEKTEWSGVFAGLDADRYNMAVNNLSYTKER-AEKYLYAAPIAQNPNVLVVKKDDSSIKSDDIGGKST--VVQATTSAKQLEAYNAEHTDNPTILNYTKADFQQIMVRLSDGFDYKIFDKIGVETVIKNQGLDNLKVIELPSDQQPYVYPLLAQGQDELKSFVDKRIKELYKDGTLEKLSKQ... 226
15 -10.500d2ylna_ c.94.1.0 (A:) automated matches {Neisseria gonorrhoeae [TaxId: 485]}  ali model 3D-neighbors follow..  10  13KGTVTVGTEGTYAPFTY---VTRAVAEKLGVKVEFKETQWDSMMAGLKAGRFDVVANQVGLTSPERQATFDKSEPYSWSGAVLVAHNDSNIKSIADIKGVKT---------QSLTSNYGEKAKAAGAQLVPVDGLAQSLTLIEQKRADATLNDELAVLDYLKKNGVKIVWSAPADEKVGSGLIVNKG--NDEAVAKFSTAINELKADGTLKKLGEQ... 231
16 -10.100d3k4ua1 c.94.1.0 (A:2-233) automated matches {Wolinella succinogenes [TaxId: 844]}  ali model 3D-neighbors follow..  10  2.GELRVGLEPGYLPFEMKD-LAREMAKAMGVKLKLVPTSWDGLIPGLVTEKFDIIISGMTISQERNLRVN-FVEPYILLVKKGL---EKGVKSYKDLDKPELTLVTKFGVSAEYAAK----RLFKNAKLKTYDTEAEAVQEVLNGKADMFIFDLFNVAFMAQKGQGYLVHLDTSLTYEPLGWAIKKG--DPDFLNWLNHFLAQIKHDG........... 214
17 -9.960d3mpka_ c.94.1.0 (A:) automated matches {Bordetella pertussis [TaxId: 257313]}  ali model 3D-neighbors follow..  12  17..VVKVAVLNLFAPFISAAVLQLLQLRT-GLDFEIIGVDTEELIAKLRSGEADMAGALFVNSARESFSRPYVRNGMVIVTRQDPDAPV----DADHLDGRTVALV-RNSAAIPLL-----QRRYPQAKVVTADNPSEAMLMVANGQADAVVQTQISASYYVNRYFAGKLRIASALDLPPAEIALATTRGQTELMSILNKALYSISNDELASIIS..... 232
18 -9.420d3kzga_ c.94.1.0 (A:) automated matches {Legionella pneumophila [TaxId: 272624]}  ali model 3D-neighbors follow..  1SLNLTIGTSKFNPPFLMQEICRRL-----HATCTFEAYIFDDLFPALKNREVDLVIASMIITDERKKHFPYMESNSQYITTVDSKISTFDDLHGKKIGVRKGTPYARQVLSENRNNQVIFYELIQDMLLGLSNNQVDASL............................................................................... 155
19 -9.410d3h7ma_ c.94.1.0 (A:) automated matches {Geobacter sulfurreducens [TaxId: 35554]}  ali model 3D-neighbors follow..  10  4HRTIVVGGDRDYPPY-YNVELTRAIAEVMGMTVEFRLGAWSEMFSALKSGRVD--VLQGISWSEKRARQIDFTPPHTIVYHAIFARRDSPPAAGEDLRGRKV-ALHRDGIMHEYL-----AERGYGKDLVLTPTPADALRLLAAGGCDYAVVAMVPGMYIRENRLTNLVPVARSIAAQRYGYAVRQG--DAELLARFSEGLAILRKTG........... 213
20 -9.300d3vvfa1 c.94.1.0 (A:1-236) automated matches {Thermus thermophilus [TaxId: 262724]}  ali model 3D-neighbors follow..  11  11SGEIRIGTEGAFPPF-FEVDLGNAIAERLGLKPRWIAQSFDTLLIQLNQGRFDFVIASHGITEERARAVD-FTNPHYCTGGV---SRKGGPRTAKDLQGKVV-----GVQVGTTYMEAAQKIPGIKEVRTYQRDP-DALQDLLAGRIDTWITDRFVAKEIKERKLENTLQVGELVFQERVAMAVAKG--NKSLLDALNRALAELMQDGTYARISQK... 227
21 -9.210d3kbra_ c.94.1.0 (A:) automated matches {Pseudomonas aeruginosa [TaxId: 287]}  ali model 3D-neighbors follow..  10  10SGVLRVATTGDYKPFSY---MAQRLAESLGAKLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQA--FSIPYLRKTPITLCSEEARFQTLEQIDQPGVTAIVNPGGTNEKFAR----ANLKKARILVHPDNVTIFQQIVDGKADLMMTDAIARLQSRLHPELCAVHPQQPFDFAEKAYLLPRDEAFKRYVDQWLHIAEQ................ 220
22 -9.150d4kqpa_ c.94.1.0 (A:) automated matches {Lactococcus lactis [TaxId: 272623]}  ali model 3D-neighbors follow..  12  7..VYTIASDNSFAPF-IDVDLLNAIAKNQGFKLKWNFIGFQAAVDSVQSGHADGMMSGMSITDARKQGSPYYSSNLTIATSSTD----DSIKSWKDLKGKTL--AKNGTASFDYLNAHAKEYGYTVKTFT----DATTMYSSLNNGSINALMDDEPVIKYAIKQGQKFATPIKPIPDGQYGFAVKKGS-NPELIEMFNNGLANLRANG........... 216
23 -9.130d2q88a1 c.94.1.0 (A:1-256) automated matches {Rhizobium meliloti (Sinorhizobium meliloti) [TaxId: 382]}  ali model 3D-neighbors follow..  15  11QGFARIAI--NEPPFTAPDVAREIFKRLGVADVVASISEYGAMIPGLQAGRHDAITAGLFMKPERCAAVA-YSQPILFALKKGNPLGLKSYKDIADNPDAKI-----GAPGGGTEEKLALEAGVPRDRVIVVPDGQSGLKMLQDGRIDVYSLPVLSINDLVSKANDPNVEVLAPAPVYCDGAAFRKG--DEALRDAFDVELAKLKESG........... 228

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.

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, Nika K, Tautz L, Saito K, Cerignoli F, Friedberg I, Godzik A, Mustelin T. Identification and characterization of DUSP27, a novel dual-specific protein phosphatase. FEBS Lett. 2007 May 29;581(13):2527-33. Epub 2007 Apr 30.