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Query: d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}, from SCOP206

Results of FFAS03 search in COG0516
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 KLQKQLLEAVEHKQLRPLDVQFALTVAGDEHPAVTLAAALLSHDAGEGHVCLPLSRLENNEASHPLLATCVSEIGELQNWEECLLASQAVSRGDEPTPMILCGDRLYLNRMWCNERTVARFFNEVNHAIEVDEALLAQTLDKLFPVSDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDALPDHARVIFLGDRDQLASVEAGAVLGDICAYANAGFTAERARQLSRLTGTHVPAGTGTEAASLRDSLCLLQKSYRLast
1 -32.400[L] COG0507 ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member  ali follow..  19  1..............................................................................................................MRTCGRRLAARLTSFVGWPAKSALAPGGRILTLKVMQFAPQQDEALKAVS-RSQLFRLFGYAGTGKTTLARHFAENV-------DGEVVFAAFTGKAAQVLRSKGA-----------------TNAKTIHSLIGKTSIAPMFAINRQSPVKAALIIVDECSMVDEALGKDLMSF---GTPILVLGDPGQLPPVSGGGYFTNHEPDFL----------LTDIHRQARDNPIIQLAMQVREG......... 223
2 -15.300[A] KOG1802 RNA helicase nonsense mRNA reducing factor (pNORF1)  ali follow..  22  365...........................................................................................................LKKFAIDKKSISGYLYYKILGHQVVDISFDVPLPKEFSIPNFAQ-QSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKD---RILVCAPSNVAVDHLAAKLRDGLKVVRLTAKSREDVESSVSALHNLVGRGAKGELKNLLKLKDTKFRTVLIDESTQA----PECLIPIVKGAKQVILVGDHQQLGPV----ILER--KAADAGLKQSLFERLISLGHVPI----------------RLEVQYR 639
3 -14.400[A] KOG1804 RNA helicase  ali follow..  19  314........................................................................................................................................................QKLAVKRILSGDCRILFGPPGTGKTVTIIEAVLQVHFALPDS--RILVCAPSNSAADLVCLRLPATMVRVNATCRFEEIVIDAVKPYFRIIITTCSSSGLFYQIGVR-HFTHVFVDEAGQSEPECLIPLGLMSDISGQIVLAGDPMQLGPV----IKSRLAM--AYGLNVSFLERLMSRPAYQRDENAFGACGAHNPLVTKLVKNYR 538
4 -14.000[L] KOG1803 DNA helicase  ali follow..  19  237................................................................................................................................................ETLNPSQVAAVSAAMNTQRNLLCIQGPPGTGKTRVIAEIVHQLMKKKK----KVLVCAPTHVAVRNAMDATTGRIEEMPEEKAEQQLCLLANTKDELAVFSTLGTSSIQKLPEYHWNADVMIVDEAAQTEPATWVPVLTTPSCK-KLILVGDQKQLPAV----VLSD--KAMKGNFKLSLMEKLAEEFSS-------------NNINILLNEQYR 478
5 -12.200[R] COG3972 Superfamily I DNA and RNA helicases  ali follow..  15  171..................................................................................................................EGAKALTRASKRIVEDPEVTPAAAALAKLESEIANFDQKQRRAALVTIDGPQRIRGLAGSGKTVILAMKAAHLHMTRPND--KILVTFFTKSLRSPIKDLVTKFYRHYKEIDPDWNNI-SNSSGTYADACRRSGRMPRSYSSARDAAYDHILIDEGQDFPYKLCFELAKGDRDKKNIVWAYDELQNILNVKMRSPAELFGQDDDGEPRISLARAEKNLPPGATNDT------------VLSKCYR 434
6 -10.800[T] COG1875 Predicted ATPase related to phosphate starvation-inducible protein PhoH  ali follow..  19  255........................................................................................................................................................QRVAIDLLNDDAVGIVSGPAGTGKS--ALALCAGLEAVMERRI-KIIVFRPLGDQEEKMGQAVFDTLSSMVSQNIIDEALSRGLIEVLPL----------THIRGRSLHDAFVIVDEAQSLERNVLLTMLSRIGQNSRVVLTHDVAQRDNLRVGRYDG................................................. 418
7 -10.300[F] COG1618 Predicted nucleotide kinase  ali follow..  16  14......................................................................................................................................................................AVTGSPGVGKSTVVAKTAEKLAEKPG--------FKIGGIRTAEIRKEGHREGFSIRDLATGKTGILSHVKGSGPRLGKYHVNLDDLERIGANAACDLVVIDEIGPMELSFVSAVEEVLESDKPVLAVLHHSSRHPLAKGFEVLTVDKGNRDELPEKITNRFLRKLG.......................... 184
8 -10.200[R] COG2842 Uncharacterized ATPase, putative transposase  ali follow..  12  3...................................................................................................LINKLKQHLSDSQITQAQLAREA-------GVNAGALSAYLNDNYKGNIADVEAKLAAYLEKKNCLATVYGMSGVGKTKAIQEFA------KSHANVWLVTASPSRSSLSEILYEI---ALELGISDAPRRKGTLSRLIARKIKGTEG----------------LLIVDEADHLPYEALEELRIM-EAGIGLVLVGNDKVYTRMKGGI.................................................... 211
9 -9.910[T] COG1702 Phosphate starvation-inducible protein PhoH, predicted ATPase  ali follow..  19  130...............................................................................................................................................................AIDTNTIVFGLGPGSGKTYLA--MAKAVQALQSKQVSRIILTRPAVEAGEKLG----------TLNEKIDPYLRPLHDALRDMVEPEVIPKLMEYMRGRTLNDAFVILDEAQNTTPAQMKMFLTRLGFGSKMVVTGDITQV-DLPGGQKSG................................................. 282
10 -9.660[S] COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain  ali follow..  15  4........................................................................................................................................KKTLGDVFKTVGLPHFGEVRADISQVGKHLLIEGPSGIGKTCVVFKVFE---ELQWSQGRDFTYVGCRDQNAEQIIDDFLKNAAAGNALSPC-----------------------------------VLVIDDFHLLSQAKRMEIGSTLKEPAKVILIGAGVSLLSDAY-DLGPRLGSYALTRASDVEIDKLISEGEQALAVLFEDRDVLLAES......... 199
11 -9.150[L] COG4098 Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein)  ali follow..  20  99........................................................................................................................................................QEKVSEGLLKQKPTLVHAVTGAGKTEMIYQVVAKVINAGG----AVCLASPR-ELYKRLQQDFSCGIALLHGESEPYFRTPLVVATTHQLL-------KFYQ------AFDLLIVDEVDAFNPMLYHAVKNSVKENGLRIFL-TNELDKKVRLGEL................................................... 252
12 -9.080[N] COG1419 Flagellar GTP-binding protein  ali follow..  17  131...................................................................................................................YKLIDFLKMKFGDLDPNSNETFKILSEQFVNLVKTN------APDFKNAKVLFVGTTGVGKTTSLAK-LAARFKIDEKKRVAI-LTLDTYRIAA--AEQLKIYADIMDIPMKIAYTPKEAEYEMMAL------------------DYDIVLVDTAGR--MSELRALSEAVKPNITFLVLSMNYKLDDMKRHIILTKMDETSVYG------TFVNISEITGLPIAFVTNGQRVPDDIFEANPV.. 355

FFAS is supported by the NIH grant R01-GM087218-01
8 2 8 1 6   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.

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