Protein Info for DDA3937_RS13000 in Dickeya dadantii 3937

Annotation: transcription-repair coupling factor

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

1 100 200 300 400 500 600 700 800 900 1000 1100 1150 PF17757: UvrB_inter" amino acids 129 to 218 (90 residues), 99.3 bits, see alignment 4.5e-32 TIGR00580: transcription-repair coupling factor" amino acids 146 to 1080 (935 residues), 1186.1 bits, see alignment E=0 PF21132: MFD_D3" amino acids 378 to 450 (73 residues), 97.8 bits, see alignment 1.1e-31 PF02559: CarD_TRCF_RID" amino acids 478 to 533 (56 residues), 70.7 bits, see alignment 3.6e-23 PF00270: DEAD" amino acids 603 to 765 (163 residues), 97.3 bits, see alignment E=3.3e-31 PF04851: ResIII" amino acids 603 to 759 (157 residues), 48.1 bits, see alignment E=5e-16 PF00271: Helicase_C" amino acids 803 to 907 (105 residues), 70.1 bits, see alignment E=7.7e-23 PF03461: TRCF" amino acids 1007 to 1099 (93 residues), 100.7 bits, see alignment E=1.9e-32

Best Hits

Swiss-Prot: 81% identical to MFD_ECOLI: Transcription-repair-coupling factor (mfd) from Escherichia coli (strain K12)

KEGG orthology group: K03723, transcription-repair coupling factor (superfamily II helicase) [EC: 3.6.4.-] (inferred from 64% identity to aat:D11S_0770)

Predicted SEED Role

"Transcription-repair coupling factor" in subsystem DNA-replication or Transcription factors bacterial

Isozymes

Compare fitness of predicted isozymes for: 3.6.4.-

Use Curated BLAST to search for 3.6.4.-

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

See E0SGZ1 at UniProt or InterPro

Protein Sequence (1150 amino acids)

>DDA3937_RS13000 transcription-repair coupling factor (Dickeya dadantii 3937)
MMPEQYRYTLPGKAGEQRLLGQLTGAACAVECAEIVERHAGLVVLITPDMQNALRLRDEI
QQFTAQPVMTLPDWETLPYDSFSPHQEIISARLSTLYQLPSLTRGVLILPVNTLMQKVCP
HEFLHGHALMLKKGQRLSRDKLRNQLEQAGYRSVDQVMEHGEFATRGALLDLFPMGSEEP
FRIDFFDDEIDSLRLFDADTQRTLNEVEQIHLLPAREFPTDKTAIELFRSQWREQFEVRR
DAEHVYQQVSKGTLPAGIEYWQPLFFSQPLPALFSYLPTDTLLVNTGDIQQGAERFWQDI
QQRHDSRRVDPMRPLLPPDTLWLPVDTLFAELKQWPRVQLRSDTLPDKAANINLGYQPLP
DLAVQHQNKSPLDALRRFVEQFGGQIVFSVESEGRRETLQELLSRIKLAPTPVKSLEQTA
SPGCYLMIGASEHGFIDTLRQRTLICESDLLGERVSRRRQDSRRTINTDTLIRNLAELRP
GQPVVHLEHGVGRYSGLTTLEAGGIKAEYLILHYAGEDKLYVPVSSLHLISRYAGGAEDS
APLHKLGGDAWTRARQKAAEKVRDVAAELLDVYAQRAAHTGFAFKHDREQYQLFCQGFPF
DTTPDQAQAINAVLSDMCRPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTT
LLAQQHFDNFRDRFANWPVRIEMLSRFRSQKEQTQVLEQTQEGKVDILIGTHKLLQSDVR
WRDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGIRDLSIIATP
PARRLAVKTFVREYDSLVVREAILREILRGGQVYYLYNDVENIEKAAQRLNELVPEARIA
IGHGQMRERDLERVMNDFHHQRFNVLVCTTIIETGIDIPSANTIIIERADHFGLAQLHQL
RGRVGRSHHQAYAYLLTPNPKAMSSDAHKRLEAIASLEDLGAGFALATHDLEIRGAGELL
GEDQSGQMESVGFSLYMDLLESAVESLKAGREPSLEDLISSQTDVELRLPALLPDDFIPD
VNTRLSFYKRIASAKNDSELDDLKAELIDRFGKLPDAARHLLQVAGLRQQAQLLGIKRIE
GNDKGGFVEFSQHNRVDPTHLIGLLQRDPKVYRLDGPSRLKFINDLSGYPQRLTFITHLL
EEMAQHTYAA