Protein Info for GFF3606 in Sphingobium sp. HT1-2

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 1158 transmembrane" amino acids 652 to 673 (22 residues), see Phobius details PF17757: UvrB_inter" amino acids 134 to 220 (87 residues), 79.3 bits, see alignment 5.9e-26 TIGR00580: transcription-repair coupling factor" amino acids 149 to 1089 (941 residues), 1026.1 bits, see alignment E=0 PF21132: MFD_D3" amino acids 392 to 464 (73 residues), 32 bits, see alignment 3e-11 PF02559: CarD_TRCF_RID" amino acids 489 to 544 (56 residues), 72.6 bits, see alignment 6.5e-24 PF00270: DEAD" amino acids 614 to 775 (162 residues), 79.6 bits, see alignment E=7.3e-26 PF00271: Helicase_C" amino acids 813 to 917 (105 residues), 64.4 bits, see alignment E=3.4e-21 PF03461: TRCF" amino acids 1018 to 1108 (91 residues), 84.5 bits, see alignment 1.6e-27

Best Hits

Predicted SEED Role

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

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

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

Compare to protein 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

Find the best match in UniProt

Protein Sequence (1158 amino acids)

>GFF3606 Transcription-repair coupling factor (Sphingobium sp. HT1-2)
MTDLQKILKAKAPLTLSGVPAGFQPWLLADIARAAHGSDATRAVFVASDEQLMRAVAETA
HYFAPEIELIEIPAWDCLPYDRASPSLRTASARLAGLHALQAKPKGPQLVLTTLNALTQR
TLTPFRVRQLVARLAPKERIAITRLADMLQSNGYVRTDTVHDRGEFAIRGGIVDLFPGGE
EQPLRLDFFGDEIETVRRFDPTDQRTTGSVDGFTLLPASEALLDEDTIKRFRGRYRETFG
ATATGDPLYQAVSEGRRLAGMEHWLPLFEEKLVPLTDHLGDDAIIVRDHGVVGAADARFE
AIRDYHANRIAAKSADPGAYRPLKPEALYLDAAEWDASAAVWPMHATTPFHEPESATVLD
FAVDGPRDFAPERAQNVNVYEAVGKHIDALRRTKKKVVIASYSAGARERLSGLLADHGVA
RLAAADSWQEALGTAAGGSAVLTVLGLDHGFTAPDVAVLTEQDMLGDRLVRRAKRKKSAD
AFLAELATLSPGDLVVHMDHGIGRYEGLTQIPVSKTAHDCVALSYAGGDKLYVPVENLEV
LSRYGSDSEGVSLDKLGGEAWQRRKARMKERIREIAGELLKTAAERALRPAEIAEPDAAG
YPAFVDRFPYQETDDQDRAIGDVIEDLGAGRPMDRLVCGDVGFGKTEVALRAAFVAAMAG
MQVVVICPTTLLARQHHMNFVERFRGFPLEIARLSRLVPDKEAKATKAGLADGTIDIVVG
THALLAKGLEFKRLGLVIVDEEQRFGVTHKERLKSLKTDVHVLTLTATPIPRTLQMAMSG
LRELSVIQTPPVDRLAVRTYIMPWDGVVIREALLREHYRGGQSFFVVPRISDLTEVEEFL
RTEVPEVKPIVAHGQMSATDVEERMSAFYDKRYDVLLSTTIVESGLDIPSANTLIIHRAD
RFGLAQLYQLRGRVGRSKTRAYAYFTTPANRIITETAEKRLKVLSDLDTLGAGFQLASHD
LDIRGAGNLVGDEQSGHIKEVGFELYQSMLEDAIMDAKAGGAGLEARRDSFSPQISVDAP
IMIPEEFVPDLDLRMGLYRRINELEDRQGLEAFAAELIDRFGKLPAPTQNLLKIIEIKQN
CLKANIAKIDVGPKGALVSFFEDRFPSPAGLVAYVQRLDGVARLRPDSKVVVTRAWPDPA
ARLNGALQLSKGLAKAAG