Protein Info for AMB_RS12390 in Magnetospirillum magneticum AMB-1

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 1159 transmembrane" amino acids 654 to 675 (22 residues), see Phobius details PF17757: UvrB_inter" amino acids 132 to 216 (85 residues), 74.1 bits, see alignment 2.8e-24 TIGR00580: transcription-repair coupling factor" amino acids 147 to 1089 (943 residues), 1025.2 bits, see alignment E=0 PF21132: MFD_D3" amino acids 398 to 465 (68 residues), 31.4 bits, see alignment 5.2e-11 PF02559: CarD_TRCF_RID" amino acids 491 to 546 (56 residues), 63 bits, see alignment 7.7e-21 PF04851: ResIII" amino acids 616 to 771 (156 residues), 34 bits, see alignment E=9.4e-12 PF00270: DEAD" amino acids 617 to 777 (161 residues), 77.8 bits, see alignment E=3e-25 PF00271: Helicase_C" amino acids 815 to 919 (105 residues), 61.9 bits, see alignment E=2.3e-20 PF03461: TRCF" amino acids 1019 to 1109 (91 residues), 91.4 bits, see alignment 1.3e-29

Best Hits

KEGG orthology group: K03723, transcription-repair coupling factor (superfamily II helicase) [EC: 3.6.4.-] (inferred from 57% identity to azc:AZC_1221)

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)

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

See Q2W4F6 at UniProt or InterPro

Protein Sequence (1159 amino acids)

>AMB_RS12390 transcription-repair coupling factor (Magnetospirillum magneticum AMB-1)
MKNIDNLIAQPGRRKLAGAPEGRDALLLAELAAGGCAQGGILHVARDEGRMARVAEALAF
FAPDLQVLEFPGWDCVPYDRVSPHVDMVARRIDTLARLADGVKGAFVVLTTVPGLAQRVP
PREALASATLDARKGSRLSMDKLIGFLSKNGYVRADTVMEPGEYAVRGGIVDLYPPGSAE
PLRLDFFGDEIDSVRSFDPMSQRTTGPMAGFVCRPVSEVGLDDASIARFRTNYREMFGVI
SGPDPLYEAISEGIKFNGMEHWLPLFHDGLDTLFAYVPEAAVVLDHQSDEALTARHALVL
EYFDARAGLAGAGLTESGMVYHPILPERLYLERAEWDRLLAARPVLHLSPFDAVEGDEGA
VDAGGRLGRDFADMRARPGVNVYDCVREHAEEQAKAGRRVVIAAWTQGSRDRLAGVLRDH
GIKGIETVESWAEAQGLDKGRVAVAVLGLDHGFATPDLAVITEQDILGDRLARPARKKKK
GAQFIAEASALAEGDLVVHVEHGIGRYDGLVALEVSGAPHDCLRVLYDGGDKLFVPVENI
DVLTRFGSEQAGVSLDKLGGTAWQARKAKLKKRIRDIADQLIGIAAQRKMRQGEALVPAE
GLYDEFCARFPFAETEDQMRAIEDSIADLASGKPMDRLICGDVGFGKTEVAMRVAFVAAL
QGLQVAVVVPTTLLARQHYRTFKERFSGLPVRVEQLSRLVTAKTASEVKAGVADGSVDVV
VGTHALLAKGIGFKRLGLLIIDEEQHFGVAHKERLKQLKADVHVLTLTATPIPRTLQMAL
SGVKEMSVIATPPIDRLAVRTFVLPYDPVVLRESILRERYRGGQVFYVCPRLADIDRVAE
RLAKLVPEVKTAVAHGRLAPADLEEVMVAFGEKQYDVLLSTNIIESGIDMPSVNTLIIHR
ADMFGLGQLYQLRGRVGRGKTRGYAYFTLPNDKVLSKAAEKRLQVMQALDTLGAGFQLAS
HDLDIRGAGNLLGEEQSGHIREVGVELYQQLLEEAVAAAKGGQGGEAAEEWSPQIAVGTP
VLIPETYVADLSVRLSLYRRIGSLADQAEIEALAAELIDRFGKLPPEVENLLEVVAIKAL
CKLAGIDKVDSGPKGAVVSLRGNVFANPAALVQFIARSAGSCKIRPDHKIVFLRAWEDPK
QRIVGLRNVIGKLAELASA