Protein Info for Atu0332 in Agrobacterium fabrum C58

Annotation: RNA polymerase sigma-54 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 50 100 150 200 250 300 350 400 450 514 signal peptide" amino acids 1 to 15 (15 residues), see Phobius details PF00309: Sigma54_AID" amino acids 7 to 51 (45 residues), 57.8 bits, see alignment 1.2e-19 TIGR02395: RNA polymerase sigma-54 factor" amino acids 11 to 502 (492 residues), 415.4 bits, see alignment E=1.5e-128 PF04963: Sigma54_CBD" amino acids 140 to 328 (189 residues), 184.8 bits, see alignment E=2.1e-58 PF04552: Sigma54_DBD" amino acids 344 to 503 (160 residues), 227.2 bits, see alignment E=1.3e-71

Best Hits

Swiss-Prot: 66% identical to RP54_SINFN: RNA polymerase sigma-54 factor (rpoN) from Sinorhizobium fredii (strain NBRC 101917 / NGR234)

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 100% identity to atu:Atu0332)

Predicted SEED Role

"RNA polymerase sigma-54 factor RpoN" in subsystem Flagellar motility or Flagellum or Transcription initiation, bacterial sigma factors

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 Q8U5M8 at UniProt or InterPro

Protein Sequence (514 amino acids)

>Atu0332 RNA polymerase sigma-54 factor (Agrobacterium fabrum C58)
MALSASLLLRQNQSLVMTPQLMQSIQLLQMTHFELTQFIAQEVERNPLLEIAANDGDLGS
DTPVDVDNFGDAEASDAAVRVTPDSDDWYGERAANLGEQLDTSFENVFPDDGEPRKADAP
ELASQWKSMPGQESGESYDLDDFVAARQSLSDHLNQQLPLAISAAEDRMIADALIGQLDE
TGYIAADAVDDVAERLGATPSAVEYVLKTLQGFDPPGIFSRSLSECLATQLAQKDRLDPA
MRAFVDNLELLAKRDFASLKKLCGVDEEDLLDMLAEIRTLNPRPGAGYDSMVSETIVPDI
IVRPSSTGGWLVEINPDTLPRVLINQSYFAEVSKHKARAGEDQDFLSECMQTAHWLTRSL
DQRARTIMKVASEIVRQQDAFLINGVDQLRPLNLKTVADAIKMHESTVSRVTSKKYMLTP
RGLFELKYFFSVSISAVEGGDSHSAEAVRHRIKAMIAQEAAEAVLSDDDIVDNLKKTGID
IARRTVAKYREAMNIPSSVQRRREKKAMAKLSAF