Protein Info for GFF1466 in Sphingobium sp. HT1-2

Annotation: RNA polymerase sigma-54 factor RpoN

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 50 100 162 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 7 to 156 (150 residues), 80.9 bits, see alignment E=4.1e-27 PF22029: PhyR_sigma2" amino acids 9 to 60 (52 residues), 46.3 bits, see alignment E=1e-15 PF04542: Sigma70_r2" amino acids 11 to 73 (63 residues), 47.1 bits, see alignment E=4.9e-16 PF07638: Sigma70_ECF" amino acids 45 to 147 (103 residues), 28.6 bits, see alignment E=3.8e-10 PF08281: Sigma70_r4_2" amino acids 103 to 154 (52 residues), 55.1 bits, see alignment E=1.4e-18 PF04545: Sigma70_r4" amino acids 107 to 153 (47 residues), 32.9 bits, see alignment E=1.1e-11

Best Hits

KEGG orthology group: K03088, RNA polymerase sigma-70 factor, ECF subfamily (inferred from 88% identity to sch:Sphch_0265)

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)

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 (162 amino acids)

>GFF1466 RNA polymerase sigma-54 factor RpoN (Sphingobium sp. HT1-2)
MSFERDLLAILPRLRRFAASLSHDRADGDDLCQAALEKGLRARDQWQPGTRLDSWMYRIM
RNLWIDEGRARQRAARTFAPEEAGADVGYAGDKAVEQAMTLSDVDRAMQALPPEQREAIA
LVLVEGLSYKEAAAILNIPMGTLTSRLVRGRGALIELLGEAA