Protein Info for Dshi_3584 in Dinoroseobacter shibae DFL-12

Annotation: RNA polymerase, sigma 54 subunit, RpoN (RefSeq)

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 50 100 150 200 250 300 350 400 438 PF00309: Sigma54_AID" amino acids 7 to 50 (44 residues), 43.9 bits, see alignment 2.5e-15 PF04963: Sigma54_CBD" amino acids 72 to 240 (169 residues), 110.6 bits, see alignment E=1.2e-35 PF04552: Sigma54_DBD" amino acids 271 to 423 (153 residues), 147.4 bits, see alignment E=4.6e-47

Best Hits

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 100% identity to dsh:Dshi_3584)

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 A8LQ77 at UniProt or InterPro

Protein Sequence (438 amino acids)

>Dshi_3584 RNA polymerase, sigma 54 subunit, RpoN (RefSeq) (Dinoroseobacter shibae DFL-12)
MRHREGLTLRQQQRLTLTPEMRTTLSVLRMSAAALEELLVRQAEENPILSLRRPGPPPAA
QATAYEVALDTTVAEVSLGDHLRAQLGLMSLAPPVHQAALALSWSLTETGYLDSTPAEIA
QECALDEATVLLGLAALQGCEPVGVGARSLAECLRLQLVDKGIAPAVAARATEVLDLLVG
SDVARAARRTGIPAEDLGAVIRLLPELSPYPGQRFSPTPQVSAPDVAVHFPDGAGPEIRV
LRGRQSDLALDPELMAAARREAADTALARYGAEAEALHRALGYRANALERIVAFLVDYQS
GFFREGGAAMRPLTREVLAARLGLHAATVGRAVADKTLAHAGGVIPLSAFFSARLGPETG
AATSAYGVQSRIAALVAAESEDAVLTDGEIAQRLKKEGVDIARRTVAKYRGCLNIPSSYD
RKRLNAAARMRGRMISSG