Protein Info for LRK54_RS12875 in Rhodanobacter denitrificans FW104-10B01

Annotation: RNA polymerase factor sigma-54

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 50 100 150 200 250 300 350 400 450 487 PF00309: Sigma54_AID" amino acids 5 to 48 (44 residues), 55.2 bits, see alignment 7.5e-19 TIGR02395: RNA polymerase sigma-54 factor" amino acids 9 to 484 (476 residues), 471 bits, see alignment E=2e-145 PF04963: Sigma54_CBD" amino acids 120 to 314 (195 residues), 180 bits, see alignment E=6.2e-57 PF04552: Sigma54_DBD" amino acids 327 to 485 (159 residues), 226.5 bits, see alignment E=2.1e-71

Best Hits

Swiss-Prot: 50% identical to RP54_PSEAE: RNA polymerase sigma-54 factor (rpoN) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 50% identity to pap:PSPA7_5035)

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

Find the best match in UniProt

Protein Sequence (487 amino acids)

>LRK54_RS12875 RNA polymerase factor sigma-54 (Rhodanobacter denitrificans FW104-10B01)
MKPALQFRLHQQLTLTPQLQQAIRLLQLSQLELEAELRQIAESNPLLEFAEEVEDDETLE
SSEPESDYPSVEAVAASSSDDGEASDWSDGGVAETPIDFSSSSVGSSGSSGSGTRGDEDF
EPQNAAPETLQQHLLWQLNLASFNPRQHLIATVLIDALNPAGYLAEGLEAILAALPADLD
ASIAEIEEVRRRLQGFDPAGVGSIDLRDCLRVQLEQFDPDTPQRELALRIVDDELDLLAR
NDIARLARRLRAGEDDVAAAAVLIRSLDPRPGAALDATPVEYVAPDVYALRDGSRWRVSL
NPDAQPRLGLNQHYCGLIAQARGEDASWMRGQLQEARWLIKSLESRAETLLKVAEAIVRR
QSAFLDYGPEAMHPLVLREVAEEVGMHESTISRVTTRKYLHTPRGTFELKYFFSSGVSTE
DGGSASATAIQAMLRKLIEAEDVRKPLSDLAIAEELQRKGIQVARRTVAKYREGLRIPTS
SERQRAG