Protein Info for HMPREF1078_RS05920 in Parabacteroides merdae CL09T00C40

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 50 100 150 200 250 300 350 400 450 489 PF00309: Sigma54_AID" amino acids 3 to 48 (46 residues), 54.5 bits, see alignment 1.2e-18 TIGR02395: RNA polymerase sigma-54 factor" amino acids 8 to 487 (480 residues), 448.8 bits, see alignment E=1.2e-138 PF04963: Sigma54_CBD" amino acids 115 to 306 (192 residues), 196.1 bits, see alignment E=7e-62 PF04552: Sigma54_DBD" amino acids 329 to 487 (159 residues), 175.8 bits, see alignment E=8.4e-56

Best Hits

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 84% identity to pdi:BDI_3169)

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 (489 amino acids)

>HMPREF1078_RS05920 RNA polymerase factor sigma-54 (Parabacteroides merdae CL09T00C40)
MLKQQLQQKLQQKLSPQQIQLIRLLELPAIELEERIKHELEDNPALEEGKEIADDFDRTD
EGGEELAANEMEGESETDTDLSLGDYMSEDDIPDYKLRELNERAEKKEDVPFSVSESLNE
YLLQQLGLRDLPEKQVKIAEYIIGNIDDDGYLRRDLSAIADDLVFQAGQDVTEKEIETVL
AIIQDFDPAGVGARNLQECLLLQLARREKTSETRLATLMLTDFFEEFTRKHYDKIIKGLD
IDETALKRAIREITTLDPKPCASWGGSMETALSQIIPDFVVEAVNGELILSMNNRGIPDM
RINREYAEMFQDYAGNKANQTTQMKEAVQFVKQKLDSAQWFIDAIKQRQETLQRTMETII
LLQRDFFLTGDEATLRPMILKDVAERAGYDISTISRVSNSKYVQTNFGIYPLKYFFSESM
QTDSGEEISTREVKKIMKEHIDGEDKRKPLTDEELASILKEKGYIIARRTVAKYREQLGI
PVARLRKEI