Protein Info for HP15_315 in Marinobacter adhaerens HP15

Annotation: RNA polymerase, sigma 70 subunit, RpoD

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 50 100 150 200 250 300 350 400 450 500 550 615 PF03979: Sigma70_r1_1" amino acids 5 to 79 (75 residues), 104.2 bits, see alignment E=8.9e-34 PF00140: Sigma70_r1_2" amino acids 99 to 129 (31 residues), 45.7 bits, see alignment (E = 1.6e-15) PF04546: Sigma70_ner" amino acids 140 to 345 (206 residues), 225.3 bits, see alignment E=2.4e-70 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 372 to 597 (226 residues), 128 bits, see alignment E=2.7e-41 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 372 to 608 (237 residues), 397.8 bits, see alignment E=1.7e-123 PF04542: Sigma70_r2" amino acids 376 to 446 (71 residues), 82.9 bits, see alignment E=3.5e-27 PF04539: Sigma70_r3" amino acids 455 to 531 (77 residues), 104 bits, see alignment E=1.1e-33 PF04545: Sigma70_r4" amino acids 544 to 597 (54 residues), 65.7 bits, see alignment 6.5e-22

Best Hits

Swiss-Prot: 72% identical to RPOD_PSEAE: RNA polymerase sigma factor RpoD (rpoD) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 93% identity to maq:Maqu_0658)

MetaCyc: 67% identical to RNA polymerase sigma factor RpoD (Escherichia coli K-12 substr. MG1655)

Predicted SEED Role

"RNA polymerase sigma factor RpoD" in subsystem Flagellum or Macromolecular synthesis operon or Transcription factors cyanobacterial RpoD-like sigma factors 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 E4PL37 at UniProt or InterPro

Protein Sequence (615 amino acids)

>HP15_315 RNA polymerase, sigma 70 subunit, RpoD (Marinobacter adhaerens HP15)
MSGNSQKSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVCEET
PDADTLLMTEGDSTADEAAAAEAAAALAAVETDAGRTTDPVRMYMREMGTVELLTREGEI
VIAKRIEEGIRDVMAAVAHFPGTAGTVIQAYDRILENEGRISDIVTGFLDPDDAEPFMGE
DTTPESSDDSDSDSDDDDDSSEEETDNGPDPEETRLRFELLNEKLEAANKALAKHGRSDK
KTQEALNELGQVFAPFKLANKAFDELVNVVRSTNDLVRENERAIMQICVRECKMPRKDFI
KSFPGNETNLDWADKIAKSKKPYAAPLAERIDEVVRLQKRIQNVQTEVDLDVADIKEINR
RVSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR
GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL
GERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREA
TRSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
SDHLRGFIDDQGNQG