Protein Info for AMB_RS03585 in Magnetospirillum magneticum AMB-1

Annotation: RNA polymerase sigma factor 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 50 100 150 200 250 300 350 400 450 500 550 600 650 679 PF03979: Sigma70_r1_1" amino acids 30 to 95 (66 residues), 82.2 bits, see alignment E=6.4e-27 PF00140: Sigma70_r1_2" amino acids 117 to 149 (33 residues), 49.6 bits, see alignment (E = 9.3e-17) PF04546: Sigma70_ner" amino acids 159 to 413 (255 residues), 146.9 bits, see alignment E=2.6e-46 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 441 to 677 (237 residues), 397.2 bits, see alignment E=2.6e-123 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 441 to 666 (226 residues), 130.3 bits, see alignment E=5.3e-42 PF04542: Sigma70_r2" amino acids 445 to 515 (71 residues), 82.4 bits, see alignment E=4.9e-27 PF04539: Sigma70_r3" amino acids 524 to 599 (76 residues), 101.7 bits, see alignment E=5.6e-33 PF04545: Sigma70_r4" amino acids 613 to 666 (54 residues), 65.2 bits, see alignment 8.9e-22

Best Hits

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to mag:amb0697)

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)

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

See Q2W9H4 at UniProt or InterPro

Protein Sequence (679 amino acids)

>AMB_RS03585 RNA polymerase sigma factor RpoD (Magnetospirillum magneticum AMB-1)
MATKSTNTAEVSENQDEAMDGPLLDTLGVAVKKMVAKGKERGYVTYDELNAAMPPEEVSS
EQIEDTMAMLSELGINVVESEEGEDNTPEAAEEETTETEGYSGAGNVDEEDLGRTDDPVR
MYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLTLRAVVDWHDALVEGKMLLR
DIIDLDATYGADPEPEELAEVEAEGVIVEEAAPAGAAEAKPEGEAEPKAEGEEGEKEEGA
EGEPEVEGEGEAEEGEENSISLAAMETELLPIVLETFEVIAATHHKLEKVQDQRLAALNK
GEAVTPAMEKKYDKLKLELVRLMDGIHLNNARIEQLVEQLNGLNRRLMMQEGRLLRLAES
CRVKRQDFLDAYYGSELDPNWIEQVTQRSKQWKDFGARHGKDAADIRATIADISAEAGLP
ISEYRRIVQTVQRGEREASRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK
AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEI
GREPTPEELAEKLSMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPLDA
AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA
LRKLKHPSRSRKLRSFLDT