Protein Info for SMc01563 in Sinorhizobium meliloti 1021

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 50 100 150 200 250 300 350 400 450 500 550 600 650 684 PF03979: Sigma70_r1_1" amino acids 27 to 99 (73 residues), 80.9 bits, see alignment E=1.6e-26 PF00140: Sigma70_r1_2" amino acids 127 to 159 (33 residues), 50 bits, see alignment (E = 7e-17) PF04546: Sigma70_ner" amino acids 169 to 418 (250 residues), 146.7 bits, see alignment E=2.8e-46 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 446 to 682 (237 residues), 397 bits, see alignment E=2.9e-123 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 447 to 671 (225 residues), 129.4 bits, see alignment E=1e-41 PF04542: Sigma70_r2" amino acids 450 to 520 (71 residues), 82.7 bits, see alignment E=4e-27 PF04539: Sigma70_r3" amino acids 529 to 604 (76 residues), 101.6 bits, see alignment E=6.3e-33 PF04545: Sigma70_r4" amino acids 618 to 671 (54 residues), 65.1 bits, see alignment 9.6e-22

Best Hits

Swiss-Prot: 100% identical to RPOD_RHIME: RNA polymerase sigma factor RpoD (rpoD) from Rhizobium meliloti (strain 1021)

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to smk:Sinme_2360)

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 Q59753 at UniProt or InterPro

Protein Sequence (684 amino acids)

>SMc01563 RNA polymerase sigma factor RpoD (Sinorhizobium meliloti 1021)
MATKVKENEEADVEREGAPDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS
EQIEDTMSMLSDMGINVIEDEEAEEAAASDDDDGADEGESEGGELAPASGTALAASKKKE
PTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRD
ELNEGQTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKVRRTRTAANDDD
ITNVGGEGQAPEEEEEDDDESNLSLAAMEAELRPQVMETLDVIAETYKKLRKLQDQQVEA
RLAATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLYDISKRLTQNEGRLLR
LAESYGVKREAFLEQYSGAELDPNWMKSISNLAGKGWKEFARAENQTIRDIRQEIQNLAT
ETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN
IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQ
MLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNAL
LPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ
IEAKALRKLKHPSRSRKLRSFLDS