Protein Info for LRK53_RS01085 in Rhodanobacter sp000427505 FW510-R12

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 50 100 150 200 250 300 350 400 450 500 550 624 PF03979: Sigma70_r1_1" amino acids 8 to 85 (78 residues), 92.5 bits, see alignment E=4e-30 PF00140: Sigma70_r1_2" amino acids 102 to 132 (31 residues), 47.1 bits, see alignment (E = 5.7e-16) PF04546: Sigma70_ner" amino acids 143 to 358 (216 residues), 194.1 bits, see alignment E=9e-61 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 385 to 610 (226 residues), 130.1 bits, see alignment E=6.1e-42 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 385 to 621 (237 residues), 399.6 bits, see alignment E=4.8e-124 PF04542: Sigma70_r2" amino acids 389 to 459 (71 residues), 82.8 bits, see alignment E=3.5e-27 PF04539: Sigma70_r3" amino acids 468 to 544 (77 residues), 103.9 bits, see alignment E=1.1e-33 PF04545: Sigma70_r4" amino acids 557 to 610 (54 residues), 68.8 bits, see alignment 6.9e-23

Best Hits

Swiss-Prot: 70% identical to RPOD_XANCP: RNA polymerase sigma factor RpoD (rpoD) from Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 70% identity to psu:Psesu_2884)

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

Find the best match in UniProt

Protein Sequence (624 amino acids)

>LRK53_RS01085 RNA polymerase sigma factor RpoD (Rhodanobacter sp000427505 FW510-R12)
MNSKAPHEQQSEIKALISKGLEQGYLTYAEINDHLPDDIVDPEQIEDIMAVLKGVGIEVH
DAAPDTDPLADKAGSSTDDEAAAEEAVALLSAVDSEVGRTTDPVRMYMREMGTVELLTRE
GEIAIAKRIEEGLGQVQTALASFPLTIELLLEEYDQHLDGKRRLSEILAGFLDLEEAADL
ARKEKEAAALLAPEVEDSEEGDEDDDETATEDEEEAGPSGPDPEEVKRRMELLREHYAKF
QKAAPRAASITDKKIVKLRDQMAEEFLKLKLPSALIDGFVRKLREVVNDIRHHERVLMDI
FVKQVKMPKAEFIKAFPSNEGNPEWVAELSRKRQKWSPNIKTHREAIDAEQEKLAAIERK
LFLPLIDIKDINRAMASGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI
GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM
LQQFGREATPEELAKEMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGNASS
PIDSATETGLMETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI
EAKALRKLRHPSRSEQLRSFLDVE