Protein Info for Ga0059261_4238 in Sphingomonas koreensis DSMZ 15582

Annotation: RNA polymerase sigma factor RpoD, C-terminal domain

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 50 100 150 200 250 300 350 400 450 500 550 600 673 PF03979: Sigma70_r1_1" amino acids 24 to 101 (78 residues), 73.5 bits, see alignment E=3.4e-24 PF00140: Sigma70_r1_2" amino acids 118 to 150 (33 residues), 49.4 bits, see alignment (E = 1.1e-16) PF04546: Sigma70_ner" amino acids 160 to 407 (248 residues), 144.6 bits, see alignment E=1.2e-45 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 435 to 671 (237 residues), 397.5 bits, see alignment E=2.1e-123 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 436 to 660 (225 residues), 130.3 bits, see alignment E=5.5e-42 PF04542: Sigma70_r2" amino acids 439 to 509 (71 residues), 82.7 bits, see alignment E=3.9e-27 PF04539: Sigma70_r3" amino acids 518 to 594 (77 residues), 100.5 bits, see alignment E=1.4e-32 PF04545: Sigma70_r4" amino acids 607 to 660 (54 residues), 65.2 bits, see alignment 9.4e-22

Best Hits

Swiss-Prot: 68% 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 83% identity to sjp:SJA_C1-14330)

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 A0A1L6JBD0 at UniProt or InterPro

Protein Sequence (673 amino acids)

>Ga0059261_4238 RNA polymerase sigma factor RpoD, C-terminal domain (Sphingomonas koreensis DSMZ 15582)
MAKAIMADDGDTTETGDAPLIDLNEGSIKKLVARAKKRGYITVDQLNEMLPQDQFTTDQI
EDVMSALSDMGVNVVENEDVGEDEQPEDDTPDEVDSSDKDDEPFEIAKKKETVDRTDDPV
RMYLREMGAVELLSREGEIAIAKRIEAGRDTMILGLCESPITFNAIIGWSDALNEGTMQL
REILDLDAMLSKGPSAEQVEGAEDDDSGEISEKTAGASFKEEEEPEEASADEDDELTERR
APRISDEEEEDNTLSLAQMEETLKPQALERFANITSIYKKFSKVQQQRLDAMAAGGELTA
ADEKKYHKLREELTAEVESVQFHQAKIEYLVDQLYSFNRRLTALGGQMLRLAERHKVNRK
DFLDRYMGHELDESFIASVEKLDKKWAAFAANEGAAVDRIRVEVSEISQQTGMALTEFRR
IVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE
YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTP
EEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANL
KETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKH
PSRSRKMRSFLDQ