Protein Info for Shew_1048 in Shewanella loihica PV-4

Annotation: RNA polymerase sigma factor RpoE (RefSeq)

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 50 100 150 192 TIGR02939: RNA polymerase sigma factor RpoE" amino acids 2 to 190 (189 residues), 334.3 bits, see alignment E=2.5e-104 PF07638: Sigma70_ECF" amino acids 9 to 186 (178 residues), 42 bits, see alignment E=1.9e-14 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 21 to 186 (166 residues), 114.8 bits, see alignment E=3.2e-37 PF04542: Sigma70_r2" amino acids 25 to 92 (68 residues), 69.9 bits, see alignment E=2.6e-23 PF08281: Sigma70_r4_2" amino acids 134 to 181 (48 residues), 60 bits, see alignment E=2.8e-20 PF04545: Sigma70_r4" amino acids 136 to 181 (46 residues), 39.4 bits, see alignment E=6.9e-14

Best Hits

Swiss-Prot: 70% identical to RPOE_ECOL6: ECF RNA polymerase sigma-E factor (rpoE) from Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

KEGG orthology group: K03088, RNA polymerase sigma-70 factor, ECF subfamily (inferred from 100% identity to slo:Shew_1048)

MetaCyc: 70% identical to RNA polymerase sigma factor RpoE (Escherichia coli K-12 substr. MG1655)

Predicted SEED Role

"RNA polymerase sigma factor RpoE" in subsystem 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 A3QBS1 at UniProt or InterPro

Protein Sequence (192 amino acids)

>Shew_1048 RNA polymerase sigma factor RpoE (RefSeq) (Shewanella loihica PV-4)
MSGQISDQQLVERVQQGDKNAFNLLVHKYQSKVINLIARYVRNQADVADVAQEAFIKAYR
ALPNFRGESAFYTWLYRIAVNTAKNHLVAQGRRAPANDVDAEEAEYYDGSDALKEFASPE
RLMLSDEIQKVVFDTLDTLPEELKMAISLRELDGMSYEEIANVMECPVGTVRSRIFRARE
AIDKKLQPLLER