Protein Info for HMPREF1078_RS16420 in Parabacteroides merdae CL09T00C40

Annotation: RNA polymerase sigma factor RpoD/SigA

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 50 100 150 200 250 286 PF00140: Sigma70_r1_2" amino acids 17 to 48 (32 residues), 44.8 bits, see alignment 2e-15 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 50 to 274 (225 residues), 118.8 bits, see alignment E=9.3e-39 PF04542: Sigma70_r2" amino acids 55 to 123 (69 residues), 67.2 bits, see alignment E=1.8e-22 PF04539: Sigma70_r3" amino acids 135 to 203 (69 residues), 53.8 bits, see alignment E=3.5e-18 PF04545: Sigma70_r4" amino acids 222 to 274 (53 residues), 62.3 bits, see alignment E=4.9e-21

Best Hits

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to pdi:BDI_0360)

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 (286 amino acids)

>HMPREF1078_RS16420 RNA polymerase sigma factor RpoD/SigA (Parabacteroides merdae CL09T00C40)
MRQLKITKSITNRESASLDKYLQEIGREDLITVEEEVELAQAIKRGDRRALEKLTRANLR
FVVSVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAE
QSRIVRLPLNQVGSLNKISKAFSKFEQENERRPSPEELADELDIPVDKISDTLKVSGRHI
SVDAPFVEGEDNSLLDVLVNDDAPIADRSLMNESLAKEIDRALATLTERECEIIKMFFGI
GCQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQGTRSKLLKSYLG