Protein Info for SO0224 in Shewanella oneidensis MR-1

Name: rpoB
Annotation: DNA-directed RNA polymerase, beta subunit (NCBI ptt file)

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

1 100 200 300 400 500 600 700 800 900 1000 1100 1200 1345 TIGR02013: DNA-directed RNA polymerase, beta subunit" amino acids 8 to 1342 (1335 residues), 1915.1 bits, see alignment E=0 PF04563: RNA_pol_Rpb2_1" amino acids 27 to 500 (474 residues), 123.4 bits, see alignment E=2.8e-39 PF04561: RNA_pol_Rpb2_2" amino acids 151 to 224 (74 residues), 32.1 bits, see alignment 2.8e-11 amino acids 357 to 455 (99 residues), 55.5 bits, see alignment 1.9e-18 PF04565: RNA_pol_Rpb2_3" amino acids 514 to 581 (68 residues), 101.8 bits, see alignment 5.6e-33 PF10385: RNA_pol_Rpb2_45" amino acids 592 to 657 (66 residues), 90.5 bits, see alignment 1.7e-29 PF00562: RNA_pol_Rpb2_6" amino acids 719 to 1267 (549 residues), 449.5 bits, see alignment E=3e-138 PF04560: RNA_pol_Rpb2_7" amino acids 1269 to 1343 (75 residues), 98.7 bits, see alignment 6.4e-32

Best Hits

KEGG orthology group: K03043, DNA-directed RNA polymerase subunit beta [EC: 2.7.7.6] (inferred from 78% identity to aap:NT05HA_1813)

MetaCyc: 80% identical to RNA polymerase subunit beta (Escherichia coli K-12 substr. MG1655)
DNA-directed RNA polymerase. [EC: 2.7.7.6]

Predicted SEED Role

"DNA-directed RNA polymerase beta subunit (EC 2.7.7.6)" in subsystem RNA polymerase bacterial (EC 2.7.7.6)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 2.7.7.6

Use Curated BLAST to search for 2.7.7.6

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 Q8EK74 at UniProt or InterPro

Protein Sequence (1345 amino acids)

>SO0224 DNA-directed RNA polymerase, beta subunit (NCBI ptt file) (Shewanella oneidensis MR-1)
MVYSYSEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKFTDQDPTGERGLEAAFRSVFPIK
SFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAGTVKDIKEQ
EVYMGDIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNARIIPYR
GSWLDFEFDPKDALFVRIDRRRKLPATIILRALEYSTQEILDLFFERVEFKIKKDTLVMT
LVPERLRGETASYDIKDAEGTVLVEAGRRVTARHIRQLEKTNTTELEVPVEYIVGKYAAQ
DYIDPDTGEVLVSANSEISLEDLAKLSLAGIKELSTLYINELDHGAYISDTLRIDPTTNR
LEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLSIPDDEGSGV
LSKEDIVAVMKNIIHIRNGFDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVRERL
SLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLT
RERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPYRKVVDGVI
TDEVEYLSAIEEGRYVIAQANIEVDSEGRMVEEQIACRHKGESTFMRASDIQYMDVSPQQ
IISVAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERTLAVDSGVVVAAK
RGGVIDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCCSVGEPVVR
GDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTIHIQELSCI
ARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPEE
KLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAIEIEEMHIAQARKD
LGEEFKILEEGVLSRARNLLLSAGFSEAQIAALPRKDVLVQVIDDEAKQTELEQLAEQHE
ELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKRTIQPGDKMAGRHGNKGVISKI
NPIEDMPYDEQGNPVDIVLNPLGVPSRMNIGQVLEVHLGAAAKGIGHKIAAMLEDQREKG
LAEVRNYIKQVYELGDEVQQRVDIDSFTDDELLRLANNLKGGIPVATPAFDGAKEKEIKQ
MLELAGLPTSGQLKLFDGRTGNEFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQ
PLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTQMYKNIVDGNHQMQP
GMPESFNVLLKEIRSLGINIELDQE