Protein Info for Shew_0152 in Shewanella loihica PV-4

Annotation: DNA-directed RNA polymerase subunit beta' (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

1 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1404 PF04997: RNA_pol_Rpb1_1" amino acids 15 to 342 (328 residues), 294.3 bits, see alignment E=3.1e-91 TIGR02386: DNA-directed RNA polymerase, beta' subunit" amino acids 20 to 1366 (1347 residues), 1803.8 bits, see alignment E=0 PF00623: RNA_pol_Rpb1_2" amino acids 344 to 381 (38 residues), 31.6 bits, see alignment (E = 4.8e-11) amino acids 390 to 485 (96 residues), 98.8 bits, see alignment 1e-31 PF04983: RNA_pol_Rpb1_3" amino acids 489 to 644 (156 residues), 114.7 bits, see alignment E=1e-36 PF05000: RNA_pol_Rpb1_4" amino acids 674 to 764 (91 residues), 75.7 bits, see alignment 6.6e-25 PF04998: RNA_pol_Rpb1_5" amino acids 766 to 1315 (550 residues), 274.7 bits, see alignment E=2.2e-85

Best Hits

Swiss-Prot: 78% identical to RPOC_ACTSZ: DNA-directed RNA polymerase subunit beta' (rpoC) from Actinobacillus succinogenes (strain ATCC 55618 / DSM 22257 / 130Z)

KEGG orthology group: K03046, DNA-directed RNA polymerase subunit beta' [EC: 2.7.7.6] (inferred from 79% identity to aap:NT05HA_1812)

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)

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 A3Q976 at UniProt or InterPro

Protein Sequence (1404 amino acids)

>Shew_0152 DNA-directed RNA polymerase subunit beta' (RefSeq) (Shewanella loihica PV-4)
MKDLLKFLKQQSKTEEFEGIKIGLASPDLIRSWSFGEVKKPETINYRTFKPEREGLFCAR
IFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIDLASPVAHIWFLKSL
PSRIGLMLDMTLRDIERVLYFESFVVIEPGMTSLERGQMLTEENYLDALEEYGDEFEAKM
GAEAVLELLRAIDLEKEIEEMREELPSINSETRRKKITKRLKLIEAFYQSGNKPEWMILK
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ
ESVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPT
LRLHQCGLPKKMALELFKPFIYGKLEGRGLATTIKAAKKMVEREVPEVWDVLDDVIREHP
VMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RSLMMSTNNILSPANGEPVITPSQDVVLGLYYTSRERINGRGEGMAFESVAEVEKAYRTG
VAELHARVKVRITETTIAEDGERTESRRIVDTTVGRALLSQVLPKGLSYDLVNQNMGKKQ
ISKLLNTCYRQLGLKDTVIFADQLMYTGFHFATVSGASVGINDMVIPDEKYSLVADAEAE
VLEIQEQFQSGLVTAGERYNKVIDIWASANEKVSKAMMDNLSTETVINRDGEEETQASFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGAR
KGLADTALKTANSGYLTRRLVDVAQDLVVIEDDCGTHEGLTMKPLIEGGDVVEPLRERVL
GRVVAEDVYYPGTEDVLAPRNTLLDEAWCDKLEEHSIDEVKVRSVISCDTDFGVCAACYG
RDLARGHLINQGEAIGVVAAQSIGEPGTQLTMRTFHIGGAASRASAENNVQVKNAGTVKL
HNAKHVTNSDGKLVIVSRSSEIAIIDELGREKERYKVPYGTVLEKLEDATVNAGEVIANR
DPHTHPIVSEVAGSIKFVDMIEGVTMTRQTDELTGLSSIVVMDVGQRPTAGKEMRPAIRL
VGADGNDLMIPGTEVPAQYFLPGKAIVNQDDNAQIAVGDALARIPQESSKTRDITGGLPR
VADLFEARKPKEPAILAEYSGTISFGKETKGKRRLVITPADGGKPYEEMIPKWRNLNVFE
GEKVERGEVIADGPEAAHDILRLRGIHKVANYIVNEVQDVYRLQGVKINDKHIEVIIRQM
LRKCEITEAGDSEFLPGEQVEVSRVKIANRELEAQGKEPAKFERELLGITKASLATESFI
SAASFQETTRVLTEAAVGGKSDKLRGLKENVIVGRLIPAGTGYAYHTSRNQAAQNGPAEE
VPAISASEAEQNLADLLNLAGSPE