Protein Info for PS417_25565 in Pseudomonas simiae WCS417

Annotation: DNA-directed RNA polymerase subunit beta'

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 1399 PF04997: RNA_pol_Rpb1_1" amino acids 15 to 342 (328 residues), 288.2 bits, see alignment E=2.7e-89 TIGR02386: DNA-directed RNA polymerase, beta' subunit" amino acids 19 to 1366 (1348 residues), 1786.9 bits, see alignment E=0 PF00623: RNA_pol_Rpb1_2" amino acids 344 to 394 (51 residues), 33.9 bits, see alignment (E = 1.1e-11) amino acids 389 to 485 (97 residues), 100 bits, see alignment 5.6e-32 PF04983: RNA_pol_Rpb1_3" amino acids 489 to 643 (155 residues), 113.9 bits, see alignment E=2.1e-36 PF05000: RNA_pol_Rpb1_4" amino acids 674 to 764 (91 residues), 77.8 bits, see alignment 1.7e-25 PF04998: RNA_pol_Rpb1_5" amino acids 766 to 1316 (551 residues), 270 bits, see alignment E=6.9e-84

Best Hits

Swiss-Prot: 72% 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 71% identity to aap:NT05HA_1812)

MetaCyc: 75% 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 A0A1N7U7I1 at UniProt or InterPro

Protein Sequence (1399 amino acids)

>PS417_25565 DNA-directed RNA polymerase subunit beta' (Pseudomonas simiae WCS417)
MKDLLNLLKNQGQVEEFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAK
IFGPVKDYECLCGKYKRLKHRGVICEKCGVEVALAKVRRERMAHIELASPVAHIWFLKSL
PSRIGLLMDMTLRDIERVLYFESYVVIDPGMTTLEKGQLLNDEQYFEALEEFGDDFDARM
GAEAVRELLHAIDLEHEIGRLREEIPQTNSETKIKKLSKRLKLMEAFQGSGNLPEWMVLT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLSAPDIIVRNEKRMLQ
EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPT
LRLHQCGLPKKMALELFKPFIFGKLEMRGLATTIKAAKKMVERELPEVWDVLAEVIREHP
VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTREAINAKGEGRVFADLQEVDRVFRAG
EAALHAKVKVRINETVNDRDGGSVTNTRIVDTTVGRALLYQVVPKGLSYDVVNLPMKKKA
ISKLINQCYRVVGLKETVIFADQLMYTGFAYSTISGVSIGVNDFVIPDEKARIIGAATDE
VKEIESQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMANLSKEKVIDRHGDEVDQESFN
SMYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLSVLQYFISTHGAR
KGLADTALKTANSGYLTRRLVDVAQDLVVTEIDCGTEHGLLMTPHIEGGDVVEPLGERVL
GRVIARDVFKPGTEEVIVPAGTLVDEKWVEFIELNSIDEVIVRSPISCETRYGICAKCYG
RDLARGHQVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRTSAADSVQVKNGGTVRL
HNLKHVERVDGHLVAVSRSGELAIADDYGRERERYKLPYGAVISVKEGDKVDAGAIVAKW
DPHTHPIVTEMKGTVTYVGMEEGITIKRQTDELTGMTNIEVLDAKDRPAAGKDIRPAVKM
VDDNGKDLLLPGTDVIAQYFLPANALVGVADGAKIAIGDVIARIPQETSKTRDITGGLPR
VADLFEARRPKEASILAEVSGTIAFGKETKGKRRLVITPNDGSDPYEELIPKWRHLNVFE
GEQVNRGEVISDGPSDPHDILRLLGVSALAKYIVNEIQDVYRLQGVKINDKHIETILRQM
LRKVEIAESGDSSFIKGDQMELTHVLVENERLAAEDKFVSKFTRVLLGITKASLSTESFI
SAASFQETTRVLTEAAVTGKRDYLRGLKENVVVGRLIPAGTGLAYHSERKRRRDADKPLR
VSASEVEAALTEALNSSGN