Protein Info for PGA1_c01440 in Phaeobacter inhibens DSM 17395

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 1413 PF04997: RNA_pol_Rpb1_1" amino acids 17 to 345 (329 residues), 289.5 bits, see alignment E=8.8e-90 TIGR02386: DNA-directed RNA polymerase, beta' subunit" amino acids 21 to 1360 (1340 residues), 1804.2 bits, see alignment E=0 PF00623: RNA_pol_Rpb1_2" amino acids 347 to 401 (55 residues), 35.9 bits, see alignment (E = 2.3e-12) amino acids 398 to 488 (91 residues), 94.6 bits, see alignment 2.1e-30 PF04983: RNA_pol_Rpb1_3" amino acids 492 to 645 (154 residues), 96.8 bits, see alignment E=3.4e-31 PF05000: RNA_pol_Rpb1_4" amino acids 674 to 760 (87 residues), 70.8 bits, see alignment 2.1e-23 PF04998: RNA_pol_Rpb1_5" amino acids 763 to 850 (88 residues), 92 bits, see alignment 1.1e-29 amino acids 891 to 1309 (419 residues), 151.5 bits, see alignment E=8.2e-48

Best Hits

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 I7EIF0 at UniProt or InterPro

Protein Sequence (1413 amino acids)

>PGA1_c01440 DNA-directed RNA polymerase subunit beta' (Phaeobacter inhibens DSM 17395)
MNQELTNNPFNPLTPPKVFDEIKVSLASPERILSWSYGEIKKPETINYRTFKPERDGLFC
ARIFGPIKDYECLCGKYKRMKYRGVVCEKCGVEVTLQKVRRERMGHIELASPVAHIWFLK
SLPSRIGLMLDMTLRDLERVLYFENYVVIEPGLTDLTYGQMMTEEEYMDAQDQFGMDAFT
ANIGAEAIREMLAAIDLEAEAEHLRAELAEATGELKPKKIIKRLKVVESFLESGNRPEWM
VMTVIPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPDIIVRNEKR
MLQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDFSGRSVIVT
GPELKLHQCGLPKKMALELFKPFIYSRLEAKGLSSTVKQAKKLVEKERPEVWDILDEVIR
EHPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCSAFNADFDGDQMAVHVPLSLEAQ
LEARVLMMSTNNVLSPANGAPIIVPSQDMILGLYYVTLEREGMPGEGKIFGTIDEVQHAL
DAGEVHLHTKITARITQIDEEGNEVLKRFETTPGRVRLGALLPKNVKAPFELVNRLLRKK
EVQQVIDTVYRYCGQKESVIFCDQIMTMGFREAFKAGISFGKDDMVIPDTKWTLVDETRD
QVKDFEQQYMDGLITQGEKYNKVVDAWSKCNDKVTDAMMGTISADKRNEAGAVMEPNSVY
MMAHSGARGSVTQMKQLGGMRGLMAKPNGDIIETPIISNFKEGLTVLEYFNSTHGARKGL
SDTALKTANSGYLTRRLVDVAQDCIVRDRDCGTEAAITAEAAVNDGEVVASLGERILGRV
AAEDIKKPGTEEIIVAVGQLIDERMADAVEEAGVQSTRIRSPLTCEAEEGVCAQCYGRDL
ARGTQVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGVAQGGQQSFLEASQEGKIVFEMPQ
TLENANGETLVVGRNMKLIIQDEHGEERASHKLGYGSKLFVKEGQSVARGDKLFEWDPYT
LPIIAEKPGTAKYVDLVSGIAVRDETDEATGMTQKIVIDWRAAPKGSDLKPEIILVDGDG
EPVRSDAGNPLTYPMSVDAILSVEEGQQIMAGDVVARIPREGAKTKDITGGLPRVAELFE
ARRPKDHAIIAEIDGYVRFGRDYKNKRRISIEPADESMEPVEYMVPKGKHIPVQEGDFVQ
KGDYIMDGNPAPHDILSIMGVEALANYMIDEVQDVYRLQGVKINDKHIEVIVRQMLQKWE
ISDSGDTTLLKGEHVDKQEFDTANEKALSRGKRPAQGEPILLGITKASLQTRSFISAASF
QETTRVLTEASVQGKRDKLVGLKENVIVGRLIPAGTGGATQRVRNIAQGRDNVVLEARRE
EAEAAAALAAPSMDDVATEDNLDNLVETPESRD