Protein Info for Atu1955 in Agrobacterium fabrum C58

Annotation: DNA-directed RNA polymerase 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 1402 PF04997: RNA_pol_Rpb1_1" amino acids 16 to 344 (329 residues), 289.1 bits, see alignment E=1.1e-89 TIGR02386: DNA-directed RNA polymerase, beta' subunit" amino acids 20 to 1017 (998 residues), 1481.5 bits, see alignment E=0 PF00623: RNA_pol_Rpb1_2" amino acids 346 to 487 (142 residues), 121.7 bits, see alignment E=9.5e-39 PF04983: RNA_pol_Rpb1_3" amino acids 491 to 644 (154 residues), 108.2 bits, see alignment E=1e-34 PF05000: RNA_pol_Rpb1_4" amino acids 673 to 760 (88 residues), 72.7 bits, see alignment 5.5e-24 PF04998: RNA_pol_Rpb1_5" amino acids 763 to 1310 (548 residues), 243.4 bits, see alignment E=7.5e-76

Best Hits

Swiss-Prot: 69% identical to RPOC_ACICJ: DNA-directed RNA polymerase subunit beta' (rpoC) from Acidiphilium cryptum (strain JF-5)

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 Q8UE09 at UniProt or InterPro

Protein Sequence (1402 amino acids)

>Atu1955 DNA-directed RNA polymerase beta (Agrobacterium fabrum C58)
MNQEVMNLFNPQVPAQHFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCA
RIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKS
LPSRISTLLDMTLKDVERVLYFENYIVTEPGLTSLKQNQLLSEEEYMIAVDEFGEDQFTA
MIGAEAIYEMLASMNLEKIAGDLRAELAETTSDLKQKKFMKRLKIVENFMESGNRPEWMI
MKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRM
LQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTG
PELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIRE
HPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQL
EARVLMMSTNNILHPANGHPIIVPSQDMVLGLYYLSIMNQNEPGEGMAFSDIGELHHALE
NKVVTLHAKIRGRFKTVDADGKPVSKIHETTPGRMLIGELLPKNVNVPFDTCNQEMTKKN
ISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACRAGISFGKDDMVIPDSKVKIVGDTEAL
VKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEEMMARIKAVEFDPETGRQKPMNSIY
MMSHSGARGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGL
ADTALKTANSGYLTRRLVDVAQDCIVNSVDCGTDKGLTMTAIVDAGQIVASIGARILGRT
ALDDIDNPVTGENIVKAGTLIDEADVAIIEKAGIQSVRIRSALTCEVQIGVCGVCYGRDL
ARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTANVVDQSFLEASYEGTIQIKNRN
ILRNSEGVLIAMGRNMSVTILDERGVERSSQRVAYGSKIFVDDGDKVKRGQRLAEWDPYT
RPMMTEVEGTVHFEDLVDGLSVLEATDESTGITKRQVIDWRSTPRGSDLKPAIIIKDASG
AVAKLSRGGEARFHLSVDAILSVEPGSKVSQGDVLARSPLESAKTKDITGGLPRVAELFE
ARRPKDHAIIAEIDGTIRLGRDYKNKRRVMIEPAEDGVEPVEYLIPKGKPFHLQEGDYIE
KGEYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVE
ITDAGDSQYIVGDNVDRIEMEDMNDRLIEEGKKPAYGEPVLLGITKASLQTPSFISAASF
QETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTGGTMTQIRRIATSRDDLILEERRK
GTGAGSANQMLQDMTDQVPAAE