Protein Info for GFF412 in Variovorax sp. SCN45

Annotation: Transcription-repair coupling factor

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 1160 PF17757: UvrB_inter" amino acids 128 to 216 (89 residues), 81.9 bits, see alignment 1e-26 TIGR00580: transcription-repair coupling factor" amino acids 146 to 1086 (941 residues), 1017 bits, see alignment E=0 PF21132: MFD_D3" amino acids 373 to 447 (75 residues), 58 bits, see alignment 2.6e-19 PF02559: CarD_TRCF_RID" amino acids 477 to 540 (64 residues), 60.5 bits, see alignment 4.7e-20 PF00270: DEAD" amino acids 610 to 770 (161 residues), 88.5 bits, see alignment E=1.5e-28 PF04851: ResIII" amino acids 611 to 766 (156 residues), 41.4 bits, see alignment E=5.3e-14 PF00271: Helicase_C" amino acids 810 to 914 (105 residues), 67.4 bits, see alignment E=4.5e-22 PF03461: TRCF" amino acids 1014 to 1105 (92 residues), 88.4 bits, see alignment E=1.2e-28

Best Hits

KEGG orthology group: K03723, transcription-repair coupling factor (superfamily II helicase) [EC: 3.6.4.-] (inferred from 86% identity to aav:Aave_1580)

Predicted SEED Role

"Transcription-repair coupling factor" in subsystem DNA-replication or Transcription factors bacterial

Isozymes

Compare fitness of predicted isozymes for: 3.6.4.-

Use Curated BLAST to search for 3.6.4.-

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

Find the best match in UniProt

Protein Sequence (1160 amino acids)

>GFF412 Transcription-repair coupling factor (Variovorax sp. SCN45)
MDLPHLTAGKRFTLPRPPLSADALLLAQLAMREKAAGRATAMFTADANDAQRLIDEIAFF
APELRCALFPDWETLPYDSFSPHQDLISERLATLWRISQKEADVVLVPATTALYRLAPPA
FLAGYTFHFKAKQKLEESKLKAQLTLAGYSHVTQVVSPGEYAVRGGLIDLFPMGSPVPFR
VDLFDDEIDSIRTFDPDTQRSLYPVPEVRLLPGREFPMDEDARGRFRGRWRELLEGDPTK
SRIYKDMGNGVATAGIEYYLPLFFDETATVFDYLGPDATVVLHGDLEPAFQHFWQDTNER
YRLVRGDPERPALPPEALFLNAEQFYQRAKPHAQLAIRGDVPTEAPYAEFDRLPPFAVVR
GAEDPLVGLKAHIAKTPHRVLLIAESDGRRESLLDFLRASGVNPPAFDSLAEFEASADEK
VGIATAALASGFAWREQGIDLVTETELFATAPTTRRRNKKQEQVSDVEALIKDLSELNVG
DPVVHTAHGIGRYRGLIHMDLGQGTDAEGKPLLQEMLHLEYADKATLYVPVSQLHQISRY
TGVSADEAPLHKLGSGQWEKAKRKAAEQVRDSAAELLNIYARRAAREGHAFRYSPADYEV
FANDFGFQETADQKAAIHAVVQDMISPQPMDRLVCGDVGFGKTEVALRAAFIAVTGGKQV
AFLAPTTLLAEQHYQTLVDRFAKWPVKVAEMSRFRSAKEITAAAKGLAEGQVDIVVGTHK
LLSQSVKFKNLGLLIIDEEHRFGVRHKEAMKAMRAEVDVLTLTATPIPRTLGMALEGLRD
LSVIATAPQRRLAIKTFVRNEGTGVIREAVLRELKRGGQVYFLHNEVETIENRRQKLEEI
LPEARIAVAHGQMPERELERVMRDFVAQRYNLLLCSTIIETGIDVPTANTIVMSRADKFG
LAQLHQLRGRVGRSHHQAYAYLMVPDTEGLTKQAAQRLDAIQQMEELGSGFYLAMHDLEI
RGTGEVLGESQSGNMTEIGFQLYNEMLSEAVRALKAGQEPDLLSPLSVTTEINLHAPALL
PDDYCGDVHLRLSFYKKLATAKTPDQIDTLLEEIVDRFGKLPPQAQTLIDTHRLRVLARP
YGVVKVDAAPGIINITFKKDPPVDGMAIIQLIQKNKHIKLAGNEKLRIERELKEPKERAQ
MVRDVLRSLGQPTVKENVTA