Protein Info for Dshi_1561 in Dinoroseobacter shibae DFL-12

Annotation: transcription-repair coupling factor (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 1160 transmembrane" amino acids 647 to 668 (22 residues), see Phobius details PF17757: UvrB_inter" amino acids 127 to 211 (85 residues), 65.7 bits, see alignment 8.5e-22 TIGR00580: transcription-repair coupling factor" amino acids 141 to 1085 (945 residues), 1014.7 bits, see alignment E=0 PF02559: CarD_TRCF_RID" amino acids 486 to 541 (56 residues), 67.1 bits, see alignment 3e-22 PF00270: DEAD" amino acids 609 to 769 (161 residues), 77.7 bits, see alignment E=2.2e-25 PF00271: Helicase_C" amino acids 806 to 913 (108 residues), 68.8 bits, see alignment E=1.1e-22 PF03461: TRCF" amino acids 1013 to 1105 (93 residues), 94.5 bits, see alignment E=1e-30

Best Hits

KEGG orthology group: K03723, transcription-repair coupling factor (superfamily II helicase) [EC: 3.6.4.-] (inferred from 54% identity to azl:AZL_012200)

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

See A8LKT9 at UniProt or InterPro

Protein Sequence (1160 amino acids)

>Dshi_1561 transcription-repair coupling factor (RefSeq) (Dinoroseobacter shibae DFL-12)
MTSQTVPTHLRVTGVPEGFDAQIVLREASRPDGQAVFVARDDKRMAAMAAALAVTAPQIP
VLRFPGWDCLPYDRSSPNPEISATRMATLAALAHGVPGPFVLLTTLSAVTQRVPARATLA
EASFSAQVGGRIDEAALRQFLTRMGFVQAPTVTEPGDYAIRGGIIDIFPPGQSGPVRLDL
FGDVLDGARRFDAATQRTTEKLDAIELAPVSEIILDPAAITRFRQSYRIEFGAAGTDDPL
YEAVSAGRKHAGMEHWLPFFHDRLETLLDYVPEASLILDDQFEAMHLSRWEGIKDQYETR
RHALAQKGQMGTVYKPAPPETLYIPPADETALLATKRTLQLSVLPSASGPGVTDAGGRIG
RNFAPERQSQATGLFEALATHITEKRKTSQVVIASWSEGARERLRGLLEDQDLSGLTEIA
RLSDIPEGTGGVHLLVWALDEGFEGPDHRSTRLTVISEQDVLGDRLIRTTKRKRRAENFL
QEATSLSAGDLVVHVDHGVGAFKGLETVTAMGAPHECLLLEYAGGDRLYLPVENIELLSR
FGQEIGMLDKLGGGAWQAKKAKLKERIREMADKLIRIAAERALRRAPMLEPPPDMWEAFS
ARFPYTETDDQLSAIEDVVHDLAAGTPMDRLICGDVGFGKTEVAMRAAFIAALSGVQVAV
IAPTTLLARQHYKSFADRFRGFPLEVRPLSRFVPAKAAADTRKGLAAGSVDIVVGTHALL
AKGVRFHNLGLLIIDEEQRFGVGHKERLKELRSDVHVLTLTATPIPRTLQLSLSGVRDLS
IIGTPPVDRLSIRTYVSEFDPVTLREALLREHYRGGQSFFVVPRIKDIPEIEAFLRDQVP
EVSFVVAHGQMAAGELDDRMNAFYDGKYDVLLATTIVESGLDIPTANTMIIHRADMFGLS
QLYQIRGRVGRAKTRAYAYLTTKPRMKLTPAAEKRLRVLGSLDSLGAGFTLASQDLDIRG
AGNLLGEAQSGQFREVGFELYQSMLEEAIGKIKSGSLEGLTDDDGQWAPQINLGVPVLIP
EAYVPDLDVRLGLYRRLSQLTTKVELEGFAAELIDRFGKLPKEVNTLLLIVRIKAMCKKA
GIAKLDGGPKGATVQFHNDKFANPAGLVKFINDQKGLAKVRDNKIVVRRDWAKESDRIKG
AFSIARDLAVEAKAAKAQAG