Protein Info for GFF2248 in Variovorax sp. SCN45

Annotation: Transcriptional regulatory protein RtcR

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 50 100 150 200 250 300 350 400 450 500 540 signal peptide" amino acids 1 to 18 (18 residues), see Phobius details PF06956: RtcR" amino acids 3 to 183 (181 residues), 272.5 bits, see alignment E=4.1e-85 PF00158: Sigma54_activat" amino acids 186 to 351 (166 residues), 167.6 bits, see alignment E=6.4e-53 PF14532: Sigma54_activ_2" amino acids 192 to 359 (168 residues), 48.3 bits, see alignment E=3.9e-16 PF01078: Mg_chelatase" amino acids 201 to 329 (129 residues), 27 bits, see alignment E=8.5e-10 PF07728: AAA_5" amino acids 208 to 330 (123 residues), 30.7 bits, see alignment E=9e-11 PF00004: AAA" amino acids 209 to 334 (126 residues), 28.2 bits, see alignment E=6.8e-10

Best Hits

Swiss-Prot: 63% identical to RTCR_ECOLI: Transcriptional regulatory protein RtcR (rtcR) from Escherichia coli (strain K12)

KEGG orthology group: K14414, transcriptional regulatory protein RtcR (inferred from 92% identity to vpe:Varpa_5107)

Predicted SEED Role

"Transcriptional regulatory protein RtcR" in subsystem RNA 3'-terminal phosphate cyclase

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

Find the best match in UniProt

Protein Sequence (540 amino acids)

>GFF2248 Transcriptional regulatory protein RtcR (Variovorax sp. SCN45)
MKPIVVIGFLGTQLDAGQGAGRWNKWRPTVSLAQHEDMVVSRMELLYTLKHKALAELVKA
DIATVSPETTVNLVPMELADPWDFGEVYSRLYDWARGYSFDTEREQYWTHITTGTHVAQI
CMFLLSESRVVPGVLAQTSPPRRQRQGEAGKCTLIDLDLSRYDVIARRFDAEQRDAVAFL
KSGIATRNARFNALIDEIERVAVRSRAPILLVGPTGAGKSFLARRMFELKQSRHQMTGPF
VEVNCATLRGDGAASTLFGHRKGSFTGAAADRAGLLRTAHQGALFLDEIGELGLDEQAML
LKAIEEKRFFPVGADKEVESDFQLIAGTNRDLRSDVADGRFREDLFARINLWTYDLPGLA
QRPEDIEPNVDHLLAIHAAENHRVVRFNAEARAAYLRFAQSGEAVWSGNFRDLSASVTRL
ATLADGGRIPVALVEAEIARLRWLWKHAGAVSPASAGGGDVDLDALLGEERVQALDLFDR
LQLEAVVRVCRQSRSLSDAGRQLFQASRTQRSVVNDADRLRKYLVKLGLDWGQVSAGPTS