Protein Info for Dshi_3411 in Dinoroseobacter shibae DFL-12

Annotation: cytochrome c-type biogenesis protein CcmF (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 50 100 150 200 250 300 350 400 450 500 550 600 664 signal peptide" amino acids 1 to 25 (25 residues), see Phobius details transmembrane" amino acids 34 to 57 (24 residues), see Phobius details amino acids 62 to 78 (17 residues), see Phobius details amino acids 96 to 114 (19 residues), see Phobius details amino acids 126 to 144 (19 residues), see Phobius details amino acids 175 to 195 (21 residues), see Phobius details amino acids 207 to 229 (23 residues), see Phobius details amino acids 249 to 265 (17 residues), see Phobius details amino acids 275 to 296 (22 residues), see Phobius details amino acids 312 to 331 (20 residues), see Phobius details amino acids 352 to 374 (23 residues), see Phobius details amino acids 393 to 413 (21 residues), see Phobius details amino acids 425 to 441 (17 residues), see Phobius details amino acids 447 to 465 (19 residues), see Phobius details amino acids 492 to 515 (24 residues), see Phobius details amino acids 621 to 641 (21 residues), see Phobius details TIGR00353: cytochrome c-type biogenesis protein CcmF" amino acids 53 to 646 (594 residues), 667 bits, see alignment E=1.5e-204 PF01578: Cytochrom_C_asm" amino acids 89 to 296 (208 residues), 176.3 bits, see alignment E=6.8e-56 PF16327: CcmF_C" amino acids 315 to 643 (329 residues), 396 bits, see alignment E=1.4e-122

Best Hits

Swiss-Prot: 55% identical to CCMF_RHIME: Cytochrome c-type biogenesis protein CycK (cycK) from Rhizobium meliloti (strain 1021)

KEGG orthology group: K02198, cytochrome c-type biogenesis protein CcmF (inferred from 100% identity to dsh:Dshi_3411)

Predicted SEED Role

"Cytochrome c heme lyase subunit CcmF" in subsystem Biogenesis of c-type cytochromes or Copper homeostasis

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 A8LP79 at UniProt or InterPro

Protein Sequence (664 amino acids)

>Dshi_3411 cytochrome c-type biogenesis protein CcmF (RefSeq) (Dinoroseobacter shibae DFL-12)
MIPEIGNFALMLALAAALVQSVLPMVGAAQRNVLWMQSAVTTALIQCGLLAVAFAALMRS
FIVSDFTVVNVVANSHSLKPMIYKVAATWGSHEGSLLLWVLILAIFGAGVAVLGKNIPAE
LRARTLSVQAWISVGFLSFMIFTSNPFDRMFPAPLNGNDLNPLLQDIGLALHPPLLYLGY
VGFSIVFSFAVAALIEGRVDPAWARWVRPWTLAAWVSLTGGIALGSWWAYYELGWGGWWF
WDPVENVSFMPWLLGTALLHSAIVTEKRDTFKSWTILLAILTFSLSLLGTFIVRSGLLTS
VHAFAVDPERGVYILGLLFVSIGGSLALYAWRAPQLEGGGLFTPISREAGLLINNLLLAT
ATAAVLFGTLYPLFLEAVTGDKISVGPPFFNASFIPIMLPLVFMMGIGPFLSWKRADLPG
VMSRLKFAIGLGLIAALWAWWMDTDGPVLAIIAMGVAGWLLVASAREWLSRIKAGEVPLA
ESLRRAKNLPRAAHGMTIAHMGVAVLILGMVGSSAWKTEQILFASPGTVVEIAGYEVRFD
RVERVRGPNYVSDMGTLTAFRDGEQVAVLQPERRWYPVAEMQTTESAIRSTLAGDLYVTI
GEPAADRASNEWTLRILFEPFVNFIWIGTVFLVIGGTFSLTDRRLRVGAPKSAARPPIQA
TPAE