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PR01411

Identifier
CCMFBIOGNSIS  [View Relations]  [View Alignment]  
Accession
PR01411
No. of Motifs
7
Creation Date
30-APR-2000
Title
Cytochrome c-type biogenesis protein CcmF signature
Database References
PRINTS; PR01410 CCBIOGENESIS
Literature References
1. DELGADO, M.J., YEOMAN, K.H., WU, G., VARGAS, C., DAVIES, A., POOLE, R.K.,
JOHNSTON, A.W.B. AND DOWNIE, J.A.
Characterization of the cycHJKL genes involved in cytochrome c
biogenesis and symbiotic nitrogen fixation in Rhizobium leguminosarum.
J.BACTERIOL. 177 4927-4934 (1995). 
 
2.THOENY-MEYER, L., FISCHER, F., KUNZLER, P., RITZ, D. AND HENNECKE, H.
Escherichia coli genes required for cytochrome c maturation.
J.BACTERIOL. 177 4321-4326 (1995).
 
3. PAGE D., PEARCE D.A., NORRIS H.A. AND FERGUSON S.J.
The Paracoccus denitrificans ccmA, B and C genes: cloning and
sequencing, and analysis of the potential of their products to form a haem
or apo-c-type cytochrome transporter.
MICROBIOLOGY 143 563-576 (1997).
 
4. HUSSAIN, H., GROVE, J., GRIFFITHS, L., BUSBY, S. AND COLE, J. 
A seven-gene operon essential for formate-dependent nitrite reduction to
ammonia by enteric bacteria.
MOL.MICROBIOL. 12 153-163 (1994). 
 
5. SCHUSTER, W., COMBETTES, B., FLIEGER, K. AND BRENNICKE, A.
A plant mitochondrial gene encodes a protein involved in cytochrome c 
biogenesis.
MOL.GEN.GENET. 239 49-57 (1993).
 
6. BECKMAN, D.L., TRAWICK, D.R. AND KRANZ, R.G.
Bacterial cytochromes c biogenesis.
GENES DEV. 6 268-283 (1992).
 
7. RITZ, D., THONY-MEYER, L. AND HENNECKE, H.
The cycHJKL gene cluster plays an essential role in the biogenesis of 
c-type cytochromes in Bradyrhizobium japonicum.
MOL.GEN.GENET. 247 27-38 (1995). 

Documentation
Within mitochondria and bacteria, a family of related proteins is involved
in the assembly of periplasmic c-type cytochromes: these include CycK [1],
CcmF [2,3], NrfE [4] and CcbS [5]. These proteins may play a role in 
guidance of apocytochromes and haem groups for their covalent linkage 
by the cytochrome-c-haem lyase. Members of the family are probably integral
membrane proteins, with up to 16 predicted transmembrane (TM) helices. 
 
The gene products of the hel and ccl loci have been shown to be required
specifically for the biogenesis of c-type cytochromes in the Gram-negative
photosynthetic bacterium Rhodobacter capsulatus [6]. The ccl locus contains
two genes, ccl1 and ccl2, each of which possesses typical signal sequences
to direct them to the periplasm [6]. Ccl1 is similar to proteins encoded
by chloroplast and mitochondrial genes, suggesting analogous functions in 
these organelles. It is believed that the hel-encoded proteins are required 
for the export of haem to the periplasm, where it is subsequently ligated
to the c-type apocytochromes [6]. 
 
The CycK and CycL proteins of Bradyrhizobium japonicum share up to 53% 
amino acid sequence identity with Rhodobacter capsulatus proteins Cc11 and
Cc12 proteins, respectively [7]. CycK and CycL proteins, which are encoded
by the cycHJKL-cluster, may form part of a cytochrome c-haem lyase complex
whose active site faces the periplasm [7]. 
 
CCMFBIOGNSIS is a 7-element fingerprint that provides a signature for 
cytochrome c-type biogenesis protein CcmF. The fingerprint was derived from
an initial alignment of 7 sequences: the motifs were drawn from conserved
regions spanning virtually the full alignment length, focusing on those
sections that characterise the CCMF proteins but distinguish them from 
the rest of the cytochrome c-type biogenesis protein family. Three 
iterations on SPTR37_10f were required to reach convergence, at which point
a true set comprising 11 sequences was identified. 
Summary Information
11 codes involving  7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
711111111111111
60000000
50000000
40000000
30000000
20000000
1234567
True Positives
CCMF_BRAJA    CCMF_ECOLI    CCMF_HAEIN    CCMF_PSEFL    
CCMF_RHIME CCMF_RHOCA O30977 Q51753
Q52732 Q52820 Q9Z646
Sequence Titles
CCMF_BRAJA  CYTOCHROME C-TYPE BIOGENESIS PROTEIN CYCK - BRADYRHIZOBIUM JAPONICUM. 
CCMF_ECOLI CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCMF - ESCHERICHIA COLI.
CCMF_HAEIN CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCMF - HAEMOPHILUS INFLUENZAE.
CCMF_PSEFL CYTOCHROME C-TYPE BIOGENESIS PROTEIN CYCK - PSEUDOMONAS FLUORESCENS.
CCMF_RHIME CYTOCHROME C-TYPE BIOGENESIS PROTEIN CYCK - RHIZOBIUM MELILOTI.
CCMF_RHOCA CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCL1 - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
O30977 CCMF - PARACOCCUS DENITRIFICANS.
Q51753 INNER MEMBRANE OR PERIPLASMIC PROTEIN - PSEUDOMONAS FLUORESCENS.
Q52732 PROBABLE CYTOCHROME C-TYPE BIOGENESIS PROTEIN CYCK - RHIZOBIUM ETLI.
Q52820 DNA FOR CYCH, CYCJ, CYCK AND CYCL GENES - RHIZOBIUM LEGUMINOSARUM.
Q9Z646 CCMF - PANTOEA CITREA.
Scan History
SPTR37_10f 3  50   NSINGLE    
Initial Motifs
Motif 1  width=25
Element Seqn Id St Int Rpt
ESGHYALVLALGLALIQSIVPLIGA CCMF_BRAJA 4 4 -
ELGNYALALSLAVSLMLAIFPLWGA CCMF_HAEIN 4 4 -
EIGNGLLCLALGIALLLSVYPLWGV CCMF_ECOLI 4 4 -
EIGNGLLCLALGIALLLSVYPLWGV CCMF_ECOLI 4 4 -
ELGQLRMILALCFAVVQAVVPLLGA CCMF_PSEFL 9 9 -
ELGHYALVLALATAIIQGVLPVLGV CCMF_RHIME 4 4 -
ETGHFALILALCVALVQAVIPLVGA CCMF_RHOCA 4 4 -

Motif 2 width=24
Element Seqn Id St Int Rpt
LSKHLPQEAVARVLGIMGIISVGF CCMF_HAEIN 113 84 -
FGNNLPLSLRAHVLAVQAWIASAF CCMF_BRAJA 113 84 -
FGGALPERLRARVLAVQGTIGVAF CCMF_RHOCA 113 84 -
FGRNLPETLKANVLAVQAWIATAF CCMF_RHIME 113 84 -
FSRQLPQVMLARVLAVMGMISIGF CCMF_PSEFL 118 84 -
FSQRIPLDIVARVLAIMGMVSVGF CCMF_ECOLI 113 84 -
FSQRIPLDIVARVLAIMGMVSVGF CCMF_ECOLI 113 84 -

Motif 3 width=16
Element Seqn Id St Int Rpt
FAVAALIEGRVDAAWA CCMF_RHOCA 189 52 -
FAIAALMEGRIDAAWA CCMF_BRAJA 189 52 -
FAIASLMTGKLDSAWA CCMF_HAEIN 190 53 -
FAIASLLSGRLDSTYA CCMF_ECOLI 190 53 -
FAIASLLSGRLDSTYA CCMF_ECOLI 190 53 -
FAIAALLGGRLDAAWA CCMF_PSEFL 195 53 -
FAVAALIEGRIDAAWA CCMF_RHIME 189 52 -

Motif 4 width=16
Element Seqn Id St Int Rpt
FILLILCLFIGGSLSL CCMF_BRAJA 313 108 -
FILFILAFFTGGALTL CCMF_RHOCA 313 108 -
FILAILIVFIGGAFSL CCMF_RHIME 313 108 -
FILIFLLFVVGGSLTL CCMF_PSEFL 319 108 -
FILAFMVLVIGGSLLL CCMF_ECOLI 314 108 -
FILAFMVLVIGGSLLL CCMF_ECOLI 314 108 -
YILAYLVVVIGGSLAL CCMF_HAEIN 314 108 -

Motif 5 width=18
Element Seqn Id St Int Rpt
LLLNNILLMTALCVVFLG CCMF_HAEIN 352 22 -
LVLNNLLLTVACAVVLFG CCMF_BRAJA 351 22 -
LVMNNVLLAVAALVVFTG CCMF_RHOCA 351 22 -
LVVNNLILTTATATVLTG CCMF_RHIME 351 22 -
LLGNNLVLVVAASMILLG CCMF_PSEFL 356 21 -
LLANNVLLVAAMLVVLLG CCMF_ECOLI 352 22 -
LLANNVLLVAAMLVVLLG CCMF_ECOLI 352 22 -

Motif 6 width=20
Element Seqn Id St Int Rpt
FAPLFALLLLAVPFGPMLAW CCMF_BRAJA 394 25 -
FLIIMTPFALLLGIGPLVKW CCMF_HAEIN 395 25 -
FTWLMVPFALLLGVGPLVRW CCMF_ECOLI 395 25 -
FTWLMVPFALLLGVGPLVRW CCMF_ECOLI 395 25 -
FIPLMGLLMVVMAVGVLVRW CCMF_PSEFL 399 25 -
FGLLMLPLIAVVPFGPLLAW CCMF_RHIME 394 25 -
FTPFMVGLALLLPLGSMMPW CCMF_RHOCA 394 25 -

Motif 7 width=14
Element Seqn Id St Int Rpt
GGLSLTDRRYRSAA CCMF_RHOCA 626 212 -
GLLCMFDRRYRFNV CCMF_HAEIN 631 216 -
GLLCLFDPRYRKRV CCMF_ECOLI 624 209 -
GLLCLFDPRYRKRV CCMF_ECOLI 624 209 -
GLLAALDRRYRVKV CCMF_PSEFL 633 214 -
GVVSLSDRRLRVGA CCMF_RHIME 633 219 -
GVLSLSDRRLRVGA CCMF_BRAJA 633 219 -
Final Motifs
Motif 1  width=25
Element Seqn Id St Int Rpt
EIGHYALVLALATALILSIVPVIGA Q52820 4 4 -
ELGNYALALSLAVSLMLAIFPLWGA CCMF_HAEIN 4 4 -
EIGNGLLCLALGIALLLSVYPLWGV CCMF_ECOLI 4 4 -
EIGNGLLCLALGIALLLSVYPLWGV CCMF_ECOLI 4 4 -
EIGSFLLCLALGWAVLLSIYPLWGA Q9Z646 4 4 -
ETGHFALLVALCVALIQSVIPLVGA O30977 4 4 -
ELGQLRMILALCFAVVQAVVPLLGA CCMF_PSEFL 9 9 -
ELGQLAMILALCFAIVQAIVPLLGA Q51753 9 9 -
ELGHYALVLALATAIIQGVLPVLGV CCMF_RHIME 4 4 -
ETGHFALILALCVALVQAVIPLVGA CCMF_RHOCA 4 4 -
EIGHYALVVRLATALIVSIVPVIAA Q52732 4 4 -
ESGHYALVLALGLALIQSIVPLIGA CCMF_BRAJA 4 4 -

Motif 2 width=24
Element Seqn Id St Int Rpt
LSKHLPQEAVARVLGIMGIISVGF CCMF_HAEIN 113 84 -
FGRNLPETLKANVLSVQAWISVAF Q52820 113 84 -
FGNNLPLSLRAHVLAVQAWIASAF CCMF_BRAJA 113 84 -
FGANLPETLKANVLAVQAWISLAF Q52732 113 84 -
FGGALPERLRARVLAVQGTIGVAF CCMF_RHOCA 113 84 -
FGRNLPETLKANVLAVQAWIATAF CCMF_RHIME 113 84 -
FSRQLPQVMLARVLAVMGMISIGF Q51753 117 83 -
FSRQLPQVMLARVLAVMGMISIGF CCMF_PSEFL 118 84 -
FGGAMPERLRARLLAVQGSIGVAF O30977 113 84 -
LSRGMPQDAIARVLAVMGMINLGF Q9Z646 113 84 -
FSQRIPLDIVARVLAIMGMVSVGF CCMF_ECOLI 113 84 -
FSQRIPLDIVARVLAIMGMVSVGF CCMF_ECOLI 113 84 -

Motif 3 width=16
Element Seqn Id St Int Rpt
FAIAALMEGRIDAAWA CCMF_BRAJA 189 52 -
FAVAALLEGRIDAAWA Q52820 189 52 -
FAIASLMTGKLDSAWA CCMF_HAEIN 190 53 -
FAIASLLSGRLDSTYA CCMF_ECOLI 190 53 -
FAIASLLSGRLDSTYA CCMF_ECOLI 190 53 -
FAIASLMTGRLDTAWA Q9Z646 190 53 -
FAVAALLEGKVDAAWA O30977 189 52 -
FAIAALLGGRLDAAWA CCMF_PSEFL 195 53 -
FAIAALLGGRLDAAWA Q51753 194 53 -
FAVAALIEGRIDAAWA CCMF_RHIME 189 52 -
FAVAALIEGRVDAAWA CCMF_RHOCA 189 52 -
FAVAALIESRIDAAWA Q52732 189 52 -

Motif 4 width=16
Element Seqn Id St Int Rpt
FILCILLIFIGGALSL Q52820 315 110 -
FILLILCLFIGGSLSL CCMF_BRAJA 313 108 -
FILSILLIFIGGALSL Q52732 313 108 -
FILFILAFFTGGALTL CCMF_RHOCA 313 108 -
FILAILIVFIGGAFSL CCMF_RHIME 313 108 -
FILIFLLCVVGGSLTL Q51753 318 108 -
FILIFLLFVVGGSLTL CCMF_PSEFL 319 108 -
FILAILAFFLGGSLTL O30977 313 108 -
FILIFLVIVIGCSLLL Q9Z646 314 108 -
FILAFMVLVIGGSLLL CCMF_ECOLI 314 108 -
FILAFMVLVIGGSLLL CCMF_ECOLI 314 108 -
YILAYLVVVIGGSLAL CCMF_HAEIN 314 108 -

Motif 5 width=18
Element Seqn Id St Int Rpt
LLLNNILLMTALCVVFLG CCMF_HAEIN 352 22 -
LVVNNPDLTVACGTVLTG Q52820 353 22 -
LVLNNLLLTVACAVVLFG CCMF_BRAJA 351 22 -
LVLNNLILTVACGTVLTG Q52732 351 22 -
LVMNNVLLAVAALVVFTG CCMF_RHOCA 351 22 -
LVVNNLILTTATATVLTG CCMF_RHIME 351 22 -
LLGNNLVLVVAASMILLG Q51753 356 22 -
LLGNNLVLVVAASMILLG CCMF_PSEFL 356 21 -
LIMNNVLIAVAALVVLTG O30977 351 22 -
LLGNNVLLIAAMLVVLLG Q9Z646 352 22 -
LLANNVLLVAAMLVVLLG CCMF_ECOLI 352 22 -
LLANNVLLVAAMLVVLLG CCMF_ECOLI 352 22 -

Motif 6 width=20
Element Seqn Id St Int Rpt
FGLLMAPLIVIVPFGPMLAW Q52820 396 25 -
FLIIMTPFALLLGIGPLVKW CCMF_HAEIN 395 25 -
FTWLMVPFALLLGVGPLVRW CCMF_ECOLI 395 25 -
FTWLMVPFALLLGVGPLVRW CCMF_ECOLI 395 25 -
FTWLMAPFALMLGIGPLVRW Q9Z646 395 25 -
FTPFMVGLALLLPIGAMVPW O30977 394 25 -
FIPLMGLLMVVMAVGVLVRW CCMF_PSEFL 399 25 -
FIPLMGLLMVVMAIGVLVRW Q51753 399 25 -
FGLLMLPLIAVVPFGPLLAW CCMF_RHIME 394 25 -
FTPFMVGLALLLPLGSMMPW CCMF_RHOCA 394 25 -
FGLLMAPLLVIVPFGPLLAW Q52732 394 25 -
FAPLFALLLLAVPFGPMLAW CCMF_BRAJA 394 25 -

Motif 7 width=14
Element Seqn Id St Int Rpt
GVLSLSDRRLRVGA CCMF_BRAJA 633 219 -
GLLCMFDRRYRFNV CCMF_HAEIN 631 216 -
GLLCLFDPRYRKRV CCMF_ECOLI 624 209 -
GLLCLFDPRYRKRV CCMF_ECOLI 624 209 -
GILCLLDPRYRSRK Q9Z646 632 217 -
GVLSLTDRRYRTAT O30977 626 212 -
GLLAALDRRYRVKV CCMF_PSEFL 633 214 -
GLLAAMDRRYRVKV Q51753 686 267 -
GVVSLSDRRLRVGA CCMF_RHIME 633 219 -
GGLSLTDRRYRSAA CCMF_RHOCA 626 212 -
GLVSLSDRRLRVGA Q52732 635 221 -
GLVSLSDRRLRVGA Q52820 635 219 -