WORKLIST ENTRIES (1):
CCMFBIOGNSIS View alignment Cytochrome c-type biogenesis protein CcmF signature
Type of fingerprint: COMPOUND with 7 elements
Links:
PRINTS; PR01410 CCBIOGENESIS; PR01412 CCBSBIOGNSIS; PR01413 NRFEBIOGNSIS
PRINTS; PR01414 CCMBBIOGNSIS; PR01386 CCMCBIOGNSIS
Creation date 30-APR-2000
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).
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 FINGERPRINT INDEX
7| 11 11 11 11 11 11 11
6| 0 0 0 0 0 0 0
5| 0 0 0 0 0 0 0
4| 0 0 0 0 0 0 0
3| 0 0 0 0 0 0 0
2| 0 0 0 0 0 0 0
--+------------------------------------
| 1 2 3 4 5 6 7
True positives..
Q52820 CCMF_BRAJA Q52732 CCMF_RHOCA
CCMF_RHIME Q51753 CCMF_PSEFL O30977
Q9Z646 CCMF_ECOLI CCMF_HAEIN
PROTEIN TITLES
Q52820 DNA FOR CYCH, CYCJ, CYCK AND CYCL GENES - RHIZOBIUM LEGUMINO
CCMF_BRAJA CYTOCHROME C-TYPE BIOGENESIS PROTEIN CYCK - BRADYRHIZOBIUM J
Q52732 PROBABLE CYTOCHROME C-TYPE BIOGENESIS PROTEIN CYCK - RHIZOBI
CCMF_RHOCA CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCL1 - RHODOBACTER CAPS
CCMF_RHIME CYTOCHROME C-TYPE BIOGENESIS PROTEIN CYCK - RHIZOBIUM MELILO
Q51753 INNER MEMBRANE OR PERIPLASMIC PROTEIN - PSEUDOMONAS FLUORESC
CCMF_PSEFL CYTOCHROME C-TYPE BIOGENESIS PROTEIN CYCK - PSEUDOMONAS FLUO
O30977 CCMF - PARACOCCUS DENITRIFICANS.
Q9Z646 CCMF - PANTOEA CITREA.
CCMF_ECOLI CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCMF - ESCHERICHIA COLI
CCMF_HAEIN CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCMF - HAEMOPHILUS INFL
SCAN HISTORY
SPTR37_10f 3 50 NSINGLE
INITIAL MOTIF SETS
CCMFBIOGNSIS1 Length of motif = 25 Motif number = 1
Cytochrome c-type biogenesis protein CcmF motif I - 1
PCODE ST INT
EIGNGLLCLALGIALLLSVYPLWGV CCMF_ECOLI 4 4
EIGNGLLCLALGIALLLSVYPLWGV CCMF_ECOLI 4 4
ELGNYALALSLAVSLMLAIFPLWGA CCMF_HAEIN 4 4
ELGQLRMILALCFAVVQAVVPLLGA CCMF_PSEFL 9 9
ELGHYALVLALATAIIQGVLPVLGV CCMF_RHIME 4 4
ETGHFALILALCVALVQAVIPLVGA CCMF_RHOCA 4 4
ESGHYALVLALGLALIQSIVPLIGA CCMF_BRAJA 4 4
CCMFBIOGNSIS2 Length of motif = 24 Motif number = 2
Cytochrome c-type biogenesis protein CcmF motif II - 1
PCODE ST INT
FSQRIPLDIVARVLAIMGMVSVGF CCMF_ECOLI 113 84
FSQRIPLDIVARVLAIMGMVSVGF CCMF_ECOLI 113 84
LSKHLPQEAVARVLGIMGIISVGF CCMF_HAEIN 113 84
FSRQLPQVMLARVLAVMGMISIGF CCMF_PSEFL 118 84
FGRNLPETLKANVLAVQAWIATAF CCMF_RHIME 113 84
FGGALPERLRARVLAVQGTIGVAF CCMF_RHOCA 113 84
FGNNLPLSLRAHVLAVQAWIASAF CCMF_BRAJA 113 84
CCMFBIOGNSIS3 Length of motif = 16 Motif number = 3
Cytochrome c-type biogenesis protein CcmF motif III - 1
PCODE ST INT
FAIASLLSGRLDSTYA CCMF_ECOLI 190 53
FAIASLLSGRLDSTYA CCMF_ECOLI 190 53
FAIASLMTGKLDSAWA CCMF_HAEIN 190 53
FAIAALLGGRLDAAWA CCMF_PSEFL 195 53
FAVAALIEGRIDAAWA CCMF_RHIME 189 52
FAVAALIEGRVDAAWA CCMF_RHOCA 189 52
FAIAALMEGRIDAAWA CCMF_BRAJA 189 52
CCMFBIOGNSIS4 Length of motif = 16 Motif number = 4
Cytochrome c-type biogenesis protein CcmF motif IV - 1
PCODE ST INT
FILAFMVLVIGGSLLL CCMF_ECOLI 314 108
FILAFMVLVIGGSLLL CCMF_ECOLI 314 108
YILAYLVVVIGGSLAL CCMF_HAEIN 314 108
FILIFLLFVVGGSLTL CCMF_PSEFL 319 108
FILAILIVFIGGAFSL CCMF_RHIME 313 108
FILFILAFFTGGALTL CCMF_RHOCA 313 108
FILLILCLFIGGSLSL CCMF_BRAJA 313 108
CCMFBIOGNSIS5 Length of motif = 18 Motif number = 5
Cytochrome c-type biogenesis protein CcmF motif V - 1
PCODE ST INT
LLANNVLLVAAMLVVLLG CCMF_ECOLI 352 22
LLANNVLLVAAMLVVLLG CCMF_ECOLI 352 22
LLLNNILLMTALCVVFLG CCMF_HAEIN 352 22
LLGNNLVLVVAASMILLG CCMF_PSEFL 356 21
LVVNNLILTTATATVLTG CCMF_RHIME 351 22
LVMNNVLLAVAALVVFTG CCMF_RHOCA 351 22
LVLNNLLLTVACAVVLFG CCMF_BRAJA 351 22
CCMFBIOGNSIS6 Length of motif = 20 Motif number = 6
Cytochrome c-type biogenesis protein CcmF motif VI - 1
PCODE ST INT
FTWLMVPFALLLGVGPLVRW CCMF_ECOLI 395 25
FTWLMVPFALLLGVGPLVRW CCMF_ECOLI 395 25
FLIIMTPFALLLGIGPLVKW CCMF_HAEIN 395 25
FIPLMGLLMVVMAVGVLVRW CCMF_PSEFL 399 25
FGLLMLPLIAVVPFGPLLAW CCMF_RHIME 394 25
FTPFMVGLALLLPLGSMMPW CCMF_RHOCA 394 25
FAPLFALLLLAVPFGPMLAW CCMF_BRAJA 394 25
CCMFBIOGNSIS7 Length of motif = 14 Motif number = 7
Cytochrome c-type biogenesis protein CcmF motif VII - 1
PCODE ST INT
GLLCLFDPRYRKRV CCMF_ECOLI 624 209
GLLCLFDPRYRKRV CCMF_ECOLI 624 209
GLLCMFDRRYRFNV CCMF_HAEIN 631 216
GLLAALDRRYRVKV CCMF_PSEFL 633 214
GVVSLSDRRLRVGA CCMF_RHIME 633 219
GGLSLTDRRYRSAA CCMF_RHOCA 626 212
GVLSLSDRRLRVGA CCMF_BRAJA 633 219
FINAL MOTIF SETS
CCMFBIOGNSIS1 Length of motif = 25 Motif number = 1
Cytochrome c-type biogenesis protein CcmF motif I - 3
PCODE ST INT
EIGHYALVLALATALILSIVPVIGA Q52820 4 4
ESGHYALVLALGLALIQSIVPLIGA CCMF_BRAJA 4 4
EIGHYALVVRLATALIVSIVPVIAA Q52732 4 4
ETGHFALILALCVALVQAVIPLVGA CCMF_RHOCA 4 4
ELGHYALVLALATAIIQGVLPVLGV CCMF_RHIME 4 4
ELGQLAMILALCFAIVQAIVPLLGA Q51753 9 9
ELGQLRMILALCFAVVQAVVPLLGA CCMF_PSEFL 9 9
ETGHFALLVALCVALIQSVIPLVGA O30977 4 4
EIGSFLLCLALGWAVLLSIYPLWGA Q9Z646 4 4
EIGNGLLCLALGIALLLSVYPLWGV CCMF_ECOLI 4 4
ELGNYALALSLAVSLMLAIFPLWGA CCMF_HAEIN 4 4
CCMFBIOGNSIS2 Length of motif = 24 Motif number = 2
Cytochrome c-type biogenesis protein CcmF motif II - 3
PCODE ST INT
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
LSKHLPQEAVARVLGIMGIISVGF CCMF_HAEIN 113 84
CCMFBIOGNSIS3 Length of motif = 16 Motif number = 3
Cytochrome c-type biogenesis protein CcmF motif III - 3
PCODE ST INT
FAVAALLEGRIDAAWA Q52820 189 52
FAIAALMEGRIDAAWA CCMF_BRAJA 189 52
FAVAALIESRIDAAWA Q52732 189 52
FAVAALIEGRVDAAWA CCMF_RHOCA 189 52
FAVAALIEGRIDAAWA CCMF_RHIME 189 52
FAIAALLGGRLDAAWA Q51753 194 53
FAIAALLGGRLDAAWA CCMF_PSEFL 195 53
FAVAALLEGKVDAAWA O30977 189 52
FAIASLMTGRLDTAWA Q9Z646 190 53
FAIASLLSGRLDSTYA CCMF_ECOLI 190 53
FAIASLMTGKLDSAWA CCMF_HAEIN 190 53
CCMFBIOGNSIS4 Length of motif = 16 Motif number = 4
Cytochrome c-type biogenesis protein CcmF motif IV - 3
PCODE ST INT
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
YILAYLVVVIGGSLAL CCMF_HAEIN 314 108
CCMFBIOGNSIS5 Length of motif = 18 Motif number = 5
Cytochrome c-type biogenesis protein CcmF motif V - 3
PCODE ST INT
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
LLLNNILLMTALCVVFLG CCMF_HAEIN 352 22
CCMFBIOGNSIS6 Length of motif = 20 Motif number = 6
Cytochrome c-type biogenesis protein CcmF motif VI - 3
PCODE ST INT
FGLLMAPLIVIVPFGPMLAW Q52820 396 25
FAPLFALLLLAVPFGPMLAW CCMF_BRAJA 394 25
FGLLMAPLLVIVPFGPLLAW Q52732 394 25
FTPFMVGLALLLPLGSMMPW CCMF_RHOCA 394 25
FGLLMLPLIAVVPFGPLLAW CCMF_RHIME 394 25
FIPLMGLLMVVMAIGVLVRW Q51753 399 25
FIPLMGLLMVVMAVGVLVRW CCMF_PSEFL 399 25
FTPFMVGLALLLPIGAMVPW O30977 394 25
FTWLMAPFALMLGIGPLVRW Q9Z646 395 25
FTWLMVPFALLLGVGPLVRW CCMF_ECOLI 395 25
FLIIMTPFALLLGIGPLVKW CCMF_HAEIN 395 25
CCMFBIOGNSIS7 Length of motif = 14 Motif number = 7
Cytochrome c-type biogenesis protein CcmF motif VII - 3
PCODE ST INT
GLVSLSDRRLRVGA Q52820 635 219
GVLSLSDRRLRVGA CCMF_BRAJA 633 219
GLVSLSDRRLRVGA Q52732 635 221
GGLSLTDRRYRSAA CCMF_RHOCA 626 212
GVVSLSDRRLRVGA CCMF_RHIME 633 219
GLLAAMDRRYRVKV Q51753 686 267
GLLAALDRRYRVKV CCMF_PSEFL 633 214
GVLSLTDRRYRTAT O30977 626 212
GILCLLDPRYRSRK Q9Z646 632 217
GLLCLFDPRYRKRV CCMF_ECOLI 624 209
GLLCMFDRRYRFNV CCMF_HAEIN 631 216
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