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PR01386

Identifier
CCMCBIOGNSIS  [View Relations]  [View Alignment]  
Accession
PR01386
No. of Motifs
6
Creation Date
29-APR-2000
Title
Cytochrome c-type biogenesis protein CcmC signature
Database References
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).

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]. Genetic and molecular
analyses show that the hel locus contains at least 4 genes, helA, helB, helC
and orf52 [6]. HelA is similar to the ABC transporters and helA, helB, and
helC are proposed to encode an export complex [4]. 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]. However,
while CcmB and CcmC have the potential to interact with CcmA, the 3 gene 
products probably associating to form a complex with (CcmA)2-CcmB-CcmC
stoichiometry, the substrate for the putative CcmABC-transporter is probably
neither haem nor c-type apocytochromes [3]. Hydropathy analysis suggests
the presence of 6 TM domains.
 
CCMCBIOGNSIS is a 6-element fingerprint that provides a signature for 
cytochrome c-type biogenesis protein CcmC. The fingerprint was derived from
an initial alignment of 6 sequences: the motifs were drawn from conserved
regions spanning virtually the full alignment length - motif 1 lies
immediately C-terminal to TM domain 1; motif 2 includes TM domain 2; motif 3
encodes the C-terminal half of TM domain 3; motif 4 encodes the N-terminal
half of TM domain 4; and motifs 5 and 6 span TM domains 5 and 6 respectively.
Two iterations on SPTR37_10f were required to reach convergence, at which 
point a true set comprising 15 sequences was identified. Three partial 
matches were also found, all of which are closely related sequences that
fail to match the C-terminal motifs.
Summary Information
  15 codes involving  6 elements
2 codes involving 5 elements
1 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
6151515151515
5222220
4111100
3000000
2000000
123456
True Positives
CCMC_BRAJA    CCMC_ECOLI    CCMC_HAEIN    CCMC_PARDE    
CCMC_RHOCA O33572 O52688 P92527
Q32751 Q35212 Q41574 Q51750
Q9Z649 Q9ZCC7 YM05_MARPO
True Positive Partials
Codes involving 5 elements
O21278 Q9ZZN0
Codes involving 4 elements
O28299
Sequence Titles
CCMC_BRAJA  HEME EXPORTER PROTEIN C (CYTOCHROME C-TYPE BIOGENESIS PROTEIN CYCZ) - BRADYRHIZOBIUM JAPONICUM. 
CCMC_ECOLI HEME EXPORTER PROTEIN C (CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCMC) - ESCHERICHIA COLI.
CCMC_HAEIN HEME EXPORTER PROTEIN C (CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCMC) - HAEMOPHILUS INFLUENZAE.
CCMC_PARDE HEME EXPORTER PROTEIN C (CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCMC) - PARACOCCUS DENITRIFICANS.
CCMC_RHOCA HEME EXPORTER PROTEIN C (CYTOCHROME C-TYPE BIOGENESIS PROTEIN HELC) - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
O33572 HYPOTHETICAL ABC TRANSPORTER - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
O52688 CYTOCHROME C MATURATION PROTEIN C - SHEWANELLA PUTREFACIENS.
P92527 CYTOCHROME C BIOGENESIS ORF256 - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
Q32751 ABC-TYPE HEME TRANSPORTER SUBUNIT - ORYZA SATIVA (RICE).
Q35212 MITOCHONDRIAL DNA FOR ORF250 - OENOTHERA BERTERIANA.
Q41574 PUTATIVE HEME ABC TRANSPORTER MEMBRANE DOMAIN - TRITICUM AESTIVUM (WHEAT).
Q51750 INNER MEMBRANE PROTEIN - PSEUDOMONAS FLUORESCENS.
Q9Z649 CCMC - PANTOEA CITREA.
Q9ZCC7 HEME EXPORTER PROTEIN C (CCMC) - RICKETTSIA PROWAZEKII.
YM05_MARPO HYPOTHETICAL 26.5 KD PROTEIN IN RPS2 3'REGION (ORF 228) - MARCHANTIA POLYMORPHA (LIVERWORT).

O21278 SUBUNIT OF ABC TRANSPORTER FOR CYTOCHROME C1 - RECLINOMONAS AMERICANA.
Q9ZZN0 SUBUNIT OF ABC TRANSPORTER FOR CYTOCHROME C1 - CYANIDIOSCHYZON MEROLAE.

O28299 HEME EXPORTER PROTEIN C (HELC) - ARCHAEOGLOBUS FULGIDUS.
Scan History
SPTR37_10f 2  100  NSINGLE    
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
PSDFQQGENYRIIYVHVP YM05_MARPO 42 42 -
PADYQQGNSYRIIYLHVP CCMC_ECOLI 45 45 -
PADYQQGNSFRIMYVHAP CCMC_HAEIN 45 45 -
PDDYQQGATVKIMFIHVP CCMC_BRAJA 42 42 -
PEDYKQGATVKIIFLHVP CCMC_PARDE 42 42 -
PVAAEFGATVKVIYVHVP CCMC_RHOCA 43 43 -

Motif 2 width=21
Element Seqn Id St Int Rpt
PAAWMSLLIYIAMAISSVLFL YM05_MARPO 59 -1 -
PAAIWSMGIYASMAVAAFIGL CCMC_ECOLI 62 -1 -
PTAIWSMGVYGSMAIAAVVAL CCMC_HAEIN 62 -1 -
PNAWLSMFVWGVMSIASLGTL CCMC_BRAJA 59 -1 -
PAALMAINIWLMMLVTSLIWL CCMC_PARDE 59 -1 -
PAATLAINIWVMMLVASLIWL CCMC_RHOCA 60 -1 -

Motif 3 width=21
Element Seqn Id St Int Rpt
GALFTLFTLVTGGFWGKPMWG YM05_MARPO 97 17 -
GAVFTFIALVTGSAWGKPMWG CCMC_ECOLI 100 17 -
GALFTFLSLVTGAIWGKPMWG CCMC_HAEIN 100 17 -
GAAFTFLALLTGSLWGRPMWG CCMC_BRAJA 97 17 -
GAVMTLIALITGAIWGQPMWG CCMC_PARDE 97 17 -
GMVMTLIALITGAFWGQPMWG CCMC_RHOCA 98 17 -

Motif 4 width=21
Element Seqn Id St Int Rpt
TFWVWDARLTSVLILFFIYLG YM05_MARPO 118 0 -
TWWVWDARLTSELVLLFLYVG CCMC_ECOLI 121 0 -
TWWVWDARLTAELILFFLYLG CCMC_HAEIN 121 0 -
TYWEWDARLTSVLILFLMYLG CCMC_BRAJA 118 0 -
TWWEWDPRLTSFLILFLFYLG CCMC_PARDE 118 0 -
TWWEWDPRLTSFLILFLFYLG CCMC_RHOCA 119 0 -

Motif 5 width=27
Element Seqn Id St Int Rpt
ADVASIFICIGLINIPIIKFSVNWWNT YM05_MARPO 147 8 -
GRAAGILVLIGVVNLPIIHYSVEWWNT CCMC_ECOLI 156 14 -
AKAAGILCITTVVILPIIHFSVEWWNT CCMC_HAEIN 156 14 -
ARAAAVLTLVGAINLPIIKFSVDWWNT CCMC_BRAJA 153 14 -
ADLTGVLCLVGSVFALLSRYAVNFWNQ CCMC_PARDE 153 14 -
ADLTGVLCLVGSVFAVLSRYAAIFWNQ CCMC_RHOCA 154 14 -

Motif 6 width=25
Element Seqn Id St Int Rpt
PIFLIFASFFFLTGIFFILETRQII YM05_MARPO 194 20 -
PLRWSIFGFLLLSATLTLMRMRNLI CCMC_ECOLI 201 18 -
PLILCIFGFLTLYIWLTLVRYRMEL CCMC_HAEIN 204 21 -
PLLVMAIAFTLLFVTLHLAAMRNEI CCMC_BRAJA 201 21 -
PLYLTMAGFFLLFLALLLIRTRTEI CCMC_PARDE 202 22 -
PLVLSIAGFGMLFVALLLLRTRTEI CCMC_RHOCA 203 22 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
PLDLQQGGNSRIPYVHVP Q35212 42 42 -
PLDLQQGGNSRILYVHVP P92527 42 42 -
PSDFQQGENYRIIYVHVP YM05_MARPO 42 42 -
PPDLQQGGNSRISYVHVP Q32751 42 42 -
PPDLQQGGNSRISYVHVP Q41574 42 42 -
PADYQQGNSYRIIYLHVP CCMC_ECOLI 45 45 -
PPDYQQGDSYRIMYIHVP Q9Z649 45 45 -
PTDYQQGDSYRIIFIHVP O52688 45 45 -
PADYQQGNSFRIMYVHAP CCMC_HAEIN 45 45 -
PIDYQQGEFVRIMYVHVP Q9ZCC7 41 41 -
PDDYQQGATVKIMFIHVP CCMC_BRAJA 42 42 -
PEDYKQGATVKIIFLHVP CCMC_PARDE 42 42 -
PPDYQQGNSFRIIYIHVP Q51750 25 25 -
PDDFKQGSTVKIIYLHVP O33572 43 43 -
PVAAEFGATVKVIYVHVP CCMC_RHOCA 43 43 -

Motif 2 width=21
Element Seqn Id St Int Rpt
PAARMSILVYIATAINTFLFL Q35212 59 -1 -
PAARMSIIVYIATAINTFLFL P92527 59 -1 -
PAAWMSLLIYIAMAISSVLFL YM05_MARPO 59 -1 -
PAARMSIVIYIATAINSSLFP Q32751 59 -1 -
PAARMSIVIYIATAINSSLFP Q41574 59 -1 -
PAAIWSMGIYASMAVAAFIGL CCMC_ECOLI 62 -1 -
PAAMWSMGVYASMAIAAFIGL Q9Z649 62 -1 -
PAASMSMAAYMGMATAAFIGL O52688 62 -1 -
PTAIWSMGVYGSMAIAAVVAL CCMC_HAEIN 62 -1 -
PASWMALGIYVFMAICSFSYL Q9ZCC7 58 -1 -
PNAWLSMFVWGVMSIASLGTL CCMC_BRAJA 59 -1 -
PAALMAINIWLMMLVTSLIWL CCMC_PARDE 59 -1 -
PAALLAQSCYVMLAVCGIVGL Q51750 42 -1 -
PSALMAINAWLMMLAASLIWL O33572 60 -1 -
PAATLAINIWVMMLVASLIWL CCMC_RHOCA 60 -1 -

Motif 3 width=21
Element Seqn Id St Int Rpt
GAFFTLFTLVTGGFRGKPMWG Q35212 97 17 -
GAFFTLFTLVTGGFRGRPMWG P92527 97 17 -
GALFTLFTLVTGGFWGKPMWG YM05_MARPO 97 17 -
GAFSTLFTLVTGGFRGRPMWG Q32751 97 17 -
GAFSTLFTLVTGGFRGRPMWG Q41574 97 17 -
GAVFTFIALVTGSAWGKPMWG CCMC_ECOLI 100 17 -
GAVFTFIALVTGSAWGKPMWG Q9Z649 100 17 -
GAVITFIALFTGATWGKPMWG O52688 100 17 -
GALFTFLSLVTGAIWGKPMWG CCMC_HAEIN 100 17 -
GAIFTLISLVTGSLWGKPIWG Q9ZCC7 96 17 -
GAAFTFLALLTGSLWGRPMWG CCMC_BRAJA 97 17 -
GAVMTLIALITGAIWGQPMWG CCMC_PARDE 97 17 -
GAWMTAVALLTGAIWGKPTWG Q51750 80 17 -
GLTFTLVALVTGAVWGQPMWG O33572 98 17 -
GMVMTLIALITGAFWGQPMWG CCMC_RHOCA 98 17 -

Motif 4 width=21
Element Seqn Id St Int Rpt
TFWVWDARLTSVFISFLIYLG Q35212 118 0 -
TFWVWDARLTSVFISFLIYLG P92527 118 0 -
TFWVWDARLTSVLILFFIYLG YM05_MARPO 118 0 -
TFRVWDARLTSVFILFLIYLG Q32751 118 0 -
TFRVWDARLTSVFILFLIYLG Q41574 118 0 -
TWWVWDARLTSELVLLFLYVG CCMC_ECOLI 121 0 -
TWWVWDARLTSELVLLFIYMG Q9Z649 121 0 -
TWWVWDARLTSELVLLFLYLG O52688 121 0 -
TWWVWDARLTAELILFFLYLG CCMC_HAEIN 121 0 -
TWWVWDARLTSMLILFLLYLS Q9ZCC7 117 0 -
TYWEWDARLTSVLILFLMYLG CCMC_BRAJA 118 0 -
TWWEWDPRLTSFLILFLFYLG CCMC_PARDE 118 0 -
SWWVWDARLTSMLILLFLYFG Q51750 101 0 -
TWWAWDPRLTSFLILALFYLG O33572 119 0 -
TWWEWDPRLTSFLILFLFYLG CCMC_RHOCA 119 0 -

Motif 5 width=27
Element Seqn Id St Int Rpt
VEPASISIRAGPIDIPIIKSSVNWWNT Q35212 147 8 -
VEPASISIRAGPIDIPIIKSSVNWWNT P92527 147 8 -
ADVASIFICIGLINIPIIKFSVNWWNT YM05_MARPO 147 8 -
VEPAPISIRAGPIDIPIIKSPVNWWNT Q32751 147 8 -
VEPAPISIRAGPIDIPIIKSPVNWWNT Q41574 147 8 -
GRAAGILVLIGVVNLPIIHYSVEWWNT CCMC_ECOLI 156 14 -
GRAAGILILVGVVNLPIIHYSVQWWNT Q9Z649 156 14 -
ARAAGILAIVGVINIPIIKYSVEWWSS O52688 156 14 -
AKAAGILCITTVVILPIIHFSVEWWNT CCMC_HAEIN 156 14 -
QNPASIIALIGLINIPIIKFSVNIWYS Q9ZCC7 152 14 -
ARAAAVLTLVGAINLPIIKFSVDWWNT CCMC_BRAJA 153 14 -
ADLTGVLCLVGSVFALLSRYAVNFWNQ CCMC_PARDE 153 14 -
AKACAVLAIVGVINIPIIKYSVEWWNT Q51750 136 14 -
ADLTSVLCIVGSVFAVLSRYAVNFWNQ O33572 154 14 -
ADLTGVLCLVGSVFAVLSRYAAIFWNQ CCMC_RHOCA 154 14 -

Motif 6 width=25
Element Seqn Id St Int Rpt
PILSNFANFPFSTRILFVLETRLPI Q35212 194 20 -
PILSNFANFPFSTRILFVLETRLPI P92527 194 20 -
PIFLIFASFFFLTGIFFILETRQII YM05_MARPO 194 20 -
PILSNFANFPFSTRILFVLETRLPI Q32751 194 20 -
PILSNFANFPFSTRILFVLETRLPI Q41574 194 20 -
PLRWSIFGFLLLSATLTLMRMRNLI CCMC_ECOLI 201 18 -
PLRWAILGYLLVFISLTLMRLRNLI Q9Z649 202 19 -
PLLINILGFGLMIGAITIVRFRAEI O52688 204 21 -
PLILCIFGFLTLYIWLTLVRYRMEL CCMC_HAEIN 204 21 -
PLITMFISFILYFLLVLLLRTVILI Q9ZCC7 200 21 -
PLLVMAIAFTLLFVTLHLAAMRNEI CCMC_BRAJA 201 21 -
PLYLTMAGFFLLFLALLLIRTRTEI CCMC_PARDE 202 22 -
PLLLMVLGFYCFFGAVLLMRMRLEV Q51750 184 21 -
PLLVCIAGFVLLFLTLVLLRTRTEI O33572 203 22 -
PLVLSIAGFGMLFVALLLLRTRTEI CCMC_RHOCA 203 22 -