WORKLIST ENTRIES (1):
CCMBBIOGNSIS View alignment Cytochrome c-type biogenesis protein CcmB signature
Type of fingerprint: COMPOUND with 7 elements
Links:
PRINTS; PR01410 CCBIOGENESIS; PR01411 CCMFBIOGNSIS; PR01412 CCBSBIOGNSIS
PRINTS; PR01413 NRFEBIOGNSIS; PR01386 CCMCBIOGNSIS
Creation date 29-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).
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.
CCMBBIOGNSIS is a 7-element fingerprint that provides a signature for
cytochrome c-type biogenesis protein CcmB (HelB). The fingerprint was derived from
an initial alignment of 5 sequences: the motifs were drawn from conserved
regions spanning virtually the full alignment length - motif 1 includes the
C-terminal half of TM domain 1; motif 2 encodes the C-terminal half of TM
domain 2; motif 3 lies immediately N-terminal to TM domain 3; motif 4 spans
TM domain 3; and motifs 5-7 encode TM domains 4-6 respectively. Two
iterations on SPTR37_10f were required to reach convergence, at which point
a true set comprising 10 sequences was identified. A single partial match
was also found, Q9Z650, a CcmB protein from Pantoea citrea that fails to
make a significant match with motif 3.
SUMMARY INFORMATION
10 codes involving 7 elements
1 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| 10 10 10 10 10 10 10
6| 1 1 0 1 1 1 1
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..
Q9Z3Z2 CCMB_RHOCA CCMB_ECOLI O52687
O33571 CCMB_HAEIN CCMB_PARDE P95488
CCMB_BRAJA Q52735
Subfamily: Codes involving 6 elements
Subfamily True positives..
Q9Z650
PROTEIN TITLES
Q9Z3Z2 CCMB PROTEIN - PSEUDOMONAS PUTIDA.
CCMB_RHOCA HEME EXPORTER PROTEIN B (CYTOCHROME C-TYPE BIOGENESIS PROTEI
CCMB_ECOLI HEME EXPORTER PROTEIN B (CYTOCHROME C-TYPE BIOGENESIS PROTEI
O52687 CYTOCHROME C MATURATION PROTEIN B - SHEWANELLA PUTREFACIENS.
O33571 HYPOTHETICAL ABC TRANSPORTER - RHODOBACTER SPHAEROIDES (RHOD
CCMB_HAEIN HEME EXPORTER PROTEIN B (CYTOCHROME C-TYPE BIOGENESIS PROTEI
CCMB_PARDE HEME EXPORTER PROTEIN B (CYTOCHROME C-TYPE BIOGENESIS PROTEI
P95488 CYT10 - PSEUDOMONAS FLUORESCENS.
CCMB_BRAJA HEME EXPORTER PROTEIN B (CYTOCHROME C-TYPE BIOGENESIS PROTEI
Q52735 CCMB - RHIZOBIUM ETLI.
Q9Z650 CCMB - PANTOEA CITREA.
SCAN HISTORY
SPTR37_10f 2 100 NSINGLE
INITIAL MOTIF SETS
CCMBBIOGNSIS1 Length of motif = 22 Motif number = 1
Cytochrome c-type biogenesis protein CcmB motif I - 1
PCODE ST INT
FFLTVVVLMPFAVGPDLALLSR CCMB_BRAJA 28 28
FFLIVITLFPLSIGPEPQLLAR CCMB_ECOLI 27 27
FFLLVITLFPLVIGPDPKLLSR CCMB_HAEIN 27 27
FFLIVCTLVPFGVGPEAGTVSR CCMB_PARDE 25 25
FFLIVVTLVPFGVGPQGEILAR CCMB_RHOCA 25 25
CCMBBIOGNSIS2 Length of motif = 18 Motif number = 2
Cytochrome c-type biogenesis protein CcmB motif II - 1
PCODE ST INT
ILWLGALLASLLTLDRLF CCMB_BRAJA 54 4
IIWVAALLSSLLALERLF CCMB_ECOLI 53 4
IAWVAALLSALLSFERLF CCMB_HAEIN 53 4
ILWVGALLSCLLSLDRIF CCMB_PARDE 50 3
ILWLGALLACLLSLDRIF CCMB_RHOCA 51 4
CCMBBIOGNSIS3 Length of motif = 24 Motif number = 3
Cytochrome c-type biogenesis protein CcmB motif III - 1
PCODE ST INT
DGSLDLITMSRTPLELACAAKALA CCMB_BRAJA 77 5
DGSLEQLMLLPLPLPAVVLAKVMA CCMB_ECOLI 76 5
DGSLEQLMLTAQPLPMTALAKVVA CCMB_HAEIN 76 5
DGSLDLLATAPLPLEGAVAIKALA CCMB_PARDE 73 5
DGSLDLLATAPIPMEAVVTIKALA CCMB_RHOCA 74 5
CCMBBIOGNSIS4 Length of motif = 19 Motif number = 4
Cytochrome c-type biogenesis protein CcmB motif IV - 1
PCODE ST INT
WLAAGLPLIVATPVLGLLL CCMB_BRAJA 102 1
WMVTGLPLLILSPLVAMLL CCMB_ECOLI 101 1
WLLTGLPLILLSPIAALLL CCMB_HAEIN 101 1
WLVTGLPLALSAPVFGLLL CCMB_PARDE 98 1
WITTGLPLVLAAPLFAVLL CCMB_RHOCA 99 1
CCMBBIOGNSIS5 Length of motif = 24 Motif number = 5
Cytochrome c-type biogenesis protein CcmB motif V - 1
PCODE ST INT
TLLAGTPALTFTGMIGAALAVTLH CCMB_BRAJA 133 12
TLLLGTPTLGFLGAPGVALTVGLK CCMB_ECOLI 132 12
TLLLGTPVLSCIGAIGVALTVGLR CCMB_HAEIN 132 12
SLLLGTPALSVLGSFGAAVTVGLR CCMB_PARDE 129 12
SLLLGTPALSVLGTFGAALTVGLK CCMB_RHOCA 130 12
CCMBBIOGNSIS6 Length of motif = 20 Motif number = 6
Cytochrome c-type biogenesis protein CcmB motif VI - 1
PCODE ST INT
RGGLLMAVLVLPLSIPVLIF CCMB_BRAJA 157 0
RGGVLLSILVLPLTIPLLIF CCMB_ECOLI 156 0
KGGVLLSLLVVPLFIPVLIF CCMB_HAEIN 156 0
RGGLLVSLLVLPLYVPTLIF CCMB_PARDE 153 0
RGGLLLSLLVLPLYVPTLIF CCMB_RHOCA 154 0
CCMBBIOGNSIS7 Length of motif = 24 Motif number = 7
Cytochrome c-type biogenesis protein CcmB motif VII - 1
PCODE ST INT
FSILCALSLVSLVIGPFAAAASLR CCMB_BRAJA 195 18
LAILGALLAGTATLSPFATAAALR CCMB_ECOLI 193 17
LAILGAMMVGAVTLSPFAIAAALR CCMB_HAEIN 193 17
LVFLAAITLATLALAFAAAAASVN CCMB_PARDE 190 17
LAMLAGITAATVALVPFASAAAIR CCMB_RHOCA 191 17
FINAL MOTIF SETS
CCMBBIOGNSIS1 Length of motif = 22 Motif number = 1
Cytochrome c-type biogenesis protein CcmB motif I - 2
PCODE ST INT
FFAIVVAMFPLAVGPESQLLQT Q9Z3Z2 27 27
FFLIVVTLVPFGVGPQGEILAR CCMB_RHOCA 25 25
FFLIVITLFPLSIGPEPQLLAR CCMB_ECOLI 27 27
FFIMVVTLFPLGIGPEPQMLAR O52687 35 35
FFLLVAVLVPLGVGPEPATLAK O33571 25 25
FFLLVITLFPLVIGPDPKLLSR CCMB_HAEIN 27 27
FFLIVCTLVPFGVGPEAGTVSR CCMB_PARDE 25 25
FFAIVVALFPLAVGPESQLLQT P95488 28 28
FFLTVVVLMPFAVGPDLALLSR CCMB_BRAJA 28 28
FFLTVVAVIPFGVGPDLKLLSR Q52735 25 25
CCMBBIOGNSIS2 Length of motif = 18 Motif number = 2
Cytochrome c-type biogenesis protein CcmB motif II - 2
PCODE ST INT
LVWVAALLAVLLSLDGLF Q9Z3Z2 53 4
ILWLGALLACLLSLDRIF CCMB_RHOCA 51 4
IIWVAALLSSLLALERLF CCMB_ECOLI 53 4
IIWVAALLASMLSLERLF O52687 61 4
ILWVGALLACLLSLDRIF O33571 51 4
IAWVAALLSALLSFERLF CCMB_HAEIN 53 4
ILWVGALLSCLLSLDRIF CCMB_PARDE 50 3
LVWVAALLAVLLSLDGLF P95488 54 4
ILWLGALLASLLTLDRLF CCMB_BRAJA 54 4
IVWIGALLSALLGLDRLF Q52735 51 4
CCMBBIOGNSIS3 Length of motif = 24 Motif number = 3
Cytochrome c-type biogenesis protein CcmB motif III - 2
PCODE ST INT
DGSLEQWVLSPHPLALLVLAKVLA Q9Z3Z2 76 5
DGSLDLLATAPIPMEAVVTIKALA CCMB_RHOCA 74 5
DGSLEQLMLLPLPLPAVVLAKVMA CCMB_ECOLI 76 5
DGSLEQMLLSPQPLAILVLAKVLA O52687 84 5
DGSLDLLATAPIPLEGVVAVKACA O33571 74 5
DGSLEQLMLTAQPLPMTALAKVVA CCMB_HAEIN 76 5
DGSLDLLATAPLPLEGAVAIKALA CCMB_PARDE 73 5
DGSLEQWVLSPHPLALLVLAKVLA P95488 77 5
DGSLDLITMSRTPLELACAAKALA CCMB_BRAJA 77 5
DGSLDLMLMQETPLVLTVLVKCFA Q52735 74 5
CCMBBIOGNSIS4 Length of motif = 19 Motif number = 4
Cytochrome c-type biogenesis protein CcmB motif IV - 2
PCODE ST INT
WIFSGLPLVLLPPLLALML Q9Z3Z2 101 1
WITTGLPLVLAAPLFAVLL CCMB_RHOCA 99 1
WMVTGLPLLILSPLVAMLL CCMB_ECOLI 101 1
WLLTGVPLILIAPLLAVLL O52687 109 1
WIVTGLPLTLVSPLLGLLM O33571 99 1
WLLTGLPLILLSPIAALLL CCMB_HAEIN 101 1
WLVTGLPLALSAPVFGLLL CCMB_PARDE 98 1
WIFSGLALVLLAPLLALML P95488 102 1
WLAAGLPLIVATPVLGLLL CCMB_BRAJA 102 1
WTATGLPLVIASPLLGLFM Q52735 99 1
CCMBBIOGNSIS5 Length of motif = 24 Motif number = 5
Cytochrome c-type biogenesis protein CcmB motif V - 2
PCODE ST INT
SLLLGTPVLSLLGAVGAALTVGLK Q9Z3Z2 132 12
SLLLGTPALSVLGTFGAALTVGLK CCMB_RHOCA 130 12
TLLLGTPTLGFLGAPGVALTVGLK CCMB_ECOLI 132 12
TLALGTPVLSLLGAIGVALTVGLR O52687 140 12
SLAIGTPALSVIGTFGAALTVGLK O33571 130 12
TLLLGTPVLSCIGAIGVALTVGLR CCMB_HAEIN 132 12
SLLLGTPALSVLGSFGAAVTVGLR CCMB_PARDE 129 12
SLLLGTPVLSLLGAVAALTVGLKR P95488 133 12
TLLAGTPALTFTGMIGAALAVTLH CCMB_BRAJA 133 12
TLLVGSPAITFIGAVGAAVAVALP Q52735 130 12
CCMBBIOGNSIS6 Length of motif = 20 Motif number = 6
Cytochrome c-type biogenesis protein CcmB motif VI - 2
PCODE ST INT
RGGLLLALLILPLYIPVLIL Q9Z3Z2 156 0
RGGLLLSLLVLPLYVPTLIF CCMB_RHOCA 154 0
RGGVLLSILVLPLTIPLLIF CCMB_ECOLI 156 0
KGGVLLSLLILPLYIPVLIF O52687 164 0
RGGLLLSLLVLPLYVPTLVF O33571 154 0
KGGVLLSLLVVPLFIPVLIF CCMB_HAEIN 156 0
RGGLLVSLLVLPLYVPTLIF CCMB_PARDE 153 0
RGGLLLRLLILPLYIPVLIL P95488 156 -1
RGGLLMAVLVLPLSIPVLIF CCMB_BRAJA 157 0
RGGLLVSILVLPLTIPVLIF Q52735 154 0
CCMBBIOGNSIS7 Length of motif = 24 Motif number = 7
Cytochrome c-type biogenesis protein CcmB motif VII - 2
PCODE ST INT
LLWLATLTALAVTLAPFAIAAGLK Q9Z3Z2 193 17
LAMLAGITAATVALVPFASAAAIR CCMB_RHOCA 191 17
LAILGALLAGTATLSPFATAAALR CCMB_ECOLI 193 17
LAIIGAMLIGSLTLAPFAIGASLR O52687 201 17
FLLLGGITAGVAALLPFASAAAVR O33571 191 17
LAILGAMMVGAVTLSPFAIAAALR CCMB_HAEIN 193 17
LVFLAAITLATLALAFAAAAASVN CCMB_PARDE 190 17
LLWLASLTALAVTLAPFAIAAGLK P95488 192 16
FSILCALSLVSLVIGPFAAAASLR CCMB_BRAJA 195 18
FLILIALTLFFAVIGPAAAALALR Q52735 192 18
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