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Conserved domains on  [gi|2279554577|ref|WP_256257736|]
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cytochrome c [Paenibacillus sp. UNCCL117]

Protein Classification

c-type cytochrome( domain architecture ID 10601782)

c-type cytochrome is an electron carrier protein that contains one or more heme groups; such as Pseudomonas putida 4-cresol dehydrogenase [hydroxylating] cytochrome c subunit that binds 1 heme c group per subunit

CATH:  1.10.760.10
Gene Ontology:  GO:0020037|GO:0009055|GO:0046872
PubMed:  12594933|10647174|18568041|10395550|31252007|22723177
SCOP:  3000815

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cytochrome_CBB3 pfam13442
Cytochrome C oxidase, cbb3-type, subunit III;
48-118 3.39e-18

Cytochrome C oxidase, cbb3-type, subunit III;


:

Pssm-ID: 463879 [Multi-domain]  Cd Length: 67  Bit Score: 72.44  E-value: 3.39e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2279554577  48 NAQAAEAIYKQSCLACHGaelEGKLGPNLqkVGGKLSDQQIYKVLLNGKGGMPAFKSTLKDEELVNLAKWL 118
Cdd:pfam13442   2 AAAAGEALYAANCASCHG---TGGAGPSL--AGRALPPEALVDIIRNGKGAMPAFGGDLSDEELEALAAYL 67
 
Name Accession Description Interval E-value
Cytochrome_CBB3 pfam13442
Cytochrome C oxidase, cbb3-type, subunit III;
48-118 3.39e-18

Cytochrome C oxidase, cbb3-type, subunit III;


Pssm-ID: 463879 [Multi-domain]  Cd Length: 67  Bit Score: 72.44  E-value: 3.39e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2279554577  48 NAQAAEAIYKQSCLACHGaelEGKLGPNLqkVGGKLSDQQIYKVLLNGKGGMPAFKSTLKDEELVNLAKWL 118
Cdd:pfam13442   2 AAAAGEALYAANCASCHG---TGGAGPSL--AGRALPPEALVDIIRNGKGAMPAFGGDLSDEELEALAAYL 67
CccA COG2010
Cytochrome c, mono- and diheme variants [Energy production and conversion];
37-119 2.26e-17

Cytochrome c, mono- and diheme variants [Energy production and conversion];


Pssm-ID: 441613 [Multi-domain]  Cd Length: 169  Bit Score: 73.44  E-value: 2.26e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279554577  37 AAAPALPDTPLNAQAAEAIYKQSCLACHGAELEGKLG--PNL-QKVGGKLSDQQIYKVLLNG--KGGMPAFKSTLKDEEL 111
Cdd:COG2010    77 AAADAPAADAEALARGKALYEQNCAACHGADGKGGLGaaPNLtDDALYGGDPEALVETILNGrpGGAMPAFGGQLSDEEI 156


                  ....*...
gi 2279554577 112 VNLAKWLA 119
Cdd:COG2010   157 AALAAYLR 164
PRK14486 PRK14486
putative bifunctional cbb3-type cytochrome c oxidase subunit II/cytochrome c; Provisional
 53-118 7.01e-09

putative bifunctional cbb3-type cytochrome c oxidase subunit II/cytochrome c; Provisional


Pssm-ID: 184704 [Multi-domain]  Cd Length: 294  Bit Score: 51.74  E-value: 7.01e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2279554577  53 EAIYKQSCLACHGAELEGKLGPNLQKVG-GKLSDQQIYKVLLNGK--GGMPAFKSTLKDEELVNLAKWL 118
Cdd:PRK14486  219 KALYDANCAACHGDEAQGQEGVALNDIDdGDLPDAAYFGMIKGGSdaKGMPGFGGDLSDDDIWAIVAYI 287
CxxCH_TIGR02603 TIGR02603
putative heme-binding domain, Pirellula/Verrucomicrobium type; This model represents a domain ...
 48-108 5.82e-04

putative heme-binding domain, Pirellula/Verrucomicrobium type; This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).


Pssm-ID: 274224  Cd Length: 133  Bit Score: 36.95  E-value: 5.82e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2279554577  48 NAQAAEAIYKQSCLACHGAELEG-KLGPNLQKVGGKlSDQQIYKVLLNGKGGMPA-FKS---TLKD 108
Cdd:TIGR02603   2 DAARGKAVFAKVCYLCHRIGGQGvDFGPNLTTVGTK-GKEYLLEAILDPSRTVAPgFETyrvTTKD 66
 
Name Accession Description Interval E-value
Cytochrome_CBB3 pfam13442
Cytochrome C oxidase, cbb3-type, subunit III;
48-118 3.39e-18

Cytochrome C oxidase, cbb3-type, subunit III;


Pssm-ID: 463879 [Multi-domain]  Cd Length: 67  Bit Score: 72.44  E-value: 3.39e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2279554577  48 NAQAAEAIYKQSCLACHGaelEGKLGPNLqkVGGKLSDQQIYKVLLNGKGGMPAFKSTLKDEELVNLAKWL 118
Cdd:pfam13442   2 AAAAGEALYAANCASCHG---TGGAGPSL--AGRALPPEALVDIIRNGKGAMPAFGGDLSDEELEALAAYL 67
CccA COG2010
Cytochrome c, mono- and diheme variants [Energy production and conversion];
37-119 2.26e-17

Cytochrome c, mono- and diheme variants [Energy production and conversion];


Pssm-ID: 441613 [Multi-domain]  Cd Length: 169  Bit Score: 73.44  E-value: 2.26e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279554577  37 AAAPALPDTPLNAQAAEAIYKQSCLACHGAELEGKLG--PNL-QKVGGKLSDQQIYKVLLNG--KGGMPAFKSTLKDEEL 111
Cdd:COG2010    77 AAADAPAADAEALARGKALYEQNCAACHGADGKGGLGaaPNLtDDALYGGDPEALVETILNGrpGGAMPAFGGQLSDEEI 156


                  ....*...
gi 2279554577 112 VNLAKWLA 119
Cdd:COG2010   157 AALAAYLR 164
CytC553 COG2863
Cytochrome c553 [Energy production and conversion];
38-122 5.83e-10

Cytochrome c553 [Energy production and conversion];


Pssm-ID: 442110 [Multi-domain]  Cd Length: 98  Bit Score: 52.04  E-value: 5.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279554577  38 AAPALPDTPLNAQAAEAiYKQSCLACHGAELEGKLGPNLQKVGGkLSDQQIYKVLLNGKGG------MPAFKSTLKDEEL 111
Cdd:COG2863     4 ALLAAPAAAGDAARGKA-YAAACAACHGADGEGNPGGGAPRLAG-QHAEYLVAQLKAFRSGarkngvMPAIAKGLSDEDI 81

                          90
                  ....*....|.
gi 2279554577 112 VNLAKWLAEKK 122
Cdd:COG2863    82 KALAAYIASLK 92
PRK14486 PRK14486
putative bifunctional cbb3-type cytochrome c oxidase subunit II/cytochrome c; Provisional
 53-118 7.01e-09

putative bifunctional cbb3-type cytochrome c oxidase subunit II/cytochrome c; Provisional


Pssm-ID: 184704 [Multi-domain]  Cd Length: 294  Bit Score: 51.74  E-value: 7.01e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2279554577  53 EAIYKQSCLACHGAELEGKLGPNLQKVG-GKLSDQQIYKVLLNGK--GGMPAFKSTLKDEELVNLAKWL 118
Cdd:PRK14486  219 KALYDANCAACHGDEAQGQEGVALNDIDdGDLPDAAYFGMIKGGSdaKGMPGFGGDLSDDDIWAIVAYI 287
CytC552 COG4654
Cytochrome c551/c552 [Energy production and conversion];
48-122 1.54e-07

Cytochrome c551/c552 [Energy production and conversion];


Pssm-ID: 443692 [Multi-domain]  Cd Length: 88  Bit Score: 45.66  E-value: 1.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279554577  48 NAQAAEAIYKQS-CLACHGAElEGKLGPNLQKVGGKLSDQ-----QIYKVLLNGKGG------MPAFKsTLKDEELVNLA 115
Cdd:COG4654     3 DAAAGKALAKKSgCLACHAVD-KKLVGPSYKDVAKKYKGKadavaKLAKKIKKGGSGvwgdvpMPPHP-QLSDAEAKALV 80


                  ....*...
gi 2279554577 116 KW-LAEKK 122
Cdd:COG4654    81 KWiLSLKK 88
PRK13697 PRK13697
cytochrome c6; Provisional
 48-121 2.58e-06

cytochrome c6; Provisional


Pssm-ID: 184253 [Multi-domain]  Cd Length: 111  Bit Score: 42.85  E-value: 2.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279554577  48 NAQAAEAIYKQSCLACHgaeLEGK----LGPNLQKVG----GKLSDQQIYKVLLNGKGGMPAFKSTLKDEELVNLAKWLA 119
Cdd:PRK13697   27 DAANGEQVFSANCASCH---AGGKnlvnAGKTLKKADlekyGMYSLEAITAQVTNGKNAMPAFKDRLSPDQIEDVAAYVL 103


                  ..
gi 2279554577 120 EK 121
Cdd:PRK13697  104 EQ 105
Cyc7 COG3474
Cytochrome c2 [Energy production and conversion];
48-119 1.67e-05

Cytochrome c2 [Energy production and conversion];


Pssm-ID: 442697 [Multi-domain]  Cd Length: 101  Bit Score: 40.64  E-value: 1.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279554577  48 NAQAAEAIYKQSCLACH--GAELEGKLGPNLQKVGGKlsdqqiykvllnGKGGMPAFK--STLKDEELV----NLAKWLA 119
Cdd:COG3474     2 DAAAGEKLFNRKCAACHsvDGGAGNRVGPNLNGVVGR------------KAGSVEGFAysDALKASGLVwdeeTLDAWLA 69
Cytochrom_C pfam00034
Cytochrome c; The Pfam entry does not include all Prosite members. The cytochrome 556 and ...
 50-119 2.78e-05

Cytochrome c; The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, pfam06181, has now been merged into this family.


Pssm-ID: 459641 [Multi-domain]  Cd Length: 89  Bit Score: 39.83  E-value: 2.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279554577  50 QAAEAIYKQSCLACHGAELEG--KLGPNLQKVGGKLSDQQIYKVLLNGK---------------GGMPAFKStLKDEELV 112
Cdd:pfam00034   1 ARGKKLFAANCAACHGVNGEGagAGGPDLAGLAARYPGDALGAIRENKHaiggggvdraggppgTGMPAFDG-LTDEEIA 79


                  ....*..
gi 2279554577 113 NLAKWLA 119
Cdd:pfam00034  80 DLVAYLL 86
PetJ COG5677
Cytochrome c6 [Energy production and conversion];
48-121 5.19e-05

Cytochrome c6 [Energy production and conversion];


Pssm-ID: 444391 [Multi-domain]  Cd Length: 112  Bit Score: 39.48  E-value: 5.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279554577  48 NAQAAEAIYKQSCLACHgaeLEGK----LGPNLQKVG----GKLSDQQIYKVLLNGKGGMPAFKSTLKDEELVNLAKWLA 119
Cdd:COG5677    27 DLANGAKIFSANCAGCH---IGGGniirRGKTLKKEAlekyGMDSLEAIATQVTNGKNAMPAFKDRLSEEQIEDVAAYVL 103


                  ..
gi 2279554577 120 EK 121
Cdd:COG5677   104 DQ 105
TsdA COG3258
Thiosulfate dehydrogenase TsdA, contains C-terminal cytochrome c domain [Inorganic ion ...
 43-115 1.03e-04

Thiosulfate dehydrogenase TsdA, contains C-terminal cytochrome c domain [Inorganic ion transport and metabolism];


Pssm-ID: 442489 [Multi-domain]  Cd Length: 216  Bit Score: 39.84  E-value: 1.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279554577  43 PDTPLNAQAAEAIYKQSCLACHGAELEGKLGPNLQKVGGKLSDQQIYkvlLNGKG--------------GMPAFK-STLK 107
Cdd:COG3258   111 PAASADVERGKALYAERCASCHGADGEGQGRADGQYGFPPLWGGDSY---NDGAGmarlgtladfikgrNMPLGKpGSLS 187


                  ....*...
gi 2279554577 108 DEELVNLA 115
Cdd:COG3258   188 DDEAWDVA 195
CxxCH_TIGR02603 TIGR02603
putative heme-binding domain, Pirellula/Verrucomicrobium type; This model represents a domain ...
 48-108 5.82e-04

putative heme-binding domain, Pirellula/Verrucomicrobium type; This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).


Pssm-ID: 274224  Cd Length: 133  Bit Score: 36.95  E-value: 5.82e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2279554577  48 NAQAAEAIYKQSCLACHGAELEG-KLGPNLQKVGGKlSDQQIYKVLLNGKGGMPA-FKS---TLKD 108
Cdd:TIGR02603   2 DAARGKAVFAKVCYLCHRIGGQGvDFGPNLTTVGTK-GKEYLLEAILDPSRTVAPgFETyrvTTKD 66
thiosulf_SoxX TIGR04485
sulfur oxidation c-type cytochrome SoxX; Members of this family are SoxX, a c-type cytochrome ...
 60-111 1.14e-03

sulfur oxidation c-type cytochrome SoxX; Members of this family are SoxX, a c-type cytochrome with a CxxCH motif, part of a heterodimer with SoxA. SoxXA, SoxYZ, and SoxB contribute to thiosulfate oxidation to sulfate.


Pssm-ID: 275278 [Multi-domain]  Cd Length: 78  Bit Score: 35.25  E-value: 1.14e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2279554577  60 CLACHG----AELEGKLGPNLQKVGGKLSD-QQIYKVLLNGK-----GGMPAFKST--LKDEEL 111
Cdd:TIGR04485   5 CLACHQipgsEVFPGNIGPSLTGYGARYPDeAYLRAKIADAKavnpcTVMPRFGKNgiLTEQEI 68
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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