NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|496247556|ref|WP_008960941|]
View 

cytochrome c3 family protein [Bradyrhizobium sp. STM 3809]

Protein Classification

Cytochrom_C3 domain-containing protein( domain architecture ID 10870893)

Cytochrom_C3 domain-containing protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Cytochrom_C3 cd08168
Heme-binding domain of the class III cytochrome C family and related proteins; This alignment ...
 48-168 4.56e-17

Heme-binding domain of the class III cytochrome C family and related proteins; This alignment models heme binding core motifs as encountered in the cytochrome C3 family and related proteins. Cytochrome C3 is a tetraheme protein found in sulfate-reducing bacteria which use either thiosulfate or sulfate as the ultimate electron acceptors. C3 is an integral part of a complex electron transfer chain. The model also contains triheme cytochromes C7 which function in electron transfer during Fe(III) respiration by Geobacter sulfurreducens (PpcA, PpcB, PpcC, PpcD, and PpcE) and four repeated core motifs as found in the 16-heme cytochrome C HmcA of Desulfovibrio vulgaris Hildenborough which plays a role in electron transfer through the membrane following periplasmic oxidation of hydrogen (resulting in sulfate reduction in the cytoplasm).


:

Pssm-ID: 173979 [Multi-domain]  Cd Length: 85  Bit Score: 73.04  E-value: 4.56e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496247556  48 QPVPFSHEHHVSGLGLDCRYCHTSVEKarfaGIPPTETCMTCHSQIWTNaemlapvreslandkpiswqrvhrLPAYVYF 127
Cdd:cd08168    2 GPVPFPHKKHAEALGIDCRTCHHKYEG----GKGEPQKCAECHSHDGTD------------------------DPDFVSL 53

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 496247556 128 DHSVHvakgVGCTTCHGDVGQMRlmrqaAPLTMQWCLDCHR 168
Cdd:cd08168   54 KDAFH----NSCIGCHKEMAKAG-----KKTGPVGCAGCHK 85
Cytochrom_C3 super family cl23752
Heme-binding domain of the class III cytochrome C family and related proteins; This alignment ...
 131-217 2.51e-03

Heme-binding domain of the class III cytochrome C family and related proteins; This alignment models heme binding core motifs as encountered in the cytochrome C3 family and related proteins. Cytochrome C3 is a tetraheme protein found in sulfate-reducing bacteria which use either thiosulfate or sulfate as the ultimate electron acceptors. C3 is an integral part of a complex electron transfer chain. The model also contains triheme cytochromes C7 which function in electron transfer during Fe(III) respiration by Geobacter sulfurreducens (PpcA, PpcB, PpcC, PpcD, and PpcE) and four repeated core motifs as found in the 16-heme cytochrome C HmcA of Desulfovibrio vulgaris Hildenborough which plays a role in electron transfer through the membrane following periplasmic oxidation of hydrogen (resulting in sulfate reduction in the cytoplasm).


The actual alignment was detected with superfamily member pfam14537:

Pssm-ID: 474044 [Multi-domain]  Cd Length: 79  Bit Score: 35.55  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496247556  131 VHVAKGVGCTTCHGDvgqmRLMRQAAPLTMQWCLDCHRApepyLRPHEAVFDPKWQPPPNqaeigpklaasyhintGHLT 210
Cdd:pfam14537   1 FHAKMGLGCADCHGK----ATPSDDSAVENEQCLSCHGT----LAELAKATKEKEANPHK----------------SHLG 56


                  ....*....
gi 496247556  211 D--CTVCHR 217
Cdd:pfam14537  57 DlaCTECHK 65
 
Name Accession Description Interval E-value
Cytochrom_C3 cd08168
Heme-binding domain of the class III cytochrome C family and related proteins; This alignment ...
 48-168 4.56e-17

Heme-binding domain of the class III cytochrome C family and related proteins; This alignment models heme binding core motifs as encountered in the cytochrome C3 family and related proteins. Cytochrome C3 is a tetraheme protein found in sulfate-reducing bacteria which use either thiosulfate or sulfate as the ultimate electron acceptors. C3 is an integral part of a complex electron transfer chain. The model also contains triheme cytochromes C7 which function in electron transfer during Fe(III) respiration by Geobacter sulfurreducens (PpcA, PpcB, PpcC, PpcD, and PpcE) and four repeated core motifs as found in the 16-heme cytochrome C HmcA of Desulfovibrio vulgaris Hildenborough which plays a role in electron transfer through the membrane following periplasmic oxidation of hydrogen (resulting in sulfate reduction in the cytoplasm).


Pssm-ID: 173979 [Multi-domain]  Cd Length: 85  Bit Score: 73.04  E-value: 4.56e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496247556  48 QPVPFSHEHHVSGLGLDCRYCHTSVEKarfaGIPPTETCMTCHSQIWTNaemlapvreslandkpiswqrvhrLPAYVYF 127
Cdd:cd08168    2 GPVPFPHKKHAEALGIDCRTCHHKYEG----GKGEPQKCAECHSHDGTD------------------------DPDFVSL 53

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 496247556 128 DHSVHvakgVGCTTCHGDVGQMRlmrqaAPLTMQWCLDCHR 168
Cdd:cd08168   54 KDAFH----NSCIGCHKEMAKAG-----KKTGPVGCAGCHK 85
Cytochrome_C7 pfam14522
Cytochrome c7 and related cytochrome c; This family includes cytochromes c7 and c7-type. In ...
 125-167 9.38e-05

Cytochrome c7 and related cytochrome c; This family includes cytochromes c7 and c7-type. In cytochromes c7 all three haems are bis-His co-ordinated, while in c7-type the last haem is His-Met co-ordinated. Desulfuromonas acetoxidans and Geobacter metallireducens cytochrome c7 participate in the anaerobic iron respiration, but Geobacter metallireducens cytochrome c7 hasn't a Fe(III) reductase activity. This entry also includes cytochrome c nitrite reductase subunit NrfH from Desulfovibrio vulgaris which forms a complex with cytochrome c nitrite reductase NrfA.


Pssm-ID: 434012 [Multi-domain]  Cd Length: 62  Bit Score: 39.20  E-value: 9.38e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 496247556  125 VYFDHSVHVAKGVGCTTCHGDVGQMRLMRQAAPLTMQWCLDCH 167
Cdd:pfam14522   1 VVFSHDVHLAGGYNCADCHNKLFASKRVTMAEMEKGKSCGACH 43
Cytochrom_c3_2 pfam14537
Cytochrome c3;
131-217 2.51e-03

Cytochrome c3;


Pssm-ID: 434025 [Multi-domain]  Cd Length: 79  Bit Score: 35.55  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496247556  131 VHVAKGVGCTTCHGDvgqmRLMRQAAPLTMQWCLDCHRApepyLRPHEAVFDPKWQPPPNqaeigpklaasyhintGHLT 210
Cdd:pfam14537   1 FHAKMGLGCADCHGK----ATPSDDSAVENEQCLSCHGT----LAELAKATKEKEANPHK----------------SHLG 56


                  ....*....
gi 496247556  211 D--CTVCHR 217
Cdd:pfam14537  57 DlaCTECHK 65
 
Name Accession Description Interval E-value
Cytochrom_C3 cd08168
Heme-binding domain of the class III cytochrome C family and related proteins; This alignment ...
 48-168 4.56e-17

Heme-binding domain of the class III cytochrome C family and related proteins; This alignment models heme binding core motifs as encountered in the cytochrome C3 family and related proteins. Cytochrome C3 is a tetraheme protein found in sulfate-reducing bacteria which use either thiosulfate or sulfate as the ultimate electron acceptors. C3 is an integral part of a complex electron transfer chain. The model also contains triheme cytochromes C7 which function in electron transfer during Fe(III) respiration by Geobacter sulfurreducens (PpcA, PpcB, PpcC, PpcD, and PpcE) and four repeated core motifs as found in the 16-heme cytochrome C HmcA of Desulfovibrio vulgaris Hildenborough which plays a role in electron transfer through the membrane following periplasmic oxidation of hydrogen (resulting in sulfate reduction in the cytoplasm).


Pssm-ID: 173979 [Multi-domain]  Cd Length: 85  Bit Score: 73.04  E-value: 4.56e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496247556  48 QPVPFSHEHHVSGLGLDCRYCHTSVEKarfaGIPPTETCMTCHSQIWTNaemlapvreslandkpiswqrvhrLPAYVYF 127
Cdd:cd08168    2 GPVPFPHKKHAEALGIDCRTCHHKYEG----GKGEPQKCAECHSHDGTD------------------------DPDFVSL 53

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 496247556 128 DHSVHvakgVGCTTCHGDVGQMRlmrqaAPLTMQWCLDCHR 168
Cdd:cd08168   54 KDAFH----NSCIGCHKEMAKAG-----KKTGPVGCAGCHK 85
Cytochrome_C7 pfam14522
Cytochrome c7 and related cytochrome c; This family includes cytochromes c7 and c7-type. In ...
 125-167 9.38e-05

Cytochrome c7 and related cytochrome c; This family includes cytochromes c7 and c7-type. In cytochromes c7 all three haems are bis-His co-ordinated, while in c7-type the last haem is His-Met co-ordinated. Desulfuromonas acetoxidans and Geobacter metallireducens cytochrome c7 participate in the anaerobic iron respiration, but Geobacter metallireducens cytochrome c7 hasn't a Fe(III) reductase activity. This entry also includes cytochrome c nitrite reductase subunit NrfH from Desulfovibrio vulgaris which forms a complex with cytochrome c nitrite reductase NrfA.


Pssm-ID: 434012 [Multi-domain]  Cd Length: 62  Bit Score: 39.20  E-value: 9.38e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 496247556  125 VYFDHSVHVAKGVGCTTCHGDVGQMRLMRQAAPLTMQWCLDCH 167
Cdd:pfam14522   1 VVFSHDVHLAGGYNCADCHNKLFASKRVTMAEMEKGKSCGACH 43
Cytochrom_c3_2 pfam14537
Cytochrome c3;
131-217 2.51e-03

Cytochrome c3;


Pssm-ID: 434025 [Multi-domain]  Cd Length: 79  Bit Score: 35.55  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496247556  131 VHVAKGVGCTTCHGDvgqmRLMRQAAPLTMQWCLDCHRApepyLRPHEAVFDPKWQPPPNqaeigpklaasyhintGHLT 210
Cdd:pfam14537   1 FHAKMGLGCADCHGK----ATPSDDSAVENEQCLSCHGT----LAELAKATKEKEANPHK----------------SHLG 56


                  ....*....
gi 496247556  211 D--CTVCHR 217
Cdd:pfam14537  57 DlaCTECHK 65
NrfA-like cd00548
cytochrome c nitrite reductase and similar proteins; This family contains cytochrome c nitrite ...
 122-175 5.68e-03

cytochrome c nitrite reductase and similar proteins; This family contains cytochrome c nitrite reductase (also known as cytochrome c552, or NrfA) and similar proteins. The pentaheme enzyme NrfA catalyzes the electron reduction of nitrite to ammonia in the nitrogen cycle. This enzyme can also transform nitrogen monoxide and hydroxylamine, two potential bound reaction intermediates, into ammonia. It is a homodimer, with each monomer containing four classical CXXCH type heme-binding sites along with an alternative CXXCK heme-binding motif, which is important for catalysis. This family also includes octaheme nitrite reductase (TvNiR) from the haloalkaliphilic bacterium Thioalkalivibrio paradoxus which catalyzes the reduction of nitrite and hydroxylamine to ammonia as well as the reduction of sulfite to sulfide.


Pssm-ID: 349426  Cd Length: 370  Bit Score: 37.16  E-value: 5.68e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496247556 122 PAYVYFDHSVHVAKGVGCTTCHgdvgqMRLMRQAA----------PLT--MQWCLDCHRAPEPYLR 175
Cdd:cd00548  219 PEFETWSGGIHAKAGVSCADCH-----MPYVREGGkkysshwvtsPLKniEQSCLTCHRESEEELK 279
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH