Heme-binding domain of the class III cytochrome C family and related proteins; This alignment ...
10-196
7.42e-119
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 TIGR02161:
Pssm-ID: 474044 Cd Length: 185 Bit Score: 334.82 E-value: 7.42e-119
periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Nearly every member of this subfamily is NapC, a predicted membrane-anchored four-heme c-type cytochrome that forms one component of the periplasmic nitrate reductase along with NapA, NapB, NapD, NapE, and NapF subunits. A single known exception at this time is NirT, which is instead a component of a nitrite reductase. This family excludes TorC subunits of trimethylamine N-oxide (TMAO) reductases.
Pssm-ID: 131216 Cd Length: 185 Bit Score: 334.82 E-value: 7.42e-119
NapC/NirT cytochrome c family, N-terminal region; Within the NapC/NirT family of cytochrome c ...
20-195
6.70e-113
NapC/NirT cytochrome c family, N-terminal region; Within the NapC/NirT family of cytochrome c proteins, some members, such as NapC and NirT, bind four haem groups, while others, such as TorC, bind five haems. This family aligns the common N-terminal region that contains four haem-binding C-X(2)-CH motifs.
Pssm-ID: 427224 Cd Length: 174 Bit Score: 319.19 E-value: 6.70e-113
periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Nearly every member of this subfamily is NapC, a predicted membrane-anchored four-heme c-type cytochrome that forms one component of the periplasmic nitrate reductase along with NapA, NapB, NapD, NapE, and NapF subunits. A single known exception at this time is NirT, which is instead a component of a nitrite reductase. This family excludes TorC subunits of trimethylamine N-oxide (TMAO) reductases.
Pssm-ID: 131216 Cd Length: 185 Bit Score: 334.82 E-value: 7.42e-119
NapC/NirT cytochrome c family, N-terminal region; Within the NapC/NirT family of cytochrome c ...
20-195
6.70e-113
NapC/NirT cytochrome c family, N-terminal region; Within the NapC/NirT family of cytochrome c proteins, some members, such as NapC and NirT, bind four haem groups, while others, such as TorC, bind five haems. This family aligns the common N-terminal region that contains four haem-binding C-X(2)-CH motifs.
Pssm-ID: 427224 Cd Length: 174 Bit Score: 319.19 E-value: 6.70e-113
trimethylamine-N-oxide reductase c-type cytochrome TorC; This family includes consists of TorC, ...
14-195
1.03e-88
trimethylamine-N-oxide reductase c-type cytochrome TorC; This family includes consists of TorC, a pentahemic c-type cytochrome subunit of periplasmic reductases for trimethylamine-N-oxide (TMAO). The N-terminal half is closely related to tetrahemic NapC (or NirT) subunits of periplasmic nitrate (or nitrite) reductases; some species have both TMAO and nitrate reductase complexes.
Pssm-ID: 274003 Cd Length: 386 Bit Score: 265.60 E-value: 1.03e-88
cytochrome c nitrite reductase, small subunit; Members of this protein family are NrfH, a ...
25-190
3.40e-12
cytochrome c nitrite reductase, small subunit; Members of this protein family are NrfH, a tetraheme cytochrome c. NrfH is the cytochrome c nitrite reductase small subunit, and forms a heterodimer with NrfA, the catalytic subunit. While NrfA can act as a monomer, NrfH can bind to and anchor NrfA in the membrane and enables electron transfer to NrfA from quinones. [Energy metabolism, Electron transport]
Pssm-ID: 274453 [Multi-domain] Cd Length: 135 Bit Score: 61.21 E-value: 3.40e-12
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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