NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1079632706|emb|SCW28640|]
View 

Rubredoxin [Ruminococcaceae bacterium YRB3002]

Protein Classification

rubredoxin( domain architecture ID 11448379)

rubredoxin is a small nonheme, iron binding protein lacking an acid-labile sulfide that contains a [Fe(SCys)4] center and participates in electron transfer

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
NorV COG1773
Flavorubredoxin [Inorganic ion transport and metabolism];
1-50 3.87e-26

Flavorubredoxin [Inorganic ion transport and metabolism];


:

Pssm-ID: 441379 [Multi-domain]  Cd Length: 53  Bit Score: 89.07  E-value: 3.87e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1079632706  1 MDKYECP-CGYVYDPEVGDPDGGIAPGTAFEDIPEDWVCPVCGLGKDAFMP 50
Cdd:COG1773    1 MKKYQCKvCGYVYDPAEGDPENGIPPGTPFEDLPDDWVCPVCGAGKEDFEP 51
 
Name Accession Description Interval E-value
NorV COG1773
Flavorubredoxin [Inorganic ion transport and metabolism];
1-50 3.87e-26

Flavorubredoxin [Inorganic ion transport and metabolism];


Pssm-ID: 441379 [Multi-domain]  Cd Length: 53  Bit Score: 89.07  E-value: 3.87e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1079632706  1 MDKYECP-CGYVYDPEVGDPDGGIAPGTAFEDIPEDWVCPVCGLGKDAFMP 50
Cdd:COG1773    1 MKKYQCKvCGYVYDPAEGDPENGIPPGTPFEDLPDDWVCPVCGAGKEDFEP 51
rubredoxin cd00730
Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are ...
 3-50 4.99e-21

Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.


Pssm-ID: 238372 [Multi-domain]  Cd Length: 50  Bit Score: 76.19  E-value: 4.99e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 1079632706  3 KYECP-CGYVYDPEVGDPDGGIAPGTAFEDIPEDWVCPVCGLGKDAFMP 50
Cdd:cd00730    1 KYECRiCGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAGKDDFEP 49
Rubredoxin pfam00301
Rubredoxin;
4-48 1.86e-19

Rubredoxin;


Pssm-ID: 459752 [Multi-domain]  Cd Length: 46  Bit Score: 72.28  E-value: 1.86e-19
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 1079632706  4 YECP-CGYVYDPEVGDPDGGIAPGTAFEDIPEDWVCPVCGLGKDAF 48
Cdd:pfam00301  1 YECKvCGYVYDPAKGDPDNGIPPGTPFEDLPDDWVCPDCGAGKDQF 46
PRK05452 PRK05452
anaerobic nitric oxide reductase flavorubredoxin; Provisional
 8-50 7.22e-18

anaerobic nitric oxide reductase flavorubredoxin; Provisional


Pssm-ID: 235475 [Multi-domain]  Cd Length: 479  Bit Score: 74.41  E-value: 7.22e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1079632706   8 CGYVYDPEVGDPDGGIAPGTAFEDIPEDWVCPVCGLGKDAFMP 50
Cdd:PRK05452  431 CQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLGKDVFDE 473
 
Name Accession Description Interval E-value
NorV COG1773
Flavorubredoxin [Inorganic ion transport and metabolism];
1-50 3.87e-26

Flavorubredoxin [Inorganic ion transport and metabolism];


Pssm-ID: 441379 [Multi-domain]  Cd Length: 53  Bit Score: 89.07  E-value: 3.87e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1079632706  1 MDKYECP-CGYVYDPEVGDPDGGIAPGTAFEDIPEDWVCPVCGLGKDAFMP 50
Cdd:COG1773    1 MKKYQCKvCGYVYDPAEGDPENGIPPGTPFEDLPDDWVCPVCGAGKEDFEP 51
rubredoxin cd00730
Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are ...
 3-50 4.99e-21

Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.


Pssm-ID: 238372 [Multi-domain]  Cd Length: 50  Bit Score: 76.19  E-value: 4.99e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 1079632706  3 KYECP-CGYVYDPEVGDPDGGIAPGTAFEDIPEDWVCPVCGLGKDAFMP 50
Cdd:cd00730    1 KYECRiCGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAGKDDFEP 49
Rubredoxin pfam00301
Rubredoxin;
4-48 1.86e-19

Rubredoxin;


Pssm-ID: 459752 [Multi-domain]  Cd Length: 46  Bit Score: 72.28  E-value: 1.86e-19
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 1079632706  4 YECP-CGYVYDPEVGDPDGGIAPGTAFEDIPEDWVCPVCGLGKDAF 48
Cdd:pfam00301  1 YECKvCGYVYDPAKGDPDNGIPPGTPFEDLPDDWVCPDCGAGKDQF 46
PRK05452 PRK05452
anaerobic nitric oxide reductase flavorubredoxin; Provisional
 8-50 7.22e-18

anaerobic nitric oxide reductase flavorubredoxin; Provisional


Pssm-ID: 235475 [Multi-domain]  Cd Length: 479  Bit Score: 74.41  E-value: 7.22e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1079632706   8 CGYVYDPEVGDPDGGIAPGTAFEDIPEDWVCPVCGLGKDAFMP 50
Cdd:PRK05452  431 CQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLGKDVFDE 473
rubredoxin_like cd00350
Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family ...
 3-50 8.44e-06

Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.


Pssm-ID: 238210 [Multi-domain]  Cd Length: 33  Bit Score: 37.53  E-value: 8.44e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 1079632706  3 KYECP-CGYVYDPEVgdpdggiapgtafedipEDWVCPVCGLGKDAFMP 50
Cdd:cd00350    1 KYVCPvCGYIYDGEE-----------------APWVCPVCGAPKDKFEK 32
YotD COG1592
Rubrerythrin [Energy production and conversion];
2-50 3.64e-03

Rubrerythrin [Energy production and conversion];


Pssm-ID: 441200 [Multi-domain]  Cd Length: 180  Bit Score: 32.48  E-value: 3.64e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1079632706   2 DKYECP-CGYVYDpevgdpdGGIAPGtafedipedwVCPVCGLGKDAFMP 50
Cdd:COG1592   146 VVWVCPvCGYIHE-------GKEAPE----------KCPVCGHPKSYFEL 178
 
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