NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1277227021|gb|PIS20935|]
View 

ferredoxin [candidate division WWE3 bacterium CG08_land_8_20_14_0_20_43_13]

Protein Classification

ferredoxin( domain architecture ID 10003036)

ferredoxin is an iron-sulfur protein transferring electrons in a wide variety of metabolic reactions

CATH:  3.30.70.20
Gene Ontology:  GO:0051536|GO:0005506|GO:0009055
PubMed:  34698119|35941298
SCOP:  4001234

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Fer COG1141
Ferredoxin [Energy production and conversion];
3-62 6.46e-16

Ferredoxin [Energy production and conversion];


:

Pssm-ID: 440756 [Multi-domain]  Cd Length: 63  Bit Score: 64.52  E-value: 6.46e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277227021  3 KLKVNQDLCIGCGLCVSLAGKTFRFNSQNKAEVVSDNSqPADPAETIQQVISSCPVGAIS 62
Cdd:COG1141    2 KVTVDRDTCIGCGLCVALAPEVFELDDDGKAVVLDEEV-PEELEEDVREAADACPVGAIT 60
 
Name Accession Description Interval E-value
Fer COG1141
Ferredoxin [Energy production and conversion];
3-62 6.46e-16

Ferredoxin [Energy production and conversion];


Pssm-ID: 440756 [Multi-domain]  Cd Length: 63  Bit Score: 64.52  E-value: 6.46e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277227021  3 KLKVNQDLCIGCGLCVSLAGKTFRFNSQNKAEVVSDNSqPADPAETIQQVISSCPVGAIS 62
Cdd:COG1141    2 KVTVDRDTCIGCGLCVALAPEVFELDDDGKAVVLDEEV-PEELEEDVREAADACPVGAIT 60
Fer4_13 pfam13370
4Fe-4S single cluster domain of Ferredoxin I; Fer4_13 is a ferredoxin I from sulfate-reducing ...
 6-62 8.59e-12

4Fe-4S single cluster domain of Ferredoxin I; Fer4_13 is a ferredoxin I from sulfate-reducing bacteria. Chemical sequence analysis suggests that this characteriztic [4Fe-4S] cluster sulfur environment is widely distributed among ferredoxins.


Pssm-ID: 433153 [Multi-domain]  Cd Length: 58  Bit Score: 53.85  E-value: 8.59e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1277227021  6 VNQDLCIGCGLCVSLAGKTFRFNSQNKAEVVSDnsQPADPAET--IQQVISSCPVGAIS 62
Cdd:pfam13370  1 VDEDTCIDCGTCRELAPEVFKYDDDGGASFVHD--QPVNEEEEdlAEEALDSCPVEAIG 57
FDH-N cd10558
The beta FeS subunit of formate dehydrogenase-N (FDH-N); This subfamily contains beta FeS ...
 7-68 7.45e-03

The beta FeS subunit of formate dehydrogenase-N (FDH-N); This subfamily contains beta FeS subunit of formate dehydrogenase-N (FDH-N), a member of the DMSO reductase family. FDH-N is involved in the major anaerobic respiratory pathway in the presence of nitrate, catalyzing the oxidation of formate to carbon dioxide at the expense of nitrate reduction to nitrite. Thus, FDH-N is a major component of nitrate respiration of Escherichia coli. This integral membrane enzyme forms a heterotrimer; the alpha-subunit (FDH-G) is the catalytic site of formate oxidation and membrane-associated, incorporating a selenocysteine (SeCys) residue and a [4Fe/4S] cluster in addition to two bis-MGD cofactors, the beta subunit (FDH-H) contains four [4Fe/4S] clusters which transfer the electrons from the alpha subunit to the gamma-subunit (FDH-I), a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups.


Pssm-ID: 319880 [Multi-domain]  Cd Length: 208  Bit Score: 32.74  E-value: 7.45e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1277227021   7 NQDLCIGCGLCVslAGKTF---RFNSQNK--------AEVVSDNSQPAdpaetiqqVISSCPVGAIS--QWENLL 68
Cdd:cd10558    99 QSDKCIGCGYCI--KGCPFdipRISKDDNkmykctlcSDRVSVGLEPA--------CVKTCPTGALHfgTKEDML 163
 
Name Accession Description Interval E-value
Fer COG1141
Ferredoxin [Energy production and conversion];
3-62 6.46e-16

Ferredoxin [Energy production and conversion];


Pssm-ID: 440756 [Multi-domain]  Cd Length: 63  Bit Score: 64.52  E-value: 6.46e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277227021  3 KLKVNQDLCIGCGLCVSLAGKTFRFNSQNKAEVVSDNSqPADPAETIQQVISSCPVGAIS 62
Cdd:COG1141    2 KVTVDRDTCIGCGLCVALAPEVFELDDDGKAVVLDEEV-PEELEEDVREAADACPVGAIT 60
Fer4_13 pfam13370
4Fe-4S single cluster domain of Ferredoxin I; Fer4_13 is a ferredoxin I from sulfate-reducing ...
 6-62 8.59e-12

4Fe-4S single cluster domain of Ferredoxin I; Fer4_13 is a ferredoxin I from sulfate-reducing bacteria. Chemical sequence analysis suggests that this characteriztic [4Fe-4S] cluster sulfur environment is widely distributed among ferredoxins.


Pssm-ID: 433153 [Multi-domain]  Cd Length: 58  Bit Score: 53.85  E-value: 8.59e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1277227021  6 VNQDLCIGCGLCVSLAGKTFRFNSQNKAEVVSDnsQPADPAET--IQQVISSCPVGAIS 62
Cdd:pfam13370  1 VDEDTCIDCGTCRELAPEVFKYDDDGGASFVHD--QPVNEEEEdlAEEALDSCPVEAIG 57
Fer4_15 pfam13459
4Fe-4S single cluster domain;
5-62 2.18e-10

4Fe-4S single cluster domain;


Pssm-ID: 404359 [Multi-domain]  Cd Length: 66  Bit Score: 50.44  E-value: 2.18e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1277227021  5 KVNQDLCIGCGLCVSLAGKTFRFNSQNKAEVVSDNSQ------PADPAETIQQVISSCPVGAIS 62
Cdd:pfam13459  2 EVDRDRCIGCGLCVALDPELFELDDDGKASVLLDDGEigegevPDDDEEAAQEAARACPVDAIR 65
Fer4_19 pfam06902
Divergent 4Fe-4S mono-cluster; Members of this family contain three highly conserved cysteine ...
 7-66 2.42e-07

Divergent 4Fe-4S mono-cluster; Members of this family contain three highly conserved cysteine residues. This family includes proteins containing divergent domains which are most likely to bind to iron-sulfur clusters.


Pssm-ID: 399707  Cd Length: 64  Bit Score: 42.73  E-value: 2.42e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277227021  7 NQDLCIGCGLCVSLAGKTfrFNSQNKAEVVSDNSqpadPAETIQQVISSCPVGAISQWEN 66
Cdd:pfam06902 11 NPALCSHAGFCVRGLPGV--FDLGRKPWIDPDGA----STEEIIKVIDRCPSGALSYVEK 64
YjdI COG3592
Uncharacterized Fe-S cluster protein YjdI [Function unknown];
7-62 1.62e-06

Uncharacterized Fe-S cluster protein YjdI [Function unknown];


Pssm-ID: 442811 [Multi-domain]  Cd Length: 71  Bit Score: 40.67  E-value: 1.62e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1277227021  7 NQDLCIGCGLCVSLAGKTFrfNSQNKAEVVSDNSqpadPAETIQQVISSCPVGAIS 62
Cdd:COG3592   18 DPELCIHSGNCVKGLPEVF--DPKRKPWINPDNA----STEEIIEQIDRCPSGALS 67
IorA COG4231
TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and ...
 3-18 4.63e-03

TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and conversion];


Pssm-ID: 443375 [Multi-domain]  Cd Length: 76  Bit Score: 31.94  E-value: 4.63e-03
                         10
                 ....*....|....*.
gi 1277227021  3 KLKVNQDLCIGCGLCV 18
Cdd:COG4231   45 KAVIDPDLCIGCGSCV 60
FDH-N cd10558
The beta FeS subunit of formate dehydrogenase-N (FDH-N); This subfamily contains beta FeS ...
 7-68 7.45e-03

The beta FeS subunit of formate dehydrogenase-N (FDH-N); This subfamily contains beta FeS subunit of formate dehydrogenase-N (FDH-N), a member of the DMSO reductase family. FDH-N is involved in the major anaerobic respiratory pathway in the presence of nitrate, catalyzing the oxidation of formate to carbon dioxide at the expense of nitrate reduction to nitrite. Thus, FDH-N is a major component of nitrate respiration of Escherichia coli. This integral membrane enzyme forms a heterotrimer; the alpha-subunit (FDH-G) is the catalytic site of formate oxidation and membrane-associated, incorporating a selenocysteine (SeCys) residue and a [4Fe/4S] cluster in addition to two bis-MGD cofactors, the beta subunit (FDH-H) contains four [4Fe/4S] clusters which transfer the electrons from the alpha subunit to the gamma-subunit (FDH-I), a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups.


Pssm-ID: 319880 [Multi-domain]  Cd Length: 208  Bit Score: 32.74  E-value: 7.45e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1277227021   7 NQDLCIGCGLCVslAGKTF---RFNSQNK--------AEVVSDNSQPAdpaetiqqVISSCPVGAIS--QWENLL 68
Cdd:cd10558    99 QSDKCIGCGYCI--KGCPFdipRISKDDNkmykctlcSDRVSVGLEPA--------CVKTCPTGALHfgTKEDML 163
FDH-O_like cd10560
beta subunit of formate dehydrogenase O (FDH-O) and similar proteins; This subfamily includes ...
 6-19 9.32e-03

beta subunit of formate dehydrogenase O (FDH-O) and similar proteins; This subfamily includes beta subunit of formate dehydrogenase family O (FDH-O), which is highly homologous to formate dehydrogenase N (FDH-N), a member of the DMSO reductase family. In E. coli three formate dehydrogenases are synthesized that are capable of oxidizing formate; Fdh-H, couples formate disproportionation to hydrogen and CO2, and is part of the cytoplasmically oriented formate hydrogenlyase complex, while FDH-N and FDH-O indicate their respective induction after growth with nitrate and oxygen. Little is known about FDH-O, although it shows formate oxidase activity during aerobic growth and is also synthesized during nitrate respiration, similar to FDH-N.


Pssm-ID: 319882 [Multi-domain]  Cd Length: 225  Bit Score: 32.36  E-value: 9.32e-03
                          10
                  ....*....|....
gi 1277227021   6 VNQDLCIGCGLCVS 19
Cdd:cd10560   105 IQPDICNGCGYCVA 118
 
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