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Conserved domains on  [gi|488937228|ref|WP_002848303|]
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MULTISPECIES: YfhL family 4Fe-4S dicluster ferredoxin [Campylobacter]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
di_4Fe-4S_YfhL super family cl41379
YfhL family 4Fe-4S dicluster ferredoxin;
1-78 1.62e-38

YfhL family 4Fe-4S dicluster ferredoxin;


The actual alignment was detected with superfamily member NF033683:

Pssm-ID: 468141 [Multi-domain]  Cd Length: 79  Bit Score: 122.59  E-value: 1.62e-38
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488937228  1 MSLMITKDCISCDACREECPDEAIYEDDPTYMIDPDRCSECISDYAEPACIVICPVDCIVPDPDNIETPEELKLKHEQ 78
Cdd:NF033683  1 MALLITDECINCDVCEPECPNEAISMGDEIYEIDPDRCTECVGHYDEPQCVQVCPVDCIIPDPDHVETQEQLMEKYER 78
 
Name Accession Description Interval E-value
di_4Fe-4S_YfhL NF033683
YfhL family 4Fe-4S dicluster ferredoxin;
1-78 1.62e-38

YfhL family 4Fe-4S dicluster ferredoxin;


Pssm-ID: 468141 [Multi-domain]  Cd Length: 79  Bit Score: 122.59  E-value: 1.62e-38
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488937228  1 MSLMITKDCISCDACREECPDEAIYEDDPTYMIDPDRCSECISDYAEPACIVICPVDCIVPDPDNIETPEELKLKHEQ 78
Cdd:NF033683  1 MALLITDECINCDVCEPECPNEAISMGDEIYEIDPDRCTECVGHYDEPQCVQVCPVDCIIPDPDHVETQEQLMEKYER 78
COG2768 COG2768
Uncharacterized Fe-S cluster protein [Function unknown];
5-67 8.21e-11

Uncharacterized Fe-S cluster protein [Function unknown];


Pssm-ID: 442050 [Multi-domain]  Cd Length: 74  Bit Score: 52.43  E-value: 8.21e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488937228  5 ITKDCISCDACREECPDEAIYEDDPTYMIDPDRCSECisdyaePACIVICPVDCIVPDPDNIE 67
Cdd:COG2768   9 DEEKCIGCGACVKVCPVGAISIEDGKAVIDPEKCIGC------GACIEVCPVGAIKIEWEEDE 65
PRK07118 PRK07118
Fe-S cluster domain-containing protein;
9-61 1.54e-04

Fe-S cluster domain-containing protein;


Pssm-ID: 235941 [Multi-domain]  Cd Length: 280  Bit Score: 37.99  E-value: 1.54e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488937228   9 CISCDACREECPDEAIYEDDPTYMIDPDRCSECisdyaePACIVICPVDCIVP 61
Cdd:PRK07118 215 CIGCGKCVKACPAGAITMENNLAVIDQEKCTSC------GKCVEKCPTKAIRI 261
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 8-60 2.56e-04

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 36.61  E-value: 2.56e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488937228   8 DCISCDACREECPDEAI-YEDDPTYMIDPDRCSECisdyaePACIVICPVDCIV 60
Cdd:cd10549   79 KCIGCGLCVKVCPVDAItLEDELEIVIDKEKCIGC------GICAEVCPVNAIK 126
 
Name Accession Description Interval E-value
di_4Fe-4S_YfhL NF033683
YfhL family 4Fe-4S dicluster ferredoxin;
1-78 1.62e-38

YfhL family 4Fe-4S dicluster ferredoxin;


Pssm-ID: 468141 [Multi-domain]  Cd Length: 79  Bit Score: 122.59  E-value: 1.62e-38
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488937228  1 MSLMITKDCISCDACREECPDEAIYEDDPTYMIDPDRCSECISDYAEPACIVICPVDCIVPDPDNIETPEELKLKHEQ 78
Cdd:NF033683  1 MALLITDECINCDVCEPECPNEAISMGDEIYEIDPDRCTECVGHYDEPQCVQVCPVDCIIPDPDHVETQEQLMEKYER 78
COG2768 COG2768
Uncharacterized Fe-S cluster protein [Function unknown];
5-67 8.21e-11

Uncharacterized Fe-S cluster protein [Function unknown];


Pssm-ID: 442050 [Multi-domain]  Cd Length: 74  Bit Score: 52.43  E-value: 8.21e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488937228  5 ITKDCISCDACREECPDEAIYEDDPTYMIDPDRCSECisdyaePACIVICPVDCIVPDPDNIE 67
Cdd:COG2768   9 DEEKCIGCGACVKVCPVGAISIEDGKAVIDPEKCIGC------GACIEVCPVGAIKIEWEEDE 65
IorA COG4231
TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and ...
 1-67 2.12e-07

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


Pssm-ID: 443375 [Multi-domain]  Cd Length: 76  Bit Score: 43.88  E-value: 2.12e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488937228  1 MSLMITKD-CISCDACREECPDEAIYEDDPTYMIDPDRCSECISdyaepaCIVICPVDCIVPDPDNIE 67
Cdd:COG4231  15 MRYVIDEDkCTGCGACVKVCPADAIEEGDGKAVIDPDLCIGCGS------CVQVCPVDAIKLEKRVPE 76
NuoI COG1143
Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy ...
 6-71 2.31e-06

Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]; Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) is part of the Pathway/BioSystem: NADH dehydrogenase


Pssm-ID: 440758 [Multi-domain]  Cd Length: 66  Bit Score: 40.88  E-value: 2.31e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488937228  6 TKDCISCDACREECPDEAIY----EDDPTYMIDPDRCSECIsdyaepACIVICPVDCIVPDPDNIETPEE 71
Cdd:COG1143   1 EDKCIGCGLCVRVCPVDAITiedgEPGKVYVIDPDKCIGCG------LCVEVCPTGAISMTPFELAVEDR 64
PreA COG1146
NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and ...
 5-64 4.95e-06

NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and metabolism];


Pssm-ID: 440761 [Multi-domain]  Cd Length: 67  Bit Score: 40.08  E-value: 4.95e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488937228  5 ITKDCISCDACREECPDEAIYEDD---PTYMIDPDRCSECisdyaePACIVICPVDCIVPDPD 64
Cdd:COG1146   6 DTDKCIGCGACVEVCPVDVLELDEegkKALVINPEECIGC------GACELVCPVGAITVEDD 62
DsrA COG2221
Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion ...
 9-62 6.53e-06

Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion transport and metabolism];


Pssm-ID: 441823 [Multi-domain]  Cd Length: 69  Bit Score: 39.65  E-value: 6.53e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 488937228  9 CISCDACREECPDEAIYEDDPTYMIDPDRCSECisdyaePACIVICPVDCIVPD 62
Cdd:COG2221  17 CIGCGLCVAVCPTGAISLDDGKLVIDEEKCIGC------GACIRVCPTGAIKGE 64
COG1149 COG1149
MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function ...
 9-59 1.22e-05

MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function prediction only];


Pssm-ID: 440763 [Multi-domain]  Cd Length: 68  Bit Score: 38.94  E-value: 1.22e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 488937228  9 CISCDACREECPDEAIY-EDDPTYMIDPDRCSECisdyaePACIVICPVDCI 59
Cdd:COG1149  13 CIGCGLCVEVCPEGAIKlDDGGAPVVDPDLCTGC------GACVGVCPTGAI 58
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
9-67 5.39e-05

Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 39.62  E-value: 5.39e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488937228   9 CISCDACREECPDEAIYEDDPTYMIDPDRCSECisdyaePACIVICPVDCIVpDPDNIE 67
Cdd:COG4624   93 CKNCYPCVRACPVKAIKVDDGKAEIDEEKCISC------GQCVAVCPFGAIT-EKSDIE 144
NapF COG1145
Ferredoxin [Energy production and conversion];
9-67 6.63e-05

Ferredoxin [Energy production and conversion];


Pssm-ID: 440760 [Multi-domain]  Cd Length: 238  Bit Score: 39.32  E-value: 6.63e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488937228   9 CISCDACREECPDEAIY--EDDPTYMIDPDRCSECisdyaePACIVICPVDCIVPDPDNIE 67
Cdd:COG1145  184 CIGCGLCVKVCPTGAIRlkDGKPQIVVDPDKCIGC------GACVKVCPVGAISLEPKEIE 238
PRK07118 PRK07118
Fe-S cluster domain-containing protein;
9-61 1.54e-04

Fe-S cluster domain-containing protein;


Pssm-ID: 235941 [Multi-domain]  Cd Length: 280  Bit Score: 37.99  E-value: 1.54e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488937228   9 CISCDACREECPDEAIYEDDPTYMIDPDRCSECisdyaePACIVICPVDCIVP 61
Cdd:PRK07118 215 CIGCGKCVKACPAGAITMENNLAVIDQEKCTSC------GKCVEKCPTKAIRI 261
PorD COG1144
Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta ...
 9-60 1.98e-04

Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta subunit [Energy production and conversion]; Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta subunit is part of the Pathway/BioSystem: Pyruvate oxidation


Pssm-ID: 440759 [Multi-domain]  Cd Length: 84  Bit Score: 36.18  E-value: 1.98e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 488937228  9 CISCDACREECPDEAIYEDD-PTYMIDPDRCSECisdyaePACIVICPVDCIV 60
Cdd:COG1144  32 CIGCGLCWIVCPDGAIRVDDgKYYGIDYDYCKGC------GICAEVCPVKAIE 78
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 8-60 2.56e-04

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 36.61  E-value: 2.56e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488937228   8 DCISCDACREECPDEAI-YEDDPTYMIDPDRCSECisdyaePACIVICPVDCIV 60
Cdd:cd10549   79 KCIGCGLCVKVCPVDAItLEDELEIVIDKEKCIGC------GICAEVCPVNAIK 126
QueG COG1600
Epoxyqueuosine reductase QueG (queuosine biosynthesis) [Translation, ribosomal structure and ...
 5-38 2.77e-04

Epoxyqueuosine reductase QueG (queuosine biosynthesis) [Translation, ribosomal structure and biogenesis]; Epoxyqueuosine reductase QueG (queuosine biosynthesis) is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441208 [Multi-domain]  Cd Length: 345  Bit Score: 37.49  E-value: 2.77e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 488937228   5 ITKDCISCDACREECPDEAIYEDdptYMIDPDRC 38
Cdd:COG1600  182 VEDHCGSCTRCLDACPTGAIVAP---YVLDARRC 212
SIMIBI_bact_arch cd03110
bacterial and archaeal subfamily of SIMIBI; Uncharacterized bacterial and archaeal subfamily ...
 9-59 5.75e-04

bacterial and archaeal subfamily of SIMIBI; Uncharacterized bacterial and archaeal subfamily of SIMIBI superfamily. Proteins in this superfamily contain an ATP-binding domain and use energy from hydrolysis of ATP to transfer electron or ion. The specific function of this family is unknown.


Pssm-ID: 349764 [Multi-domain]  Cd Length: 246  Bit Score: 36.59  E-value: 5.75e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488937228   9 CISCDACREECPDEAIYEDDPTYMIDPDRCSECisdyaePACIVICPVDCI 59
Cdd:cd03110   66 CIRCGNCERVCKFGAILEFFQKLIVDESLCEGC------GACVIICPRGAI 110
FDH-N cd10558
The beta FeS subunit of formate dehydrogenase-N (FDH-N); This subfamily contains beta FeS ...
 9-60 1.05e-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: 35.83  E-value: 1.05e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488937228   9 CISCDACREECP-DEAIYEDDPTYMIDPDRCSECISDYAEPACIVICPVDCIV 60
Cdd:cd10558  103 CIGCGYCIKGCPfDIPRISKDDNKMYKCTLCSDRVSVGLEPACVKTCPTGALH 155
PRK13795 PRK13795
hypothetical protein; Provisional
 9-56 1.50e-03

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 35.36  E-value: 1.50e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 488937228   9 CISCDACREECPDEAIYEDDPT--YMIDPDRCSECIsdyaepACIVICPV 56
Cdd:PRK13795 583 CVGCGVCVGACPTGAIRIEEGKrkISVDEEKCIHCG------KCTEVCPV 626
PRK06991 PRK06991
electron transport complex subunit RsxB;
9-59 3.85e-03

electron transport complex subunit RsxB;


Pssm-ID: 235903 [Multi-domain]  Cd Length: 270  Bit Score: 34.00  E-value: 3.85e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488937228   9 CISCDACREECPDEAIYeDDPTYM--IDPDRCSECisdyaePACIVICPVDCI 59
Cdd:PRK06991  87 CIGCTLCMQACPVDAIV-GAPKQMhtVLADLCTGC------DLCVPPCPVDCI 132
 
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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