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Conserved domains on  [gi|497293920|ref|WP_009608137|]
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MULTISPECIES: 4Fe-4S dicluster domain-containing protein [Eggerthella]

Protein Classification

4Fe-4S dicluster domain-containing protein( domain architecture ID 11611512)

4Fe-4S dicluster domain-containing protein such as Desulfovibrio desulfuricans NapG protein, which may provide an alternative direct electron donor to NapA, a single subunit periplasmic nitrate reductase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DMSOR_beta_like cd16373
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 46-207 6.66e-47

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


:

Pssm-ID: 319895 [Multi-domain]  Cd Length: 154  Bit Score: 151.64  E-value: 6.66e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  46 LRPPGGQDEEQLARGCLHCEKCREVCPKHAIAPAHLEDGILNARTPRMDFKSGWCDFCENEpggpkCVAACPTHALSCPD 125
Cdd:cd16373    1 LRPPGALDEEEFLALCIRCGLCVEACPTGVIQPAGLEDGLEGGRTPYLDPREGPCDLCCDA-----CVEVCPTGALRPLD 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920 126 PS--QAIIGKAEINRDWCLAAKG-MGCHECVDVCNYEALEL---GADNVPVVDVDACNGCGACELACISLsagsitagaT 199
Cdd:cd16373   76 LEeqKVKMGVAVIDKDRCLAWQGgTDCGVCVEACPTEAIAIvleDDVLRPVVDEDKCVGCGLCEYVCPVE---------P 146


                 ....*...
gi 497293920 200 DRAIVVRP 207
Cdd:cd16373  147 PKAIVVEP 154
 
Name Accession Description Interval E-value
DMSOR_beta_like cd16373
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 46-207 6.66e-47

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319895 [Multi-domain]  Cd Length: 154  Bit Score: 151.64  E-value: 6.66e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  46 LRPPGGQDEEQLARGCLHCEKCREVCPKHAIAPAHLEDGILNARTPRMDFKSGWCDFCENEpggpkCVAACPTHALSCPD 125
Cdd:cd16373    1 LRPPGALDEEEFLALCIRCGLCVEACPTGVIQPAGLEDGLEGGRTPYLDPREGPCDLCCDA-----CVEVCPTGALRPLD 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920 126 PS--QAIIGKAEINRDWCLAAKG-MGCHECVDVCNYEALEL---GADNVPVVDVDACNGCGACELACISLsagsitagaT 199
Cdd:cd16373   76 LEeqKVKMGVAVIDKDRCLAWQGgTDCGVCVEACPTEAIAIvleDDVLRPVVDEDKCVGCGLCEYVCPVE---------P 146


                 ....*...
gi 497293920 200 DRAIVVRP 207
Cdd:cd16373  147 PKAIVVEP 154
napG PRK09476
quinol dehydrogenase periplasmic component; Provisional
 16-209 1.06e-20

quinol dehydrogenase periplasmic component; Provisional


Pssm-ID: 236534 [Multi-domain]  Cd Length: 254  Bit Score: 86.60  E-value: 1.06e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  16 VSRRTFALGAVGACAVIGLGGVKY-------LPSATLLRPPGGQDEEQLARGCLHCEKCREVCPKHAIAPAHLEDGILNA 88
Cdd:PRK09476   9 NGRRRFLRDVVRTAGGLAAVGVALglqqqqaRASGVALRPPGALNENDFLSACIRCGLCVQACPYDTLKLATLASGLSAG 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  89 rTPRMDFKSGWCDFCENEPggpkCVAACPTHALSCP--DPSQAIIGKA-EINRDWCLAAKGMGCHECVDVCNY--EALEL 163
Cdd:PRK09476  89 -TPYFVARDIPCEMCEDIP----CVKACPSGALDRElvDIDDARMGLAvLVDQENCLNFQGLRCDVCYRVCPLidKAITL 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 497293920 164 ----------GADNVPVVDVDACNGCGACELACISLSAgsitagatdrAIVVRPTE 209
Cdd:PRK09476 164 elernertgkHAFFLPTVHSDACTGCGKCEKACVLEKA----------AIKVLPRS 209
COG1149 COG1149
MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function ...
 130-186 5.64e-10

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


Pssm-ID: 440763 [Multi-domain]  Cd Length: 68  Bit Score: 53.58  E-value: 5.64e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 497293920 130 IIGKAEINRDWClaakgMGCHECVDVCNYEALELGADNVPVVDVDACNGCGACELAC 186
Cdd:COG1149    2 KRKIPVIDEEKC-----IGCGLCVEVCPEGAIKLDDGGAPVVDPDLCTGCGACVGVC 53
napF TIGR00402
ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of ...
 38-126 2.42e-04

ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation. [Energy metabolism, Electron transport]


Pssm-ID: 273060 [Multi-domain]  Cd Length: 101  Bit Score: 39.16  E-value: 2.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920   38 KYLPSATLLRPPGGQDEEQLARGCLHCEKCREVCPKHAIAPAhledgilNARTPRMDFKSGWCDFCEnepggpKCVAACP 117
Cdd:TIGR00402  13 SSTIEKTQIRPPWSARESLFSAVCTRCGECASACENNILQLG-------QQGQPTVEFDNAECDFCG------KCAEACP 79


                  ....*....
gi 497293920  118 THALSCPDP 126
Cdd:TIGR00402  80 TNAFHPRFP 88
 
Name Accession Description Interval E-value
DMSOR_beta_like cd16373
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 46-207 6.66e-47

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319895 [Multi-domain]  Cd Length: 154  Bit Score: 151.64  E-value: 6.66e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  46 LRPPGGQDEEQLARGCLHCEKCREVCPKHAIAPAHLEDGILNARTPRMDFKSGWCDFCENEpggpkCVAACPTHALSCPD 125
Cdd:cd16373    1 LRPPGALDEEEFLALCIRCGLCVEACPTGVIQPAGLEDGLEGGRTPYLDPREGPCDLCCDA-----CVEVCPTGALRPLD 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920 126 PS--QAIIGKAEINRDWCLAAKG-MGCHECVDVCNYEALEL---GADNVPVVDVDACNGCGACELACISLsagsitagaT 199
Cdd:cd16373   76 LEeqKVKMGVAVIDKDRCLAWQGgTDCGVCVEACPTEAIAIvleDDVLRPVVDEDKCVGCGLCEYVCPVE---------P 146


                 ....*...
gi 497293920 200 DRAIVVRP 207
Cdd:cd16373  147 PKAIVVEP 154
NapF_like cd10564
NapF, iron-sulfur subunit of periplasmic nitrate reductase; This family contains NapF protein, ...
 47-186 1.77e-22

NapF, iron-sulfur subunit of periplasmic nitrate reductase; This family contains NapF protein, the iron-sulfur subunit of periplasmic nitrate reductase. The periplasmic nitrate reductase NapABC of Escherichia coli likely functions during anaerobic growth in low-nitrate environments; napF operon expression is activated by cyclic AMP receptor protein (Crp). NapF is a subfamily of the beta subunit of DMSO reductase (DMSOR) family. DMSOR family members have a large, periplasmic molybdenum-containing alpha subunit as well as a small beta FeS subunit, and may also have a small gamma subunit. The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319886 [Multi-domain]  Cd Length: 139  Bit Score: 88.45  E-value: 1.77e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  47 RPPGGQDEEQLARGCLHCEKCREVCPKHAIApahledgILNARTPRMDFKSGWCDFCEnepggpKCVAACPTHALScPDP 126
Cdd:cd10564    1 RPPWAVDEALFLDLCTRCGDCVEACPEGIIV-------RGDGGFPELDFSRGECTFCG------ACAEACPEGALD-PAR 66

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497293920 127 SQAIIGKAEINrDWCLAAKGMGCHECVDVCNYEA----LELGADNVPVVDVDACNGCGACELAC 186
Cdd:cd10564   67 EAPWPLRAEIG-DSCLALQGVECRSCQDACPTQAirfrPRLGGIALPELDADACTGCGACVSVC 129
napG PRK09476
quinol dehydrogenase periplasmic component; Provisional
 16-209 1.06e-20

quinol dehydrogenase periplasmic component; Provisional


Pssm-ID: 236534 [Multi-domain]  Cd Length: 254  Bit Score: 86.60  E-value: 1.06e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  16 VSRRTFALGAVGACAVIGLGGVKY-------LPSATLLRPPGGQDEEQLARGCLHCEKCREVCPKHAIAPAHLEDGILNA 88
Cdd:PRK09476   9 NGRRRFLRDVVRTAGGLAAVGVALglqqqqaRASGVALRPPGALNENDFLSACIRCGLCVQACPYDTLKLATLASGLSAG 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  89 rTPRMDFKSGWCDFCENEPggpkCVAACPTHALSCP--DPSQAIIGKA-EINRDWCLAAKGMGCHECVDVCNY--EALEL 163
Cdd:PRK09476  89 -TPYFVARDIPCEMCEDIP----CVKACPSGALDRElvDIDDARMGLAvLVDQENCLNFQGLRCDVCYRVCPLidKAITL 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 497293920 164 ----------GADNVPVVDVDACNGCGACELACISLSAgsitagatdrAIVVRPTE 209
Cdd:PRK09476 164 elernertgkHAFFLPTVHSDACTGCGKCEKACVLEKA----------AIKVLPRS 209
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 60-186 2.07e-17

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: 75.13  E-value: 2.07e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  60 GCLHCEKCREVCPKHAIapaHLEDGILNARTPRMDFKSgwCDFCENepggpkCVAACPTHALSCPDPSQAI---IGKAEI 136
Cdd:cd10549    7 KCIGCGICVKACPTDAI---ELGPNGAIARGPEIDEDK--CVFCGA------CVEVCPTGAIELTPEGKEYvpkEKEAEI 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 497293920 137 NRDWClaakgMGCHECVDVCNYEALELGADNVPVVDVDACNGCGACELAC 186
Cdd:cd10549   76 DEEKC-----IGCGLCVKVCPVDAITLEDELEIVIDKEKCIGCGICAEVC 120
PRK10194 PRK10194
ferredoxin-type protein NapF;
46-186 2.98e-11

ferredoxin-type protein NapF;


Pssm-ID: 182296 [Multi-domain]  Cd Length: 163  Bit Score: 59.65  E-value: 2.98e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  46 LRPPGGQDEEQLARGCLHCEKCREVCpkhaiapahlEDGILNART---PRMDFKSGWCDFCENepggpkCVAACPtHALS 122
Cdd:PRK10194  21 IRPPWSGDESHFLTHCTRCDACINAC----------ENNILQRGAggyPSVNFKNNECSFCYA------CAQACP-ESLF 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 497293920 123 CPDPSQA-----IIGKAeinrdwCLAAKGMGCHECVDVCNYEAL----ELGADNVPVVDVDACNGCGACELAC 186
Cdd:PRK10194  84 SPRHTRAwdlqfTIGDA------CLAYQSVECRRCQDSCEPMAIifrpTLSGIYQPQLNSQLCNGCGACAASC 150
COG1149 COG1149
MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function ...
 130-186 5.64e-10

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


Pssm-ID: 440763 [Multi-domain]  Cd Length: 68  Bit Score: 53.58  E-value: 5.64e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 497293920 130 IIGKAEINRDWClaakgMGCHECVDVCNYEALELGADNVPVVDVDACNGCGACELAC 186
Cdd:COG1149    2 KRKIPVIDEEKC-----IGCGLCVEVCPEGAIKLDDGGAPVVDPDLCTGCGACVGVC 53
DMSOR_beta-like cd04410
Beta subunit of the DMSO Reductase (DMSOR) family; This family consists of the small beta ...
 61-188 1.43e-08

Beta subunit of the DMSO Reductase (DMSOR) family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319870 [Multi-domain]  Cd Length: 136  Bit Score: 51.62  E-value: 1.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  61 CLHCEKCREVCPK-HAIAPAHLEDGI--LNARTPRMDFKSGWCDFCENepggPKCVAACPTHALScPDPSqaiiGKAEIN 137
Cdd:cd04410    8 CIGCGTCEVACKQeHGLRPGPDWSRIkvIEGGGLERAFLPVSCMHCED----PPCVKACPTGAIY-KDED----GIVLID 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920 138 RDWClaakgMGCHECVDVCNYEALELGADNvpvVDVDACNGCG---------ACELACIS 188
Cdd:cd04410   79 EDKC-----IGCGSCVEACPYGAIVFDPEP---GKAVKCDLCGdrldeglepACVKACPT 130
HdrA COG1148
Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion];
134-186 4.28e-08

Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion];


Pssm-ID: 440762 [Multi-domain]  Cd Length: 563  Bit Score: 52.55  E-value: 4.28e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 497293920 134 AEINRDWClaakgMGCHECVDVCNYEALELGADNVPVVDVDACNGCGACELAC 186
Cdd:COG1148  491 AEVDPEKC-----TGCGRCVEVCPYGAISIDEKGVAEVNPALCKGCGTCAAAC 538
RnfB COG2878
Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit [Energy production and ...
 129-186 6.87e-07

Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit [Energy production and conversion]; Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit is part of the Pathway/BioSystem: Na+-translocating Fd:NADH oxidoreductase


Pssm-ID: 442125 [Multi-domain]  Cd Length: 254  Bit Score: 48.45  E-value: 6.87e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 497293920 129 AIIGKAEINRDWCLaakgmGCHECVDVCNYEALELGADNVPVVDVDACNGCGACELAC 186
Cdd:COG2878  127 AVIGGPKGCEYGCI-----GCGDCIKACPFDAIVGAAKGMHTVDEDKCTGCGLCVEAC 179
IorA COG4231
TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and ...
 133-186 1.72e-06

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


Pssm-ID: 443375 [Multi-domain]  Cd Length: 76  Bit Score: 44.26  E-value: 1.72e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 497293920 133 KAEINRDWClaakgMGCHECVDVCNYEALELGaDNVPVVDVDACNGCGACELAC 186
Cdd:COG4231   16 RYVIDEDKC-----TGCGACVKVCPADAIEEG-DGKAVIDPDLCIGCGSCVQVC 63
PreA COG1146
NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and ...
 132-186 6.14e-06

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


Pssm-ID: 440761 [Multi-domain]  Cd Length: 67  Bit Score: 42.77  E-value: 6.14e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 497293920 132 GKAEINRDWClaakgMGCHECVDVCNYEALELGADNVP--VVDVDACNGCGACELAC 186
Cdd:COG1146    1 MMPVIDTDKC-----IGCGACVEVCPVDVLELDEEGKKalVINPEECIGCGACELVC 52
DsrA COG2221
Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion ...
 129-186 8.19e-06

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


Pssm-ID: 441823 [Multi-domain]  Cd Length: 69  Bit Score: 42.35  E-value: 8.19e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920 129 AIIG--KAEINRDWClaakgMGCHECVDVCNYEALELgADNVPVVDVDACNGCGACELAC 186
Cdd:COG2221    3 GIIGtwPPKIDEEKC-----IGCGLCVAVCPTGAISL-DDGKLVIDEEKCIGCGACIRVC 56
HycB_like cd10554
HycB, HydN and similar proteins; This family includes HycB, the FeS subunit of a ...
 61-123 1.10e-05

HycB, HydN and similar proteins; This family includes HycB, the FeS subunit of a membrane-associated formate hydrogenlyase system (FHL-1) in Escherichia coli that breaks down formate, produced during anaerobic fermentation, to H2 and CO2. FHL-1 consists of formate dehydrogenase H (FDH-H) and the hydrogenase 3 complex (Hyd-3). HycB is thought to code for the [4Fe-4S] ferredoxin subunit of hydrogenase 3, which functions as an intermediate electron carrier protein between hydrogenase 3 and formate dehydrogenase. HydN codes for the [4Fe-4S] ferredoxin subunit of FDH-H; a hydN in-frame deletion mutation causes only weak reduction in hydrogenase activity, but loss of more than 60% of FDH-H activity. This pathway is only active at low pH and high formate concentrations, and is thought to provide a detoxification/de-acidification system countering the buildup of formate during fermentation.


Pssm-ID: 319876 [Multi-domain]  Cd Length: 149  Bit Score: 43.79  E-value: 1.10e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497293920  61 CLHCEKCREVCPKHAIAPAH-LEDGILNARTPRMdfKSGWCDFCENEPGGPKCVAACPTHALSC 123
Cdd:cd10554   87 CIGCKLCVLACPFGAIEMAPtTVPGVDWERGPRA--VAVKCDLCAGREGGPACVEACPTKALTL 148
HycB COG1142
Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];
61-126 1.93e-05

Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];


Pssm-ID: 440757 [Multi-domain]  Cd Length: 138  Bit Score: 42.72  E-value: 1.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  61 CLHCE--KCREVCPKHAI-----APAHLED--------------GILNARTPRMDFKSGWCDFCENEPGGPKCVAACPTH 119
Cdd:COG1142   52 CRHCEdaPCAEVCPVGAItrddgAVVVDEEkcigcglcvlacpfGAITMVGEKSRAVAVKCDLCGGREGGPACVEACPTG 131


                 ....*..
gi 497293920 120 ALSCPDP 126
Cdd:COG1142  132 ALRLVDV 138
NapF COG1145
Ferredoxin [Energy production and conversion];
1-186 3.65e-05

Ferredoxin [Energy production and conversion];


Pssm-ID: 440760 [Multi-domain]  Cd Length: 238  Bit Score: 43.17  E-value: 3.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920   1 MDEHGIEPKRDTGPCVSRRTFALGAVGACAVIGLGGVKYLPSATLLRPPGGQDEEQLARGCLHCEKCREVCPKHAIAPAH 80
Cdd:COG1145   44 LGGLLPIIGILAKEAFDALKDVLGILGAIVIGIGAGEIVRVGIAAADLNLKAVALVLLLALAVAGAAKRLIISAVKLVAG 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  81 LEDGILNARTPRMDFKSGWCDFCENEPGGPKCVAACPTHALSCPDPSQAIIGKAEINRDWClaakgMGCHECVDVCNYEA 160
Cdd:COG1145  124 LVVAAGEVLLVIAAALAEAGLAILGAAAPVDALAISGGKKIEEELKIAIKKAKAVIDAEKC-----IGCGLCVKVCPTGA 198

                        170       180
                 ....*....|....*....|....*..
gi 497293920 161 LELGADNVP-VVDVDACNGCGACELAC 186
Cdd:COG1145  199 IRLKDGKPQiVVDPDKCIGCGACVKVC 225
PorD COG1144
Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta ...
 133-186 4.93e-05

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: 40.42  E-value: 4.93e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 497293920 133 KAEINRDWCLaakgmGCHECVDVCNYEALELGADNVPVVDVDACNGCGACELAC 186
Cdd:COG1144   24 RPVVDEDKCI-----GCGLCWIVCPDGAIRVDDGKYYGIDYDYCKGCGICAEVC 72
PRK12769 PRK12769
putative oxidoreductase Fe-S binding subunit; Reviewed
 52-121 8.59e-05

putative oxidoreductase Fe-S binding subunit; Reviewed


Pssm-ID: 183733 [Multi-domain]  Cd Length: 654  Bit Score: 42.81  E-value: 8.59e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  52 QDEEQLARGCLHCEK--CREVCPKHAIApaHLEDGI-LNAR---------------------TPRMDFKSGW----CDFC 103
Cdd:PRK12769  47 HQQQRSAVTCHHCEDapCARSCPNGAIS--HVDDSIqVNQQkcigckscvvacpfgtmqivlTPVAAGKVKAtahkCDLC 124

                         90
                 ....*....|....*...
gi 497293920 104 ENEPGGPKCVAACPTHAL 121
Cdd:PRK12769 125 AGRENGPACVENCPADAL 142
PRK07118 PRK07118
Fe-S cluster domain-containing protein;
60-186 9.74e-05

Fe-S cluster domain-containing protein;


Pssm-ID: 235941 [Multi-domain]  Cd Length: 280  Bit Score: 42.23  E-value: 9.74e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  60 GCLHCEKCREVCPKHAIapaHLEDGIlnartPRMDfkSGWCDFCENepggpkCVAACPTHALSCPDPSQAII------GK 133
Cdd:PRK07118 140 GCLGLGSCVAACPFDAI---HIENGL-----PVVD--EDKCTGCGA------CVKACPRNVIELIPKSARVFvacnskDK 203

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 497293920 134 AEINRDWClAAKGMGCHECVDVCNYEALELgADNVPVVDVDACNGCGACELAC 186
Cdd:PRK07118 204 GKAVKKVC-EVGCIGCGKCVKACPAGAITM-ENNLAVIDQEKCTSCGKCVEKC 254
SIMIBI_bact_arch cd03110
bacterial and archaeal subfamily of SIMIBI; Uncharacterized bacterial and archaeal subfamily ...
 124-206 1.38e-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: 41.60  E-value: 1.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920 124 PDPSQAIIG--KAEINRDWCLaakgmGCHECVDVCNYEALELGADNVPVvDVDACNGCGACELAC----ISL---SAGSI 194
Cdd:cd03110   47 PEEEEDFVGgkKAFIDQEKCI-----RCGNCERVCKFGAILEFFQKLIV-DESLCEGCGACVIICprgaIYLkdrDTGKI 120

                         90
                 ....*....|..
gi 497293920 195 TAGATDRAIVVR 206
Cdd:cd03110  121 FISSSDGGPLVH 132
porD PRK09624
pyruvate ferredoxin oxidoreductase subunit delta; Reviewed
 133-186 1.54e-04

pyruvate ferredoxin oxidoreductase subunit delta; Reviewed


Pssm-ID: 170017 [Multi-domain]  Cd Length: 105  Bit Score: 39.63  E-value: 1.54e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 497293920 133 KAEINRDWCLAakgmgCHECVDVCNYEALELGADNVPVVDVDACNGCGACELAC 186
Cdd:PRK09624  45 MPEFNRDKCVR-----CYLCYIYCPEPAIYLDEEGYPVFDYDYCKGCGICANEC 93
DMSOR_beta_like cd10550
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 100-186 1.64e-04

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319872 [Multi-domain]  Cd Length: 130  Bit Score: 40.25  E-value: 1.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920 100 CDFCENepggPKCVAACPTHALSCPDPSQAIIgkaeINRDWClaakgMGCHECVDVCNYEALELGADNVPVVDVDACNGC 179
Cdd:cd10550   49 CRQCED----APCVEACPVGAISRDEETGAVV----VDEDKC-----IGCGMCVEACPFGAIRVDPETGKAIKCDLCGGD 115


                 ....*..
gi 497293920 180 GACELAC 186
Cdd:cd10550  116 PACVKVC 122
PRK13795 PRK13795
hypothetical protein; Provisional
 143-186 1.99e-04

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 41.52  E-value: 1.99e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 497293920 143 AAKGMGCHECVDVCNYEALELGADNVPV-VDVDACNGCGACELAC 186
Cdd:PRK13795 580 AAECVGCGVCVGACPTGAIRIEEGKRKIsVDEEKCIHCGKCTEVC 624
napF TIGR00402
ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of ...
 38-126 2.42e-04

ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation. [Energy metabolism, Electron transport]


Pssm-ID: 273060 [Multi-domain]  Cd Length: 101  Bit Score: 39.16  E-value: 2.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920   38 KYLPSATLLRPPGGQDEEQLARGCLHCEKCREVCPKHAIAPAhledgilNARTPRMDFKSGWCDFCEnepggpKCVAACP 117
Cdd:TIGR00402  13 SSTIEKTQIRPPWSARESLFSAVCTRCGECASACENNILQLG-------QQGQPTVEFDNAECDFCG------KCAEACP 79


                  ....*....
gi 497293920  118 THALSCPDP 126
Cdd:TIGR00402  80 TNAFHPRFP 88
PRK10330 PRK10330
electron transport protein HydN;
61-125 3.93e-04

electron transport protein HydN;


Pssm-ID: 182382 [Multi-domain]  Cd Length: 181  Bit Score: 39.87  E-value: 3.93e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  61 CLHCEKCREVCPKHA----IAPAHLEDGI-LNARTPRMDfkSGWCDFCENEPGGPKCVAACPTHALSCPD 125
Cdd:PRK10330  89 CIGCKTCVVACPYGAmevvVRPVIRNSGAgLNVRAEKAE--ANKCDLCNHREDGPACMAACPTHALICVD 156
DMSOR_beta-like cd04410
Beta subunit of the DMSO Reductase (DMSOR) family; This family consists of the small beta ...
 28-121 5.16e-04

Beta subunit of the DMSO Reductase (DMSOR) family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319870 [Multi-domain]  Cd Length: 136  Bit Score: 38.91  E-value: 5.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  28 ACAVIGLGGVKYLPSATLLRPPGGQDEEQLARGCLHCE--KCREVCPKHAIAPAhlEDGILNART--------------- 90
Cdd:cd04410   17 ACKQEHGLRPGPDWSRIKVIEGGGLERAFLPVSCMHCEdpPCVKACPTGAIYKD--EDGIVLIDEdkcigcgscveacpy 94

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 497293920  91 --PRMDFKSGW---CDFC---ENEPGGPKCVAACPTHAL 121
Cdd:cd04410   95 gaIVFDPEPGKavkCDLCgdrLDEGLEPACVKACPTGAL 133
DMSOR_beta_like cd16371
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 61-121 1.55e-03

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319893 [Multi-domain]  Cd Length: 140  Bit Score: 37.54  E-value: 1.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  61 CLHCEK--CREVCPKHAIApaHLEDGI------------------------LNARTPRMDfKsgwCDFCEN--EPG-GPK 111
Cdd:cd16371   54 CNHCENpaCVKVCPTGAIT--KREDGIvvvdqdkcigcgycvwacpygapqYNPETGKMD-K---CDMCVDrlDEGeKPA 127

                         90
                 ....*....|
gi 497293920 112 CVAACPTHAL 121
Cdd:cd16371  128 CVAACPTRAL 137
HybA COG0437
Fe-S-cluster-containing dehydrogenase component (DMSO reductase) [Energy production and ...
 57-121 1.78e-03

Fe-S-cluster-containing dehydrogenase component (DMSO reductase) [Energy production and conversion];


Pssm-ID: 440206 [Multi-domain]  Cd Length: 184  Bit Score: 38.00  E-value: 1.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  57 LARGCLHCEK--CREVCPKHAIApaHLEDGI------------------------LNARTPRMDfKsgwCDFCEN---EP 107
Cdd:COG0437   56 VPVLCNHCDDppCVKVCPTGATY--KREDGIvlvdydkcigcrycvaacpygaprFNPETGVVE-K---CTFCADrldEG 129

                         90
                 ....*....|....
gi 497293920 108 GGPKCVAACPTHAL 121
Cdd:COG0437  130 LLPACVEACPTGAL 143
PRK12809 PRK12809
putative oxidoreductase Fe-S binding subunit; Reviewed
 58-188 2.28e-03

putative oxidoreductase Fe-S binding subunit; Reviewed


Pssm-ID: 183762 [Multi-domain]  Cd Length: 639  Bit Score: 38.47  E-value: 2.28e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293920  58 ARGCLHCEKCREVCpkhaiAPAHLEDGILNART---PRMDF-------KSGWCDFCENEPggpkCVAACPTHALSCPDPS 127
Cdd:PRK12809   9 AAECIGCHACEIAC-----AVAHNQENWPLSHSdfrPRIHVvgkgqaaNPVACHHCNNAP----CVTACPVNALTFQSDS 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 497293920 128 QAIIgkaeinrdwclAAKGMGCHECVDVCNYEALELgADNVpVVDVDACNGCGACELACIS 188
Cdd:PRK12809  80 VQLD-----------EQKCIGCKRCAIACPFGVVEM-VDTI-AQKCDLCNQRSSGTQACIE 127
FDH_b_like cd10562
uncharacterized subfamily of beta subunit of formate dehydrogenase; This subfamily includes ...
 152-186 6.32e-03

uncharacterized subfamily of beta subunit of formate dehydrogenase; This subfamily includes the beta-subunit of formate dehydrogenases that are as yet uncharacterized. Members of the DMSO reductase family include formate dehydrogenase N and O (FDH-N, FDH-O) and tungsten-containing formate dehydrogenase (W-FDH) and other similar proteins. FDH-N, a major component of nitrate respiration of Escherichia coli, 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. It 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. W-FDH contains a tungsten instead of molybdenum at the catalytic center. This enzyme seems to be exclusively found in organisms such as hyperthermophilic archaea that live in extreme environments. It is a heterodimer of a large and a small subunit; the large subunit harbors the W site and one [4Fe-4S] center and the small subunit, containing three [4Fe-4S] clusters, functions to transfer electrons.


Pssm-ID: 319884 [Multi-domain]  Cd Length: 161  Bit Score: 36.13  E-value: 6.32e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 497293920 152 CVDVCNYEALELGADNVPVVDVDACNGCGACELAC 186
Cdd:cd10562   78 CVKVCPTGALYKTENGAVVVDEDKCIGCGYCVAAC 112
PRK13409 PRK13409
ribosome biogenesis/translation initiation ATPase RLI;
134-182 8.91e-03

ribosome biogenesis/translation initiation ATPase RLI;


Pssm-ID: 184037 [Multi-domain]  Cd Length: 590  Bit Score: 36.71  E-value: 8.91e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 497293920 134 AEINRDWCLAAKgmgC-HECVDVC-----NYEALEL-GADNVPVVDVDACNGCGAC 182
Cdd:PRK13409   5 AVVDYDRCQPKK---CnYECIKYCpvvrtGEETIEIdEDDGKPVISEELCIGCGIC 57
 
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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