NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2229004154|ref|WP_247037659|]
View 

MULTISPECIES: formate dehydrogenase subunit gamma [unclassified Neorhizobium]

Protein Classification

formate dehydrogenase subunit gamma( domain architecture ID 10792715)

formate dehydrogenase subunit gamma is an NAD-dependent formate dehydrogenase that catalyzes the oxidation of formate to carbon dioxide, donating the electrons to a second substrate NAD+

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK05988 PRK05988
formate dehydrogenase subunit gamma; Validated
 4-159 4.23e-95

formate dehydrogenase subunit gamma; Validated


:

Pssm-ID: 180339  Cd Length: 156  Bit Score: 271.83  E-value: 4.23e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154   4 RISAGEFTERSLQIIRDLKHLEGPMLPILHAIQAEFGYVPEEVKPVIASELNLSRAEVHGVVTFYHEFRDHPAGRHVLKL 83
Cdd:PRK05988    1 MPDEPWDAARIAAIIAEHKHLEGALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHGVITFYHDFRTHPPGRHVLKL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2229004154  84 CRAEACQSMGSDRIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGLNR 159
Cdd:PRK05988   81 CRAEACQAMGGDALAAHAKARLGIDFHQTTADGAVTLEPVYCLGLCACSPAAMLDGEVHGRLDPQRLDALLAEARR 156
 
Name Accession Description Interval E-value
PRK05988 PRK05988
formate dehydrogenase subunit gamma; Validated
 4-159 4.23e-95

formate dehydrogenase subunit gamma; Validated


Pssm-ID: 180339  Cd Length: 156  Bit Score: 271.83  E-value: 4.23e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154   4 RISAGEFTERSLQIIRDLKHLEGPMLPILHAIQAEFGYVPEEVKPVIASELNLSRAEVHGVVTFYHEFRDHPAGRHVLKL 83
Cdd:PRK05988    1 MPDEPWDAARIAAIIAEHKHLEGALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHGVITFYHDFRTHPPGRHVLKL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2229004154  84 CRAEACQSMGSDRIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGLNR 159
Cdd:PRK05988   81 CRAEACQAMGGDALAAHAKARLGIDFHQTTADGAVTLEPVYCLGLCACSPAAMLDGEVHGRLDPQRLDALLAEARR 156
NuoE COG1905
NADH:ubiquinone oxidoreductase 24 kD subunit (chain E) [Energy production and conversion]; ...
 1-157 9.60e-69

NADH:ubiquinone oxidoreductase 24 kD subunit (chain E) [Energy production and conversion]; NADH:ubiquinone oxidoreductase 24 kD subunit (chain E) is part of the Pathway/BioSystem: NADH dehydrogenase


Pssm-ID: 441509  Cd Length: 159  Bit Score: 204.99  E-value: 9.60e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154   1 MNMRISAGEFTERSLQIIRDLKHLEGPMLPILHAIQAEFGYVPEEVKPVIASELNLSRAEVHGVVTFYHEFRDHPAGRHV 80
Cdd:COG1905     1 MSERELSEELLAEIDEIIAKYPRKRSALIPILHLVQEEFGYLPEEAIEEIAEALGLPPAEVYGVATFYSMFRLKPVGKHV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2229004154  81 LKLCRAEACQSMGSDRIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGL 157
Cdd:COG1905    81 IRVCTGTACHLRGAEELLEALEEKLGIKPGETTADGKFTLEEVECLGACGLAPVMMVNDDVYGRLTPEKVDEILDEL 157
2Fe-2S_thioredx pfam01257
Thioredoxin-like [2Fe-2S] ferredoxin;
16-157 1.73e-56

Thioredoxin-like [2Fe-2S] ferredoxin;


Pssm-ID: 460139  Cd Length: 145  Bit Score: 173.43  E-value: 1.73e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154  16 QIIRDLKHLEGPMLPILHAIQAEFGYVPEEVKPVIASELNLSRAEVHGVVTFYHEFRDHPAGRHVLKLCRAEACQSMGSD 95
Cdd:pfam01257   3 EIIAKYPRKRSALIPILHLAQEEYGYLPPEAIEYVAELLGIPPARVYEVATFYTMFSLKPVGKYHIQVCTGTPCHLRGSD 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2229004154  96 RIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGL 157
Cdd:pfam01257  83 EILEALEKKLGIKPGETTPDGKFTLEEVECLGACDNAPVMQINDDYYGDLTPEKVDEILEEL 144
TRX_Fd_NuoE_FDH_gamma cd03081
TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E ...
 78-157 2.34e-41

TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidation of formate.


Pssm-ID: 239379  Cd Length: 80  Bit Score: 132.89  E-value: 2.34e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154  78 RHVLKLCRAEACQSMGSDRIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGL 157
Cdd:cd03081     1 RHVLKLCRAEACQAMGAEALAAHIKARLGIDFHETTADGSVTLEPVYCLGLCACSPAAMIDGEVHGRVDPEKFDALLAEL 80
 
Name Accession Description Interval E-value
PRK05988 PRK05988
formate dehydrogenase subunit gamma; Validated
 4-159 4.23e-95

formate dehydrogenase subunit gamma; Validated


Pssm-ID: 180339  Cd Length: 156  Bit Score: 271.83  E-value: 4.23e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154   4 RISAGEFTERSLQIIRDLKHLEGPMLPILHAIQAEFGYVPEEVKPVIASELNLSRAEVHGVVTFYHEFRDHPAGRHVLKL 83
Cdd:PRK05988    1 MPDEPWDAARIAAIIAEHKHLEGALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHGVITFYHDFRTHPPGRHVLKL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2229004154  84 CRAEACQSMGSDRIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGLNR 159
Cdd:PRK05988   81 CRAEACQAMGGDALAAHAKARLGIDFHQTTADGAVTLEPVYCLGLCACSPAAMLDGEVHGRLDPQRLDALLAEARR 156
NuoE COG1905
NADH:ubiquinone oxidoreductase 24 kD subunit (chain E) [Energy production and conversion]; ...
 1-157 9.60e-69

NADH:ubiquinone oxidoreductase 24 kD subunit (chain E) [Energy production and conversion]; NADH:ubiquinone oxidoreductase 24 kD subunit (chain E) is part of the Pathway/BioSystem: NADH dehydrogenase


Pssm-ID: 441509  Cd Length: 159  Bit Score: 204.99  E-value: 9.60e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154   1 MNMRISAGEFTERSLQIIRDLKHLEGPMLPILHAIQAEFGYVPEEVKPVIASELNLSRAEVHGVVTFYHEFRDHPAGRHV 80
Cdd:COG1905     1 MSERELSEELLAEIDEIIAKYPRKRSALIPILHLVQEEFGYLPEEAIEEIAEALGLPPAEVYGVATFYSMFRLKPVGKHV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2229004154  81 LKLCRAEACQSMGSDRIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGL 157
Cdd:COG1905    81 IRVCTGTACHLRGAEELLEALEEKLGIKPGETTADGKFTLEEVECLGACGLAPVMMVNDDVYGRLTPEKVDEILDEL 157
2Fe-2S_thioredx pfam01257
Thioredoxin-like [2Fe-2S] ferredoxin;
16-157 1.73e-56

Thioredoxin-like [2Fe-2S] ferredoxin;


Pssm-ID: 460139  Cd Length: 145  Bit Score: 173.43  E-value: 1.73e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154  16 QIIRDLKHLEGPMLPILHAIQAEFGYVPEEVKPVIASELNLSRAEVHGVVTFYHEFRDHPAGRHVLKLCRAEACQSMGSD 95
Cdd:pfam01257   3 EIIAKYPRKRSALIPILHLAQEEYGYLPPEAIEYVAELLGIPPARVYEVATFYTMFSLKPVGKYHIQVCTGTPCHLRGSD 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2229004154  96 RIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGL 157
Cdd:pfam01257  83 EILEALEKKLGIKPGETTPDGKFTLEEVECLGACDNAPVMQINDDYYGDLTPEKVDEILEEL 144
PRK07539 PRK07539
NADH-quinone oxidoreductase subunit NuoE;
10-157 8.31e-43

NADH-quinone oxidoreductase subunit NuoE;


Pssm-ID: 181024  Cd Length: 154  Bit Score: 139.14  E-value: 8.31e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154  10 FTERSLQIIRD-LKHLEGP---MLPILHAIQAEFGYVPEEVKPVIASELNLSRAEVHGVVTFYHEFRDHPAGRHVLKLCR 85
Cdd:PRK07539    2 LSAEELAAIEReIAKYPRPrsaVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVEEVATFYSMIFRQPVGRHVIQVCT 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2229004154  86 AEACQSMGSDRIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGL 157
Cdd:PRK07539   82 STPCWLRGGEAILAALKKKLGIKPGETTADGRFTLLEVECLGACDNAPVVMINDDTYEDLTPEKIDELLDEL 153
TRX_Fd_NuoE_FDH_gamma cd03081
TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E ...
 78-157 2.34e-41

TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidation of formate.


Pssm-ID: 239379  Cd Length: 80  Bit Score: 132.89  E-value: 2.34e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154  78 RHVLKLCRAEACQSMGSDRIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGL 157
Cdd:cd03081     1 RHVLKLCRAEACQAMGAEALAAHIKARLGIDFHETTADGSVTLEPVYCLGLCACSPAAMIDGEVHGRVDPEKFDALLAEL 80
TRX_Fd_NuoE cd03064
TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E ...
 78-157 1.03e-31

TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] cluster and also binds the NADH substrate and FMN.


Pssm-ID: 239362 [Multi-domain]  Cd Length: 80  Bit Score: 108.37  E-value: 1.03e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154  78 RHVLKLCRAEACQSMGSDRIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGL 157
Cdd:cd03064     1 KHVIRVCTGTACHLRGAEALLEALEKKLGIKPGETTPDGRFTLEEVECLGACDLAPVMMINDDVYGRLTPEKVDAILEAL 80
PRK07571 PRK07571
bidirectional hydrogenase complex protein HoxE; Reviewed
 28-146 1.62e-31

bidirectional hydrogenase complex protein HoxE; Reviewed


Pssm-ID: 236053  Cd Length: 169  Bit Score: 111.00  E-value: 1.62e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154  28 MLPILHAIQAEFGYVPEEVKPVIASELNLSRAEVHGVVTFYHEFRDHPAGRHVLKLCRAEACQSMGSDRIADHARQLLGI 107
Cdd:PRK07571   38 LIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVYGVATFYHLFSLKPSGEHTCVVCTGTACYVKGSAAILEDLENELGI 117

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2229004154 108 DFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVD 146
Cdd:PRK07571  118 KAGETTADGKLSLLTARCLGACGIAPAVVFDGKVAGKQT 156
TRX_Fd_family cd02980
Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX ...
 79-157 2.05e-16

Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.


Pssm-ID: 239278 [Multi-domain]  Cd Length: 77  Bit Score: 69.58  E-value: 2.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154  79 HVLKLCRAEACQSMGSDRIADHARQLLGIDFhqttLDGAVTLEPVYCLGLCACAPAAML--DGEVFGRVDELCLSEIVAG 156
Cdd:cd02980     1 HHILVCTGTACGLRGAEELLEALEKELGIRG----GDGRVTVERVGCLGACGLAPVVVVypDGVWYGRVTPEDVEEIVEE 76


                  .
gi 2229004154 157 L 157
Cdd:cd02980    77 L 77
PRK12373 PRK12373
NADH-quinone oxidoreductase subunit E;
29-137 1.39e-10

NADH-quinone oxidoreductase subunit E;


Pssm-ID: 237082 [Multi-domain]  Cd Length: 400  Bit Score: 58.27  E-value: 1.39e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004154  29 LPILHAIQAEFGYVpeeVKPVI---ASELNLSRAEVHGVVTFYHEFRDHPAGR--HVlKLCRAEACQSMGSDRIADHARQ 103
Cdd:PRK12373   40 IPLLMRAQEQEGWV---TRAAIekvADMLDMAYIRVLEVATFYTQFQLQPVGTraHI-QVCGTTPCMLRGSEALMAVCKS 115

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2229004154 104 LLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAML 137
Cdd:PRK12373  116 KIHAHPHELNADGTLSWEEVECLGACVNAPMVQI 149
TRX_Fd_NuoE_hoxF cd03083
TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E ...
 93-157 3.73e-06

TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase catalyzing the oxidation of molecular hydrogen accompanied by the reduction of NAD. It is composed of four structural subunits encoded by the genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or alpha subunit) is a fusion protein containing an N-terminal NuoE-like domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. HoxF may be involved in the electron transport chain during the NAD-dependent oxidation of hydrogen through its NuoF domain. The NuoE-like domain of hoxF contains only one conserved cysteine in its putative active site, compared to four cysteines in NuoE, and may have lost the ability to bind [2Fe-2S] clusters.


Pssm-ID: 239381  Cd Length: 80  Bit Score: 42.78  E-value: 3.73e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2229004154  93 GSDRIADHARQLLGIDFHQTTLDGAVTLEPVYCLGLCACAPAAMLDGEVFGRVDELCLSEIVAGL 157
Cdd:cd03083    16 GYKAVLDALCRELGIRFGEVDEDGMVGLFFTSCTGLCDQGPALLINNRVFTRLTPGRIDQIAELI 80
 
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