SII-SWORD/CoKE huggingface dataset:
Predicted [NiFe]-hydrogenase-3-type complex Eha, membrane protein EhaL (Prd_NiFe_hyd_3_EhaL)
Type: Family

[NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster .

Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family . Members of this subgroup include:

Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli

CO-induced hydrogenase (Coo) from Rhodospirillum rubrum

Mbh hydrogenase from Pyrococcus furiosus

Eha and Ehb hydrogenases from Methanothermobacter species

Ech hydrogenase from Methanosarcina barkeri

Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps.

Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA

, EhaB

, EhaC

, EhaD

, EhaE

, EhaF

, EhaG

, EhaI

, EhaK

, EhaL

and

) and four hydrophilic subunits (EhaM, EhaR, EhS, EhT) . The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases.

Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar
eha
operon structure.

This entry represents small membrane proteins that are predicted to be the EhaL transmembrane subunits of multisubunit membrane-bound [NiFe]-hydrogenase Eha complexes.
Probable [NiFe]-hydrogenase-type-3 Eha complex membrane subunit A (Prd_NiFe_hyd_3_EhaA)
Type: Family

[NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster .

Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family . Members of this subgroup include:

Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli

CO-induced hydrogenase (Coo) from Rhodospirillum rubrum

Mbh hydrogenase from Pyrococcus furiosus

Eha and Ehb hydrogenases from Methanothermobacter species

Ech hydrogenase from Methanosarcina barkeri

Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps.

Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA

, EhaB

, EhaC

, EhaD

, EhaE

, EhaF

, EhaG

, EhaI

, EhaK

, EhaL

and

) and four hydrophilic subunits (EhaM, EhaR, EhS, EhT) . The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases.

Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar
eha
operon structure.

This entry represents small membrane proteins that are predicted to be the EhaA transmembrane subunits of multisubunit membrane-bound [NiFe]-hydrogenase Eha complexes.
Tetrahydromethanopterin S-methyltransferase, subunit F (MeTrfase_F)
Type: Family

This group represents a tetrahydromethanopterin S-methyltransferase, subunit F which forms part of a complex that catalyzes the formation of methyl-coenzyme M and tetrahydromethanopterin from coenzyme M and methyl-tetrahydromethanopterin. This is an energy-conserving, sodium-ion translocating step . The complex is composed of 8 subunits; mtrA, mtrB, mtrC, mtrD, mtrE, mtrF, mtrG and mtrH and plays a role in methanogenesis from carbon dioxide.
Predicted [NiFe]-hydrogenase-3-type complex Eha, membrane protein EhaD (Prd_NiFe_hyd_3_EhaD)
Type: Family

[NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster .

Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family . Members of this subgroup include:

Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli

CO-induced hydrogenase (Coo) from Rhodospirillum rubrum

Mbh hydrogenase from Pyrococcus furiosus

Eha and Ehb hydrogenases from Methanothermobacter species

Ech hydrogenase from Methanosarcina barkeri

Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps.

Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA

, EhaB

, EhaC

, EhaD

, EhaE

, EhaF

, EhaG

, EhaI

, EhaK

, EhaL

and

) and four hydrophilic subunits (EhaM, EhaR, EhS, EhT) . The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases.

Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar
eha
operon structure.

This entry represents small membrane proteins that are predicted to be EhaD transmembrane subunits of multisubunit membrane-bound [NiFe]-hydrogenase Eha complexes.
Lipopolysaccharide core heptose(II)-phosphate phosphatase (LipoPS_heptP_Pase)
Type: Family

This entry represents lipopolysaccharide core heptose(II)-phosphate phosphatase, which catalyzes the dephosphorylation of heptose(II) of the outer membrane lipopolysaccharide core.

These proteins are related to cofactor-dependent phosphoglucomutases so distantly that the characteristic domain (

) is not detected. Nonetheless, the relationship has been shown by sequence analysis and molecular modelling , on the basis of which it is predicted that these proteins are phosphatases acting on large substrates, perhaps phosphoproteins. Sequence analysis also predicts that they are periplasmic, having a signal sequence and two pairs of Cys residues close enough to form disulphide bonds. Known properties of these proteins are rather disparate. AfrS is required for the transcriptional activation of AfrA, the major protein of AF/R1 pili in Escherichia coli RDEC-1. Ais proteins are aluminium-inducible proteins of unknown function.
Predicted [NiFe]-hydrogenase-3-type complex Eha, membrane protein EhaG (Prd_NiFe_hyd_3_EhaG)
Type: Family

[NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster .

Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family . Members of this subgroup include:

Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli

CO-induced hydrogenase (Coo) from Rhodospirillum rubrum

Mbh hydrogenase from Pyrococcus furiosus

Eha and Ehb hydrogenases from Methanothermobacter species

Ech hydrogenase from Methanosarcina barkeri

Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps.

Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA

, EhaB

, EhaC

, EhaD

, EhaE

, EhaF

, EhaG

, EhaI

, EhaK

, EhaL

and

) and four hydrophilic subunits (EhaM, EhaR, EhS, EhT) . The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases.

Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar
eha
operon structure.

This entry represents small membrane proteins that are predicted to be the EhaG transmembrane subunits of multi-subunit membrane-bound [NiFe]-hydrogenase Eha complexes.
Methanogenesis marker 7 protein (Menthan_mark_7)
Type: Family

Members of this protein family, to date, are found in a completed prokaryotic genome if, and only if, the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it .
Predicted [NiFe]-hydrogenase-3-type complex Eha, membrane protein EhaF (Prd_NiFe_hyd_3_EhaF)
Type: Family

[NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster .

Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family . Members of this subgroup include:

Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli

CO-induced hydrogenase (Coo) from Rhodospirillum rubrum

Mbh hydrogenase from Pyrococcus furiosus

Eha and Ehb hydrogenases from Methanothermobacter species

Ech hydrogenase from Methanosarcina barkeri

Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps.

Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA

, EhaB

, EhaC

, EhaD

, EhaE

, EhaF

, EhaG

, EhaI

, EhaK

, EhaL

and

) and four hydrophilic subunits (EhaM, EhaR, EhS, EhT) . The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases.

Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar
eha
operon structure.

This entry represents small membrane proteins that are predicted to be the EhaF transmembrane subunits of multi-subunit membrane-bound [NiFe]-hydrogenase Eha complexes.
Predicted [NiFe]-hydrogenase-3-type complex Eha, membrane protein EhaB (Prd_NiFe_hyd_3_EhaB)
Type: Family

[NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster .

Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family . Members of this subgroup include:

Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli

CO-induced hydrogenase (Coo) from Rhodospirillum rubrum

Mbh hydrogenase from Pyrococcus furiosus

Eha and Ehb hydrogenases from Methanothermobacter species

Ech hydrogenase from Methanosarcina barkeri

Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps.

Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA

, EhaB

, EhaC

, EhaD

, EhaE

, EhaF

, EhaG

, EhaI

, EhaK

, EhaL

and

) and four hydrophilic subunits (EhaM, EhaR, EhS, EhT) . The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases.

Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar
eha
operon structure.

This entry represents small membrane proteins that are predicted to be the EhaB transmembrane subunits of multi-subunit membrane-bound [NiFe]-hydrogenase Eha complexes.
NTP pyrophosphohydrolase MazG-related, Rhizobiaceae-type (MazG-related_Rhizo-type)
Type: Family

Members of this group are distantly related to MazG-type NTP pyrophosphohydrolase. Conserved residues of the MazG domain (at least three of the Glu residues, Asp, Lys and Arg), including those shown to be functionally important , are also conserved here. MazG protein of Thermotoga maritima has been shown to have both nucleoside triphosphate pyrophosphohydrolase and pyrophosphatase activities, while Escherichia coli MazG has only NTP pyrophosphohydrolase activity . Therefore, members of this group are tentatively predicted to be pyrophosphohydrolases.
Predicted [NiFe]-hydrogenase-3-type complex Eha, membrane protein EhaC (Prd_NiFe_hyd_3_EhaC)
Type: Family

[NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster .

Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family . Members of this subgroup include:

Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli

CO-induced hydrogenase (Coo) from Rhodospirillum rubrum

Mbh hydrogenase from Pyrococcus furiosus

Eha and Ehb hydrogenases from Methanothermobacter species

Ech hydrogenase from Methanosarcina barkeri

Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps.

Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA

, EhaB

, EhaC

, EhaD

, EhaE

, EhaF

, EhaG

, EhaI

, EhaK

, EhaL

and

) and four hydrophilic subunits (EhaM, EhaR, EhS, EhT) . The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases.

Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar
eha
operon structure.

This entry represents small membrane proteins that are predicted to be EhaC transmembrane subunits of multisubunit membrane-bound [NiFe]-hydrogenase Eha complexes.