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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 952992920  8 VVVDTEKCKGCNLCVVECPTNVLALSPNvngkgYNYAYMENPDACIGCANCGLVCPDNVITV 69
Cdd:COG1146   3 PVIDTDKCIGCGACVEVCPVDVLELDEE-----GKKALVINPEECIGCGACELVCPVGAITV 59

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 952992920  8 VVVDTEKCKGCNLCVVECPTNVLALSPNvngkgYNYAYMENPDACIGCANCGLVCPDNVITV 69
Cdd:COG1146   3 PVIDTDKCIGCGACVEVCPVDVLELDEE-----GKKALVINPEECIGCGACELVCPVGAITV 59

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 952992920   9 VVDTEKCKGCNLCVVECPTNVLALSPNvngKGYNYAYMENPDACIGCANCGLVCPDNVITV 69
Cdd:cd10549    2 KYDPEKCIGCGICVKACPTDAIELGPN---GAIARGPEIDEDKCVFCGACVEVCPTGAIEL 59

ferredoxin III, nif-specific; Members of this family are homodimeric ferredoxins from nitrogen fixation regions of many nitrogen-fixing bacteria. As characterized in Rhodobacter capsulatus, these proteins are homodimeric, with two 4Fe-4S clusters bound per monomer. Although nif-specific, this protein family is not usiveral, as other nitrogenase systems may substitute flavodoxins, or different types of ferredoxin. [Central intermediary metabolism, Nitrogen fixation]

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 952992920  10 VDTEKCKGCNLCVVECPTNVLAL----------SPNVNGKGYNYAYM--ENPDACIGCANCGLVCPDNVIT 68
Cdd:TIGR02936 18 IDQEKCIGCGRCYKVCGRDVLTLkgineegelvASDDDDDEIERKVMvvANPGNCIGCGACARVCPKKCQT 88

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 952992920  8 VVVDTEKCKGCNLCVVECPTNVLALSPNvngkgYNYAYMENPDACIGCANCGLVCPDNVITV 69
Cdd:COG1146   3 PVIDTDKCIGCGACVEVCPVDVLELDEE-----GKKALVINPEECIGCGACELVCPVGAITV 59

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 952992920  7 AVVVDTEKCKGCNLCVVECPTNVLALSPNVngkgynyaYMENPDACIGCANCGLVCPDNVITVYK 71
Cdd:COG4231  16 RYVIDEDKCTGCGACVKVCPADAIEEGDGK--------AVIDPDLCIGCGSCVQVCPVDAIKLEK 72

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 952992920  8 VVVDTEKCKGCNLCVVECPTNVLALSPnvngkgyNYAYMENPDACIGCANCGLVCPDNVITVYKVK 73
Cdd:COG1149   6 PVIDEEKCIGCGLCVEVCPEGAIKLDD-------GGAPVVDPDLCTGCGACVGVCPTGAITLEERE 64

Ferredoxin [Energy production and conversion];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 952992920   2 AKVKGAVVVDTEKCKGCNLCVVECPTNVLALSPNvngkgyNYAYMENPDACIGCANCGLVCPDNVITVYKVKLQ 75
Cdd:COG1145  171 AIKKAKAVIDAEKCIGCGLCVKVCPTGAIRLKDG------KPQIVVDPDKCIGCGACVKVCPVGAISLEPKEIE 238

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 952992920  8 VVVDTEKCKGCNLCVVECPTNVLALSpnvngkgyNYAYMENPDACIGCANCGLVCPDNVITVYKVK 73
Cdd:COG2221  10 PKIDEEKCIGCGLCVAVCPTGAISLD--------DGKLVIDEEKCIGCGACIRVCPTGAIKGEKPK 67

Polyferredoxin NapH [Energy production and conversion];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 952992920   8 VVVDTEKCKGCNLCVVECPTNVlalspnVNGKGYNyaymeNPDACIGCANCGLVCPDNVIT 68
Cdd:COG0348  205 VRYDRGDCIDCGLCVKVCPMGI------DIRKGEI-----NQSECINCGRCIDACPKDAIR 254

hypothetical protein; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 952992920  14 KCKGCNLCVVECPTNVLALspnvngKGYNYAYMENPDACIGCANCGLVCPdnvITVYKVKLQEA 77
Cdd:PRK13795 582 ECVGCGVCVGACPTGAIRI------EEGKRKISVDEEKCIHCGKCTEVCP---VVKYKDKRNGS 636

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 952992920   3 KVKGAVVVDTEKCKGCNLCVVECPTNVLalspnvnGKGYNYAYMeNPDACIGCANCGLVCPDNVITV 69
Cdd:COG4624   81 KRGPSIIRDKEKCKNCYPCVRACPVKAI-------KVDDGKAEI-DEEKCISCGQCVAVCPFGAITE 139

4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 952992920  15 CKGCNLCVVECPTNVLALSPNVNGKGYNYAYMeNPDACIGCANCGLVCP 63
Cdd:pfam12838  1 CIGCGACVAACPVGAITLDEVGEKKGTKTVVI-DPERCVGCGACVAVCP 48

putative glutamate synthase (NADPH) small subunit; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 952992920  15 CKGCNLCVVECPTN-VLALSPnvnGKGYNYAYmenpDACIGCANCGLVCP 63
Cdd:PRK12771 512 CFECDNCYGACPQDaIIKLGP---GRRYHFDY----DKCTGCHICADVCP 554

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 952992920   9 VVDTEKCKGCNLCVVECPTNVLALSPNvngkgynyAYMENPDACIGCANCGLVCPDNVIT 68
Cdd:cd03110   60 FIDQEKCIRCGNCERVCKFGAILEFFQ--------KLIVDESLCEGCGACVIICPRGAIY 111

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 952992920   8 VVVDTEKCKGCNLCVVECPTNVLALSPnvNGKGYNYAYME---NPDACIGCANCGLVCPDNVITV 69
Cdd:cd10549   35 PEIDEDKCVFCGACVEVCPTGAIELTP--EGKEYVPKEKEaeiDEEKCIGCGLCVKVCPVDAITL 97

photosystem I subunit VII; Provisional

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 952992920 15 CKGCNLCVVECPTNVLALSPNVNGKGYNYAYMENPDACIGCANCGLVCPDNVITV 69
Cdd:PLN00071 11 CIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPTDFLSV 65

photosystem I subunit VII

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 952992920 15 CKGCNLCVVECPTNVLALSPNVNGKGYNYAYMENPDACIGCANCGLVCPDNVITV 69
Cdd:CHL00065 11 CIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPTDFLSV 65

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.

                         10        20        30
                 ....*....|....*....|....*....|..
gi 952992920   6 GAVVVDTEKCKGCNLCVVECPTNVLALSPNVN 37
Cdd:cd10562   93 GAVVVDEDKCIGCGYCVAACPFDVPRYDETTN 124

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

                        10        20        30
                ....*....|....*....|....*....|
gi 952992920  5 KGAVVVDTEKCKGCNLCVVECPTNVLALSP 34
Cdd:COG1144  52 GKYYGIDYDYCKGCGICAEVCPVKAIEMVP 81

Acetyl-CoA synthase (ACS), also known as acetyl-CoA decarbonylase, is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA. ACS forms a heterotetramer with carbon monoxide dehydrogenase (CODH) consisting of two ACS and two CODH subunits. CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide, CoA, and a methyl group donated by another protein (CoFeSP). ACS has three structural domains, an N-terminal rossman fold domain with a helical region at its N-terminus which interacts with CODH, and two alpha + beta fold domains. A Ni-Fe-S center referred to as the A-cluster is located in the C-terminal domain. A large cavity exists between the three domains which may bind CoA.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 952992920  14 KCKGCNLCVVECPTNVLALSPNVNGKGYNYAYMENP-DACIGCANCGLVCPDNV 66
Cdd:cd01916  366 KCTDCGWCTRACPNSLRIKEAMEAAKEGDFSGLADLfDQCVGCGRCEQECPKEI 419

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

                         10        20
                 ....*....|....*....|....*...
gi 952992920   5 KGAVVVDTEKCKGCNLCVVECPTNVLAL 32
Cdd:COG1148  518 KGVAEVNPALCKGCGTCAAACPSGAISL 545

3-methyl-2-oxobutanoate dehydrogenase subunit delta;

                         10        20        30
                 ....*....|....*....|....*....|
gi 952992920   3 KVKGAVVVDTEKCKGCNLCVVECPTNVLAL 32
Cdd:PRK09623  71 KEDGYVAIDYDYCKGCGICANECPTKAITM 100

electron transport complex, RnfABCDGE type, B subunit; The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit. [Energy metabolism, Electron transport]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 952992920    8 VVVDTEKCKGCNLCVVECPTNVLalspnVNGKGYNYAYMEnpDACIGCANCGLVCPDNVITVYKV 72
Cdd:TIGR01944 108 ALIDEDNCIGCTKCIQACPVDAI-----VGAAKAMHTVIA--DECTGCDLCVEPCPTDCIEMIPV 165

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

                        10        20        30
                ....*....|....*....|....*....|....
gi 952992920  6 GAVVVDTEKCKGCNLCVVECPTNVLALSPNVNGK 39
Cdd:COG1149  34 GAPVVDPDLCTGCGACVGVCPTGAITLEEREAGK 67

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;

                         10        20        30
                 ....*....|....*....|....*....|....
gi 952992920   9 VVDTEKCKGCNLCVVECPT-NVLALSPNVNGKGY 41
Cdd:PRK08318 373 EVIEEECVGCNLCAHVCPVeGCITMGEVKFGKPY 406

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

                         10        20
                 ....*....|....*....|....*....
gi 952992920   6 GAVVVDTEKCKGCNLCVVECPTNVLALSP 34
Cdd:cd10560  101 GTVYIQPDICNGCGYCVAACPFGVIDRNE 129

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 952992920  14 KCKGCNLCVVECPTNVLALSPNVNG-KGYNYAYMeNPD--ACIGCAN-CGLVCPDNVITVYKVKLQEA 77
Cdd:cd16373   15 LCIRCGLCVEACPTGVIQPAGLEDGlEGGRTPYL-DPRegPCDLCCDaCVEVCPTGALRPLDLEEQKV 81

succinate dehydrogenase/fumarate reductase iron-sulfur subunit;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 952992920  15 CKGCNLCVVECPTNVLA---LSPNVNGKGYNYAY--------------MENPDACIGCANCGLVCPDNV 66
Cdd:PRK12576 154 CIWCGLCVSACPVVAIDpefLGPAAHAKGYRFLAdprdtiteermkilIDSSWRCTYCYSCSNVCPRDI 222

NADH dehydrogenase subunit I

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 952992920  13 EKCKGCNLCVVECPTNVlalsPNVN-------GKGYNYAYMENPDACIGCANCGLVCPDN 65
Cdd:CHL00014  59 DKCIACEVCVRVCPIDL----PVVDwkletdiRKKRLLNYSIDFGVCIFCGNCVEYCPTN 114

4Fe-4S binding domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich.

                         10        20
                 ....*....|....*....|...
gi 952992920   8 VVVDTEKCKGCNLCVVECPTNVL 30
Cdd:pfam00037  1 VVIDEEKCIGCGACVEVCPVGAI 23