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Conserved domains on  [gi|343098758|emb|CCA63472|]
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nitrogenase Fe protein, partial [alpha proteobacterium R45977]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 1-58 3.27e-27

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member pfam00142:

Pssm-ID: 476819  Cd Length: 271  Bit Score: 98.28  E-value: 3.27e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 343098758    1 IVGCDPKADSTRLILNSKAQDTVLDLAA**GSVEBLELEDVLKIGYKGIKCVESGGPE 58
Cdd:pfam00142  33 VVGCDPKADSTRLLLGGKLQPTVLDTAREKGYVEDVEVEDVVYKGYGGVKCVESGGPE 90
 
Name Accession Description Interval E-value
Fer4_NifH pfam00142
4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family;
1-58 3.27e-27

4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family;


Pssm-ID: 395090  Cd Length: 271  Bit Score: 98.28  E-value: 3.27e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 343098758    1 IVGCDPKADSTRLILNSKAQDTVLDLAA**GSVEBLELEDVLKIGYKGIKCVESGGPE 58
Cdd:pfam00142  33 VVGCDPKADSTRLLLGGKLQPTVLDTAREKGYVEDVEVEDVVYKGYGGVKCVESGGPE 90
NifH cd02040
nitrogenase component II NifH; NifH gene encodes component II (iron protein) of nitrogenase. ...
 1-58 1.82e-26

nitrogenase component II NifH; NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.


Pssm-ID: 349759  Cd Length: 265  Bit Score: 96.04  E-value: 1.82e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 343098758   1 IVGCDPKADSTRLILNSKAQDTVLDLAA**GSVEblELEDVLKIGYKGIKCVESGGPE 58
Cdd:cd02040   33 HVGCDPKADSTRLLLGGKAIPTVLDTLREKGEVE--ELEDVIKEGFNGIKCVESGGPE 88
nifH PRK13233
nitrogenase iron protein;
1-58 2.04e-19

nitrogenase iron protein;


Pssm-ID: 183905  Cd Length: 275  Bit Score: 77.94  E-value: 2.04e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 343098758   1 IVGCDPKADSTRLILNSKAQDTVLDLAA**GSvEBLELEDVLKIGYKGIKCVESGGPE 58
Cdd:PRK13233  36 IHGCDPKADSTRLILGGKPQTTMMDTLRELGE-EKVTPDKVIKTGFKDIRCVESGGPE 92
 
Name Accession Description Interval E-value
Fer4_NifH pfam00142
4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family;
1-58 3.27e-27

4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family;


Pssm-ID: 395090  Cd Length: 271  Bit Score: 98.28  E-value: 3.27e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 343098758    1 IVGCDPKADSTRLILNSKAQDTVLDLAA**GSVEBLELEDVLKIGYKGIKCVESGGPE 58
Cdd:pfam00142  33 VVGCDPKADSTRLLLGGKLQPTVLDTAREKGYVEDVEVEDVVYKGYGGVKCVESGGPE 90
NifH cd02040
nitrogenase component II NifH; NifH gene encodes component II (iron protein) of nitrogenase. ...
 1-58 1.82e-26

nitrogenase component II NifH; NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.


Pssm-ID: 349759  Cd Length: 265  Bit Score: 96.04  E-value: 1.82e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 343098758   1 IVGCDPKADSTRLILNSKAQDTVLDLAA**GSVEblELEDVLKIGYKGIKCVESGGPE 58
Cdd:cd02040   33 HVGCDPKADSTRLLLGGKAIPTVLDTLREKGEVE--ELEDVIKEGFNGIKCVESGGPE 88
nifH PRK13233
nitrogenase iron protein;
1-58 2.04e-19

nitrogenase iron protein;


Pssm-ID: 183905  Cd Length: 275  Bit Score: 77.94  E-value: 2.04e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 343098758   1 IVGCDPKADSTRLILNSKAQDTVLDLAA**GSvEBLELEDVLKIGYKGIKCVESGGPE 58
Cdd:PRK13233  36 IHGCDPKADSTRLILGGKPQTTMMDTLRELGE-EKVTPDKVIKTGFKDIRCVESGGPE 92
NifH-like cd02117
NifH family; This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) ...
 1-58 3.95e-18

NifH family; This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase, and the BchX subunit of the Chlorophyllide reductase. Members of this family use energy from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for substrate reduction


Pssm-ID: 349761  Cd Length: 266  Bit Score: 74.32  E-value: 3.95e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 343098758   1 IVGCDPKADSTRLILNSKAQDTVLDLAA**GSVEBLELEDVLKIGYKGIKCVESGGPE 58
Cdd:cd02117   33 HVGCDPKHDSTLLLTGGKVPPTIDEMLTEDGTAEELRREDLLFSGFNGVDCVEAGGPE 90
PRK13230 PRK13230
nitrogenase reductase-like protein; Reviewed
 1-58 2.20e-13

nitrogenase reductase-like protein; Reviewed


Pssm-ID: 183903  Cd Length: 279  Bit Score: 61.71  E-value: 2.20e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 343098758   1 IVGCDPKADSTRLILNSKAqDTVLDLAA**GsVEBLELEDVLKIGYKGIKCVESGGPE 58
Cdd:PRK13230  34 VVGCDPKADCTRNLVGEKI-PTVLDVLREKG-IDNLGLEDIIYEGFNGIYCVESGGPE 89
chlL PRK13185
protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional
 2-57 4.14e-11

protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional


Pssm-ID: 237293  Cd Length: 270  Bit Score: 55.35  E-value: 4.14e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 343098758   2 VGCDPKADSTrLILNSKAQDTVLD-LAA**GSVEBLELEDVLKIGYKGIKCVESGGP 57
Cdd:PRK13185  36 IGCDPKHDST-FTLTGKLVPTVIDiLEEVDFHSEELRPEDFVYEGYNGVDCVEAGGP 91
Bchl-like cd02032
L-subunit of protochlorophyllide reductase; This family of proteins contains BchL and ChlL. ...
 2-57 2.91e-10

L-subunit of protochlorophyllide reductase; This family of proteins contains BchL and ChlL. Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.


Pssm-ID: 349752  Cd Length: 267  Bit Score: 53.07  E-value: 2.91e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 343098758   2 VGCDPKADSTrLILNSKAQDTVLD-LAA**GSVEBLELEDVLKIGYKGIKCVESGGP 57
Cdd:cd02032   34 IGCDPKHDST-FTLTGFLIPTVIDvLQSVDFHYEEVWPEDVIFTGYGGVDCVEAGGP 89
PRK13231 PRK13231
nitrogenase reductase-like protein; Reviewed
 1-58 1.58e-09

nitrogenase reductase-like protein; Reviewed


Pssm-ID: 183904  Cd Length: 264  Bit Score: 50.95  E-value: 1.58e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 343098758   1 IVGCDPKADSTRlILNSKAQDTVLDLAA**gsvEBLELEDVLKIGYKGIKCVESGGPE 58
Cdd:PRK13231  34 VIGCDPKADTTR-TLCGKRIPTVLDTLKDN---RKPELEDIIHEGFNGILCVESGGPE 87
chlL CHL00072
photochlorophyllide reductase subunit L
 2-57 1.69e-07

photochlorophyllide reductase subunit L


Pssm-ID: 177011  Cd Length: 290  Bit Score: 45.50  E-value: 1.69e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 343098758   2 VGCDPKADSTrLILNSKAQDTVLD-LAA**GSVEBLELEDVLKIGYKGIKCVESGGP 57
Cdd:CHL00072  34 IGCDPKHDST-FTLTGFLIPTIIDtLQSKDYHYEDVWPEDVIYKGYGGVDCVEAGGP 89
BchX cd02033
X-subunit of protochlorophyllide reductase; Chlorophyllide reductase converts chlorophylls ...
 1-58 1.71e-04

X-subunit of protochlorophyllide reductase; Chlorophyllide reductase converts chlorophylls into bacteriochlorophylls by reducing the chlorin B-ring. This family contains the X subunit of this three-subunit enzyme. Sequence and structure similarity between bchX, protochlorophyllide reductase L subunit (bchL and chlL) and nitrogenase Fe protein (nifH gene) suggest their functional similarity. Members of the BchX family serve as the unique electron donors to their respective catalytic subunits (bchN-bchB, bchY-bchZ and nitrogenase component 1). Mechanistically, they hydrolyze ATP and transfer electrons through a Fe4-S4 cluster.


Pssm-ID: 349753  Cd Length: 329  Bit Score: 36.73  E-value: 1.71e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 343098758   1 IVGCDPKADSTRLILNSKAQDTVLDLAA**GSV-EBLELEDV-LKIGykGIKCVESGGPE 58
Cdd:cd02033   64 LIGCDPKSDTTSLLFGGKACPTIIETSTRKKLAgEEVKIGDVcFKRG--GVFAMELGGPE 121
 
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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