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Conserved domains on  [gi|1739014304|emb|VAU12900|]
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nifX protein [Klebsiella variicola]

Protein Classification

NifB/NifX family molybdenum-iron cluster-binding protein( domain architecture ID 10096243)

NifB/NifX family molybdenum-iron cluster-binding protein may serve as a transient reservoir of FeMo-co (the iron-molybdenum cofactor of nitrogenase) precursors and help control their flux during FeMo-co synthesis; similar to Azotobacter vinelandii NafY protein (nitrogenase accessory factor Y)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NifX cd00853
NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and ...
 19-119 1.90e-37

NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein is part of the nitrogen fixation gene cluster in nitrogen-fixing bacteria and has sequence similarity to other members of the cluster.


:

Pssm-ID: 238433  Cd Length: 102  Bit Score: 123.87  E-value: 1.90e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  19 KVAFASSDYRHVDQHFGATPRLVVYGVKADRVTLLRVVEFPVAS-GHQTEKIAERIHALEDCVTLFCVAIGEAVFRQLLQ 97
Cdd:cd00853     1 KVAFASSDLERVDAHFGSARRFAIYEVSPEGARLVEVRSFGGALeDGNEDKLAARLEALEDCAILYCAAIGGPAAARLVR 80

                          90       100
                  ....*....|....*....|..
gi 1739014304  98 VGVRAERVPDQTTILGLLQEIQ 119
Cdd:cd00853    81 AGIHPIKVPEGEPIAELLEELQ 102
 
Name Accession Description Interval E-value
NifX cd00853
NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and ...
 19-119 1.90e-37

NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein is part of the nitrogen fixation gene cluster in nitrogen-fixing bacteria and has sequence similarity to other members of the cluster.


Pssm-ID: 238433  Cd Length: 102  Bit Score: 123.87  E-value: 1.90e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  19 KVAFASSDYRHVDQHFGATPRLVVYGVKADRVTLLRVVEFPVAS-GHQTEKIAERIHALEDCVTLFCVAIGEAVFRQLLQ 97
Cdd:cd00853     1 KVAFASSDLERVDAHFGSARRFAIYEVSPEGARLVEVRSFGGALeDGNEDKLAARLEALEDCAILYCAAIGGPAAARLVR 80

                          90       100
                  ....*....|....*....|..
gi 1739014304  98 VGVRAERVPDQTTILGLLQEIQ 119
Cdd:cd00853    81 AGIHPIKVPEGEPIAELLEELQ 102
NifX COG1433
Predicted Fe-Mo cluster-binding protein, NifX family [Posttranslational modification, protein ...
 18-109 1.84e-17

Predicted Fe-Mo cluster-binding protein, NifX family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441042  Cd Length: 108  Bit Score: 73.00  E-value: 1.84e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  18 MKVAFASSDYRHVDQHFGATPRLVVYGVKADRVTLLRVVEFP-VASGHQTEKIAERIHAlEDCVTLFCVAIGEAVFRQLL 96
Cdd:COG1433     1 MKIAIPSDGGSRVSPHFGRAPYFLIYDVEDGEIVLVEVIENPgEAGGGAGGLLAQLLAE-LGVDVVIAGGIGPGALEALE 79

                          90
                  ....*....|...
gi 1739014304  97 QVGVRAERVPDQT 109
Cdd:COG1433    80 AAGIKVYTGAEGT 92
nifX TIGR02663
nitrogen fixation protein NifX; Members of this family are NifX proteins encoded within ...
 18-119 8.00e-17

nitrogen fixation protein NifX; Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation]


Pssm-ID: 131711  Cd Length: 119  Bit Score: 71.61  E-value: 8.00e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  18 MKVAFASSDYRHVDQHFGATPRLVVYGVKADRVTLLRVVEFPVASGHQTE--KIAERIHALEDCVTLFCVAIGEAVFRQL 95
Cdd:TIGR02663   1 MKVAFATQDLENLNAHFGSAKQFAIYDVTAEGARFVEAIQFDGASDEDGEedKIAPKIEALKDCAILYCLAIGGPAAAKV 80

                          90       100
                  ....*....|....*....|....
gi 1739014304  96 LQVGVRAERVPDQTTILGLLQEIQ 119
Cdd:TIGR02663  81 VAAKIHPIKVNEPESISELLERLQ 104
Nitro_FeMo-Co pfam02579
Dinitrogenase iron-molybdenum cofactor; This family contains several NIF (B, Y and X) proteins ...
 29-119 4.97e-12

Dinitrogenase iron-molybdenum cofactor; This family contains several NIF (B, Y and X) proteins which are iron-molybdenum cofactors (FeMo-co) in the dinitrogenase enzyme which catalyzes the reduction of dinitrogen to ammonium. Dinitrogenase is a hetero-tetrameric (alpha(2)beta(2)) enzyme which contains the iron-molybdenum cofactor (FeMo-co) at its active site.


Pssm-ID: 460602  Cd Length: 93  Bit Score: 58.42  E-value: 4.97e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  29 HVDQHFGATPRLVVYGVKADRVTLLRVVEFPV-ASGHQTEKIAERIHAlEDCVTLFCVAIGEAVFRQLLQVGVRAERVPD 107
Cdd:pfam02579   4 RVDQHFGRAPYFAIYDVEEGGVEVVENREPACaAGGGGGGKLAQLLAD-EGVDAVIVGGIGPNAAARLKAAGIKVYKGAG 82

                          90
                  ....*....|..
gi 1739014304 108 qTTILGLLQEIQ 119
Cdd:pfam02579  83 -GTVEEALEAYL 93
 
Name Accession Description Interval E-value
NifX cd00853
NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and ...
 19-119 1.90e-37

NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein is part of the nitrogen fixation gene cluster in nitrogen-fixing bacteria and has sequence similarity to other members of the cluster.


Pssm-ID: 238433  Cd Length: 102  Bit Score: 123.87  E-value: 1.90e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  19 KVAFASSDYRHVDQHFGATPRLVVYGVKADRVTLLRVVEFPVAS-GHQTEKIAERIHALEDCVTLFCVAIGEAVFRQLLQ 97
Cdd:cd00853     1 KVAFASSDLERVDAHFGSARRFAIYEVSPEGARLVEVRSFGGALeDGNEDKLAARLEALEDCAILYCAAIGGPAAARLVR 80

                          90       100
                  ....*....|....*....|..
gi 1739014304  98 VGVRAERVPDQTTILGLLQEIQ 119
Cdd:cd00853    81 AGIHPIKVPEGEPIAELLEELQ 102
NifX_NifB cd00562
This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, ...
 19-119 3.17e-25

This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea).


Pssm-ID: 238315  Cd Length: 102  Bit Score: 92.69  E-value: 3.17e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  19 KVAFASSDYRHVDQHFGATPRLVVYGVKADRVTLLRVVEFPVAS-GHQTEKIAERIHALEDCVTLFCVAIGEAVFRQLLQ 97
Cdd:cd00562     1 KIAVASSDGGRVDQHFGRAPEFLIYEVEPGGIKLVEVRENPAACgGGGEGKLAARLLALEGCDAVLVGGIGGPAAAKLEA 80

                          90       100
                  ....*....|....*....|..
gi 1739014304  98 VGVRAERVPDQTTILGLLQEIQ 119
Cdd:cd00562    81 AGIKPIKAAEGGTIEEALEALQ 102
NifX COG1433
Predicted Fe-Mo cluster-binding protein, NifX family [Posttranslational modification, protein ...
 18-109 1.84e-17

Predicted Fe-Mo cluster-binding protein, NifX family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441042  Cd Length: 108  Bit Score: 73.00  E-value: 1.84e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  18 MKVAFASSDYRHVDQHFGATPRLVVYGVKADRVTLLRVVEFP-VASGHQTEKIAERIHAlEDCVTLFCVAIGEAVFRQLL 96
Cdd:COG1433     1 MKIAIPSDGGSRVSPHFGRAPYFLIYDVEDGEIVLVEVIENPgEAGGGAGGLLAQLLAE-LGVDVVIAGGIGPGALEALE 79

                          90
                  ....*....|...
gi 1739014304  97 QVGVRAERVPDQT 109
Cdd:COG1433    80 AAGIKVYTGAEGT 92
nifX TIGR02663
nitrogen fixation protein NifX; Members of this family are NifX proteins encoded within ...
 18-119 8.00e-17

nitrogen fixation protein NifX; Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation]


Pssm-ID: 131711  Cd Length: 119  Bit Score: 71.61  E-value: 8.00e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  18 MKVAFASSDYRHVDQHFGATPRLVVYGVKADRVTLLRVVEFPVASGHQTE--KIAERIHALEDCVTLFCVAIGEAVFRQL 95
Cdd:TIGR02663   1 MKVAFATQDLENLNAHFGSAKQFAIYDVTAEGARFVEAIQFDGASDEDGEedKIAPKIEALKDCAILYCLAIGGPAAAKV 80

                          90       100
                  ....*....|....*....|....
gi 1739014304  96 LQVGVRAERVPDQTTILGLLQEIQ 119
Cdd:TIGR02663  81 VAAKIHPIKVNEPESISELLERLQ 104
Nitro_FeMo-Co pfam02579
Dinitrogenase iron-molybdenum cofactor; This family contains several NIF (B, Y and X) proteins ...
 29-119 4.97e-12

Dinitrogenase iron-molybdenum cofactor; This family contains several NIF (B, Y and X) proteins which are iron-molybdenum cofactors (FeMo-co) in the dinitrogenase enzyme which catalyzes the reduction of dinitrogen to ammonium. Dinitrogenase is a hetero-tetrameric (alpha(2)beta(2)) enzyme which contains the iron-molybdenum cofactor (FeMo-co) at its active site.


Pssm-ID: 460602  Cd Length: 93  Bit Score: 58.42  E-value: 4.97e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  29 HVDQHFGATPRLVVYGVKADRVTLLRVVEFPV-ASGHQTEKIAERIHAlEDCVTLFCVAIGEAVFRQLLQVGVRAERVPD 107
Cdd:pfam02579   4 RVDQHFGRAPYFAIYDVEEGGVEVVENREPACaAGGGGGGKLAQLLAD-EGVDAVIVGGIGPNAAARLKAAGIKVYKGAG 82

                          90
                  ....*....|..
gi 1739014304 108 qTTILGLLQEIQ 119
Cdd:pfam02579  83 -GTVEEALEAYL 93
NifB cd00852
NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and ...
 19-102 6.68e-12

NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of nitrogen fixation in bacteria. This domain is sometimes found fused to a N-terminal domain (the Radical SAM domain) in nifB-like proteins.


Pssm-ID: 238432  Cd Length: 106  Bit Score: 58.40  E-value: 6.68e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  19 KVAFASSDYRHVDQHFGATPRLVVYGVKADRVTLL--RVVEFP---VASGHQTEKIAERIHALEDCVTLFCVAIGEAVFR 93
Cdd:cd00852     1 LVAVASKGGGRVNQHFGHATEFQIYEVSGSGVKFVehRKVDPYcggGDCGDEEDRLDAIIKLLSDCDAVLCAKIGDEPKE 80


                  ....*....
gi 1739014304  94 QLLQVGVRA 102
Cdd:cd00852    81 KLEEAGIEV 89
MTH1175 cd00851
This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding ...
 18-109 8.67e-06

This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea).


Pssm-ID: 238431  Cd Length: 103  Bit Score: 42.26  E-value: 8.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739014304  18 MKVAFASSDYR-HVDQHFGATPRLVVYGVKADRVTLLRVVEFPVA--SGHQTEKIAERIHAlEDCVTLFCVAIGEAVFRQ 94
Cdd:cd00851     1 MKIAIPVSGNGgKVSPHFGRAPYFLIYDVETGKIKNVEVIENPAAhaTGGAGGKAAEFLAD-EGVDVVIVGGIGPRALNK 79

                          90
                  ....*....|....*
gi 1739014304  95 LLQVGVRAERVPDQT 109
Cdd:cd00851    80 LRNAGIKVYKGAEGT 94
 
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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