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Conserved domains on  [gi|2178610477|ref|NP_001386725|]
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zinc-regulated GTPase metalloprotein activator 1A isoform 4 [Homo sapiens]

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 ...
43-113 7.50e-36

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 cd03112:

Pssm-ID: 476819  Cd Length: 198  Bit Score: 121.09  E-value: 7.50e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2178610477  43 PVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNEFGEGSaLEKSLAVSQGGelYEEWLELRNGCLCCSVK 113
Cdd:cd03112     1 PVTLLTGFLGAGKTTLLNHILSEQHGKRIAVIVNEFGEVG-IDAALLADSGG--GEEVVELSNGCICCTLK 68
 
Name Accession Description Interval E-value
CobW-like cd03112
cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino ...
43-113 7.50e-36

cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.


Pssm-ID: 349766  Cd Length: 198  Bit Score: 121.09  E-value: 7.50e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2178610477  43 PVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNEFGEGSaLEKSLAVSQGGelYEEWLELRNGCLCCSVK 113
Cdd:cd03112     1 PVTLLTGFLGAGKTTLLNHILSEQHGKRIAVIVNEFGEVG-IDAALLADSGG--GEEVVELSNGCICCTLK 68
YejR COG0523
Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction ...
40-112 2.45e-28

Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction only];


Pssm-ID: 440289 [Multi-domain]  Cd Length: 318  Bit Score: 104.48  E-value: 2.45e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2178610477  40 AKIPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNEFGE---GSALekslaVSQGGelyEEWLELRNGCLCCSV 112
Cdd:COG0523     2 KRIPVTVLTGFLGAGKTTLLNHLLANPEGRRIAVIVNEFGEvgiDAAL-----VRDTD---EEIVELSNGCICCTL 69
cobW pfam02492
CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase ...
43-113 4.26e-25

CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans.


Pssm-ID: 396860  Cd Length: 179  Bit Score: 93.09  E-value: 4.26e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2178610477  43 PVTIITGYLGAGKTTLLNYIL-TEQHSKRVAVILNEFGEGSaLEKSLAVSQGgelyEEWLELRNGCLCCSVK 113
Cdd:pfam02492   1 PVTVITGFLGSGKTTLLNHLLkQNRAGLRIAVIVNEFGETG-IDAELLSETG----VLIVELSNGCICCTIR 67
CobW TIGR02475
cobalamin biosynthesis protein CobW; The family of proteins identified by this model is ...
40-112 1.41e-20

cobalamin biosynthesis protein CobW; The family of proteins identified by this model is generally found proximal to the trimeric cobaltochelatase subunit CobN which is essential for vitamin B12 (cobalamin) biosynthesis. The protein contains an P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. A broader CobW family is delineated by two Pfam models which identify the N- and C-terminal domains (pfam02492 and pfam07683). [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]


Pssm-ID: 274151 [Multi-domain]  Cd Length: 341  Bit Score: 84.03  E-value: 1.41e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2178610477  40 AKIPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNEFGE----GSALeKSLAVSQGGElyEEWLELRNGCLCCSV 112
Cdd:TIGR02475   2 AKIPVTIVTGFLGAGKTTLIRHLLQNAAGRRIAVIVNEFGDlgidGEIL-KACGIEGCSE--ENIVELANGCICCTV 75
PRK11537 PRK11537
putative GTP-binding protein YjiA; Provisional
42-111 1.17e-18

putative GTP-binding protein YjiA; Provisional


Pssm-ID: 183183 [Multi-domain]  Cd Length: 318  Bit Score: 78.59  E-value: 1.17e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2178610477  42 IPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNEFGEGSALEKSLavsqgGELYEEWLELRNGCLCCS 111
Cdd:PRK11537    4 IAVTLLTGFLGAGKTTLLRHILNEQHGYKIAVIENEFGEVSVDDQLI-----GDRATQIKTLTNGCICCS 68
 
Name Accession Description Interval E-value
CobW-like cd03112
cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino ...
43-113 7.50e-36

cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.


Pssm-ID: 349766  Cd Length: 198  Bit Score: 121.09  E-value: 7.50e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2178610477  43 PVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNEFGEGSaLEKSLAVSQGGelYEEWLELRNGCLCCSVK 113
Cdd:cd03112     1 PVTLLTGFLGAGKTTLLNHILSEQHGKRIAVIVNEFGEVG-IDAALLADSGG--GEEVVELSNGCICCTLK 68
YejR COG0523
Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction ...
40-112 2.45e-28

Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction only];


Pssm-ID: 440289 [Multi-domain]  Cd Length: 318  Bit Score: 104.48  E-value: 2.45e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2178610477  40 AKIPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNEFGE---GSALekslaVSQGGelyEEWLELRNGCLCCSV 112
Cdd:COG0523     2 KRIPVTVLTGFLGAGKTTLLNHLLANPEGRRIAVIVNEFGEvgiDAAL-----VRDTD---EEIVELSNGCICCTL 69
cobW pfam02492
CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase ...
43-113 4.26e-25

CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans.


Pssm-ID: 396860  Cd Length: 179  Bit Score: 93.09  E-value: 4.26e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2178610477  43 PVTIITGYLGAGKTTLLNYIL-TEQHSKRVAVILNEFGEGSaLEKSLAVSQGgelyEEWLELRNGCLCCSVK 113
Cdd:pfam02492   1 PVTVITGFLGSGKTTLLNHLLkQNRAGLRIAVIVNEFGETG-IDAELLSETG----VLIVELSNGCICCTIR 67
CobW TIGR02475
cobalamin biosynthesis protein CobW; The family of proteins identified by this model is ...
40-112 1.41e-20

cobalamin biosynthesis protein CobW; The family of proteins identified by this model is generally found proximal to the trimeric cobaltochelatase subunit CobN which is essential for vitamin B12 (cobalamin) biosynthesis. The protein contains an P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. A broader CobW family is delineated by two Pfam models which identify the N- and C-terminal domains (pfam02492 and pfam07683). [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]


Pssm-ID: 274151 [Multi-domain]  Cd Length: 341  Bit Score: 84.03  E-value: 1.41e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2178610477  40 AKIPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNEFGE----GSALeKSLAVSQGGElyEEWLELRNGCLCCSV 112
Cdd:TIGR02475   2 AKIPVTIVTGFLGAGKTTLIRHLLQNAAGRRIAVIVNEFGDlgidGEIL-KACGIEGCSE--ENIVELANGCICCTV 75
PRK11537 PRK11537
putative GTP-binding protein YjiA; Provisional
42-111 1.17e-18

putative GTP-binding protein YjiA; Provisional


Pssm-ID: 183183 [Multi-domain]  Cd Length: 318  Bit Score: 78.59  E-value: 1.17e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2178610477  42 IPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNEFGEGSALEKSLavsqgGELYEEWLELRNGCLCCS 111
Cdd:PRK11537    4 IAVTLLTGFLGAGKTTLLRHILNEQHGYKIAVIENEFGEVSVDDQLI-----GDRATQIKTLTNGCICCS 68
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
43-73 6.47e-05

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 40.35  E-value: 6.47e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2178610477  43 PVTIITGYLGAGKTTLLNYIL--TEQHSKRVAV 73
Cdd:COG0507   141 RVSVLTGGAGTGKTTTLRALLaaLEALGLRVAL 173
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
43-73 7.66e-04

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 36.76  E-value: 7.66e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2178610477  43 PVTIITGYLGAGKTTLLNYILT--EQHSKRVAV 73
Cdd:cd17933    13 RVSVLTGGAGTGKTTTLKALLAalEAEGKRVVL 45
NACHT COG5635
Predicted NTPase, NACHT family domain [Signal transduction mechanisms];
23-106 1.01e-03

Predicted NTPase, NACHT family domain [Signal transduction mechanisms];


Pssm-ID: 444362 [Multi-domain]  Cd Length: 935  Bit Score: 37.09  E-value: 1.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2178610477  23 VPIETTQSEEEEKSGLGAKIPVTIITGYLGAGKTTLLNYI---LTEQHSKRVAVI-----LNEFGEGSALEKSLA--VSQ 92
Cdd:COG5635   161 LNLLERIESLKRLELLEAKKKRLLILGEPGSGKTTLLRYLaleLAERYLDAEDPIpilieLRDLAEEASLEDLLAeaLEK 240
                          90
                  ....*....|....*.
gi 2178610477  93 GGELYEEWLE--LRNG 106
Cdd:COG5635   241 RGGEPEDALErlLRNG 256
MobB COG1763
Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme transport and metabolism]; ...
47-74 7.18e-03

Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme transport and metabolism]; Molybdopterin-guanine dinucleotide biosynthesis protein is part of the Pathway/BioSystem: Molybdopterin biosynthesis


Pssm-ID: 441369 [Multi-domain]  Cd Length: 162  Bit Score: 34.00  E-value: 7.18e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 2178610477  47 ITGYLGAGKTTLLNYILTE--QHSKRVAVI 74
Cdd:COG1763     6 IVGYSGSGKTTLLEKLIPElkARGLRVGTI 35
PRK13949 PRK13949
shikimate kinase; Provisional
47-80 9.90e-03

shikimate kinase; Provisional


Pssm-ID: 140006 [Multi-domain]  Cd Length: 169  Bit Score: 33.93  E-value: 9.90e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2178610477  47 ITGYLGAGKTTL--------------LNYILTEQHSKRVAVILNEFGE 80
Cdd:PRK13949    6 LVGYMGAGKTTLgkalarelglsfidLDFFIENRFHKTVGDIFAERGE 53
 
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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