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Conserved domains on  [gi|146327060|gb|AAI41857|]
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CBWD5 protein [Homo sapiens]

Protein Classification

GTP-binding protein( domain architecture ID 10123105)

GTP-binding protein similar to GTPase YjiA, a GTP dependent regulatory protein, and CobW, which is involved in the synthesis of cobalamin

Gene Ontology:  GO:0005525|GO:0003924
PubMed:  11916378

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CobW-like cd03112
cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino ...
 43-176 5.52e-66

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: 200.44  E-value: 5.52e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060  43 PVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNESGEGSaLEKSLAVSQGGelYEEWLELRNGCLCCSVKDNGLRAIEN 122
Cdd:cd03112    1 PVTLLTGFLGAGKTTLLNHILSEQHGKRIAVIVNEFGEVG-IDAALLADSGG--GEEVVELSNGCICCTLKGDLVKALEQ 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 146327060 123 LMQKKGKFDDILLETTGLADPGAVTSMFWVDAELGSDIYLDGIITIVDSKYGLK 176
Cdd:cd03112   78 LLERRGKFDYILIETTGLADPGPIAQTLWSDEELESRLRLDGVVTVVDAKNFLK 131
 
Name Accession Description Interval E-value
CobW-like cd03112
cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino ...
 43-176 5.52e-66

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: 200.44  E-value: 5.52e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060  43 PVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNESGEGSaLEKSLAVSQGGelYEEWLELRNGCLCCSVKDNGLRAIEN 122
Cdd:cd03112    1 PVTLLTGFLGAGKTTLLNHILSEQHGKRIAVIVNEFGEVG-IDAALLADSGG--GEEVVELSNGCICCTLKGDLVKALEQ 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 146327060 123 LMQKKGKFDDILLETTGLADPGAVTSMFWVDAELGSDIYLDGIITIVDSKYGLK 176
Cdd:cd03112   78 LLERRGKFDYILIETTGLADPGPIAQTLWSDEELESRLRLDGVVTVVDAKNFLK 131
YejR COG0523
Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction ...
 40-176 2.68e-47

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


Pssm-ID: 440289 [Multi-domain]  Cd Length: 318  Bit Score: 156.49  E-value: 2.68e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060  40 AKIPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNESGE---GSALekslaVSQGGelyEEWLELRNGCLCCSVKDNG 116
Cdd:COG0523    2 KRIPVTVLTGFLGAGKTTLLNHLLANPEGRRIAVIVNEFGEvgiDAAL-----VRDTD---EEIVELSNGCICCTLREDL 73

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060 117 LRAIENLMqKKGKFDDILLETTGLADPGAVTSMFWVDAELGSDIYLDGIITIVDSKYGLK 176
Cdd:COG0523   74 LPALRRLL-RRGRFDRLLIETTGLADPAPVAQTFTFDPELRDRLRLDGVVTVVDARNLLD 132
cobW pfam02492
CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase ...
 43-172 1.14e-43

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: 143.16  E-value: 1.14e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060   43 PVTIITGYLGAGKTTLLNYIL-TEQHSKRVAVILNESGEGSaLEKSLAVSQGgelyEEWLELRNGCLCCSVKDNGLRAIE 121
Cdd:pfam02492   1 PVTVITGFLGSGKTTLLNHLLkQNRAGLRIAVIVNEFGETG-IDAELLSETG----VLIVELSNGCICCTIREDLSMALE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 146327060  122 NLMQKKGKFDDILLETTGLADPGAVTSMFWVDaELGSDIYLDGIITIVDSK 172
Cdd:pfam02492  76 ALLEREGRLDVIFIETTGLAEPAPVAQTFLSP-ELRSPVLLDGVITVVDAA 125
CobW TIGR02475
cobalamin biosynthesis protein CobW; The family of proteins identified by this model is ...
 40-171 8.76e-32

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: 116.77  E-value: 8.76e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060   40 AKIPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNESGE----GSALeKSLAVSQGGElyEEWLELRNGCLCCSVKDN 115
Cdd:TIGR02475   2 AKIPVTIVTGFLGAGKTTLIRHLLQNAAGRRIAVIVNEFGDlgidGEIL-KACGIEGCSE--ENIVELANGCICCTVADD 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 146327060  116 GLRAIENLMQKKGKFDDILLETTGLADPGAVTSMF-WvdAELGSDIYLDGIITIVDS 171
Cdd:TIGR02475  79 FIPTMTKLLARRQRPDHILIETSGLALPKPLVQAFqW--PEIRSRVTVDGVVTVVDG 133
PRK11537 PRK11537
putative GTP-binding protein YjiA; Provisional
 42-171 6.97e-29

putative GTP-binding protein YjiA; Provisional


Pssm-ID: 183183 [Multi-domain]  Cd Length: 318  Bit Score: 108.64  E-value: 6.97e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060  42 IPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNESGEGSALEKSLavsqgGELYEEWLELRNGCLCCS----VKDNGL 117
Cdd:PRK11537   4 IAVTLLTGFLGAGKTTLLRHILNEQHGYKIAVIENEFGEVSVDDQLI-----GDRATQIKTLTNGCICCSrsneLEDALL 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 146327060 118 RAIENLMQKKGKFDDILLETTGLADPGAVTSMFWVDAELGSDIYLDGIITIVDS 171
Cdd:PRK11537  79 DLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQRYLLDGVIALVDA 132
 
Name Accession Description Interval E-value
CobW-like cd03112
cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino ...
 43-176 5.52e-66

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: 200.44  E-value: 5.52e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060  43 PVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNESGEGSaLEKSLAVSQGGelYEEWLELRNGCLCCSVKDNGLRAIEN 122
Cdd:cd03112    1 PVTLLTGFLGAGKTTLLNHILSEQHGKRIAVIVNEFGEVG-IDAALLADSGG--GEEVVELSNGCICCTLKGDLVKALEQ 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 146327060 123 LMQKKGKFDDILLETTGLADPGAVTSMFWVDAELGSDIYLDGIITIVDSKYGLK 176
Cdd:cd03112   78 LLERRGKFDYILIETTGLADPGPIAQTLWSDEELESRLRLDGVVTVVDAKNFLK 131
YejR COG0523
Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction ...
 40-176 2.68e-47

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


Pssm-ID: 440289 [Multi-domain]  Cd Length: 318  Bit Score: 156.49  E-value: 2.68e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060  40 AKIPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNESGE---GSALekslaVSQGGelyEEWLELRNGCLCCSVKDNG 116
Cdd:COG0523    2 KRIPVTVLTGFLGAGKTTLLNHLLANPEGRRIAVIVNEFGEvgiDAAL-----VRDTD---EEIVELSNGCICCTLREDL 73

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060 117 LRAIENLMqKKGKFDDILLETTGLADPGAVTSMFWVDAELGSDIYLDGIITIVDSKYGLK 176
Cdd:COG0523   74 LPALRRLL-RRGRFDRLLIETTGLADPAPVAQTFTFDPELRDRLRLDGVVTVVDARNLLD 132
cobW pfam02492
CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase ...
 43-172 1.14e-43

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: 143.16  E-value: 1.14e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060   43 PVTIITGYLGAGKTTLLNYIL-TEQHSKRVAVILNESGEGSaLEKSLAVSQGgelyEEWLELRNGCLCCSVKDNGLRAIE 121
Cdd:pfam02492   1 PVTVITGFLGSGKTTLLNHLLkQNRAGLRIAVIVNEFGETG-IDAELLSETG----VLIVELSNGCICCTIREDLSMALE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 146327060  122 NLMQKKGKFDDILLETTGLADPGAVTSMFWVDaELGSDIYLDGIITIVDSK 172
Cdd:pfam02492  76 ALLEREGRLDVIFIETTGLAEPAPVAQTFLSP-ELRSPVLLDGVITVVDAA 125
CobW TIGR02475
cobalamin biosynthesis protein CobW; The family of proteins identified by this model is ...
 40-171 8.76e-32

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: 116.77  E-value: 8.76e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060   40 AKIPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNESGE----GSALeKSLAVSQGGElyEEWLELRNGCLCCSVKDN 115
Cdd:TIGR02475   2 AKIPVTIVTGFLGAGKTTLIRHLLQNAAGRRIAVIVNEFGDlgidGEIL-KACGIEGCSE--ENIVELANGCICCTVADD 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 146327060  116 GLRAIENLMQKKGKFDDILLETTGLADPGAVTSMF-WvdAELGSDIYLDGIITIVDS 171
Cdd:TIGR02475  79 FIPTMTKLLARRQRPDHILIETSGLALPKPLVQAFqW--PEIRSRVTVDGVVTVVDG 133
PRK11537 PRK11537
putative GTP-binding protein YjiA; Provisional
 42-171 6.97e-29

putative GTP-binding protein YjiA; Provisional


Pssm-ID: 183183 [Multi-domain]  Cd Length: 318  Bit Score: 108.64  E-value: 6.97e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146327060  42 IPVTIITGYLGAGKTTLLNYILTEQHSKRVAVILNESGEGSALEKSLavsqgGELYEEWLELRNGCLCCS----VKDNGL 117
Cdd:PRK11537   4 IAVTLLTGFLGAGKTTLLRHILNEQHGYKIAVIENEFGEVSVDDQLI-----GDRATQIKTLTNGCICCSrsneLEDALL 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 146327060 118 RAIENLMQKKGKFDDILLETTGLADPGAVTSMFWVDAELGSDIYLDGIITIVDS 171
Cdd:PRK11537  79 DLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQRYLLDGVIALVDA 132
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 43-73 2.93e-04

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: 2.93e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 146327060  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 3.28e-03

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: 36.38  E-value: 3.28e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 146327060  43 PVTIITGYLGAGKTTLLNYILT--EQHSKRVAV 73
Cdd:cd17933   13 RVSVLTGGAGTGKTTTLKALLAalEAEGKRVVL 45
 
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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