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Conserved domains on  [gi|490374875|ref|WP_004254476|]
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MULTISPECIES: hypothetical protein [Providencia]

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 ...
 2-176 3.63e-26

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 PRK08118:

Pssm-ID: 476819  Cd Length: 167  Bit Score: 97.76  E-value: 3.63e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490374875   2 KINIIGTSGSGKSTLCQQLSLLLNVPSIELDSLYWLANWQGSSddalNQKLTAALDKAVSG--WVLDGNYTRTQPIKWKE 79
Cdd:PRK08118   3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWKPNWEGVP----KEEQITVQNELVKEdeWIIDGNYGGTMDIRLNA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490374875  80 VDMVVWLDYSLPRTLYQSITRTLS-RIRSGQELwaNTGNKERWKNAFFSrdsiilWLLKtyYPNKKR--------NLSHM 150
Cdd:PRK08118  79 ADTIIFLDIPRTICLYRAFKRRVQyRGKTRPDM--GAGCEEKFDLQFFK------WIWE--YPKTKRpsilkrlnQLSEE 148

                        170       180
                 ....*....|....*....|....*.
gi 490374875 151 ANInlrhiqfVRLTSPKETNLFLQQM 176
Cdd:PRK08118 149 KDI-------VILKSRNEVRLFLEKI 167
 
Name Accession Description Interval E-value
PRK08118 PRK08118
DNA topology modulation protein;
2-176 3.63e-26

DNA topology modulation protein;


Pssm-ID: 181235  Cd Length: 167  Bit Score: 97.76  E-value: 3.63e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490374875   2 KINIIGTSGSGKSTLCQQLSLLLNVPSIELDSLYWLANWQGSSddalNQKLTAALDKAVSG--WVLDGNYTRTQPIKWKE 79
Cdd:PRK08118   3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWKPNWEGVP----KEEQITVQNELVKEdeWIIDGNYGGTMDIRLNA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490374875  80 VDMVVWLDYSLPRTLYQSITRTLS-RIRSGQELwaNTGNKERWKNAFFSrdsiilWLLKtyYPNKKR--------NLSHM 150
Cdd:PRK08118  79 ADTIIFLDIPRTICLYRAFKRRVQyRGKTRPDM--GAGCEEKFDLQFFK------WIWE--YPKTKRpsilkrlnQLSEE 148

                        170       180
                 ....*....|....*....|....*.
gi 490374875 151 ANInlrhiqfVRLTSPKETNLFLQQM 176
Cdd:PRK08118 149 KDI-------VILKSRNEVRLFLEKI 167
UMPK cd02023
Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or ...
 3-35 3.58e-04

Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.


Pssm-ID: 238981 [Multi-domain]  Cd Length: 198  Bit Score: 39.46  E-value: 3.58e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 490374875   3 INIIGTSGSGKSTLCQQLSLLLNVPS---IELDSLY 35
Cdd:cd02023    2 IGIAGGSGSGKTTVAEEIIEQLGNPKvviISQDSYY 37
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 1-30 8.48e-04

Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase is part of the Pathway/BioSystem: NAD biosynthesis


Pssm-ID: 442405 [Multi-domain]  Cd Length: 178  Bit Score: 38.26  E-value: 8.48e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 490374875   1 MKINIIGTSGSGKSTLCQQLSLLLNVPSIE 30
Cdd:COG3172    9 KKIVLLGAESTGKTTLARALAAHYNTPWVP 38
PduV-EutP pfam10662
Ethanolamine utilization - propanediol utilization; Members of this family function in ...
 2-21 6.88e-03

Ethanolamine utilization - propanediol utilization; Members of this family function in ethanolamine and propanediol degradation pathways. PduV may be involved in the association of the bacterial microcompartments (BMCs) to filaments.


Pssm-ID: 402341 [Multi-domain]  Cd Length: 137  Bit Score: 35.33  E-value: 6.88e-03
                          10        20
                  ....*....|....*....|
gi 490374875    2 KINIIGTSGSGKSTLCQQLS 21
Cdd:pfam10662   3 KIMLIGPTGCGKTTLCQALS 22
 
Name Accession Description Interval E-value
PRK08118 PRK08118
DNA topology modulation protein;
2-176 3.63e-26

DNA topology modulation protein;


Pssm-ID: 181235  Cd Length: 167  Bit Score: 97.76  E-value: 3.63e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490374875   2 KINIIGTSGSGKSTLCQQLSLLLNVPSIELDSLYWLANWQGSSddalNQKLTAALDKAVSG--WVLDGNYTRTQPIKWKE 79
Cdd:PRK08118   3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWKPNWEGVP----KEEQITVQNELVKEdeWIIDGNYGGTMDIRLNA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490374875  80 VDMVVWLDYSLPRTLYQSITRTLS-RIRSGQELwaNTGNKERWKNAFFSrdsiilWLLKtyYPNKKR--------NLSHM 150
Cdd:PRK08118  79 ADTIIFLDIPRTICLYRAFKRRVQyRGKTRPDM--GAGCEEKFDLQFFK------WIWE--YPKTKRpsilkrlnQLSEE 148

                        170       180
                 ....*....|....*....|....*.
gi 490374875 151 ANInlrhiqfVRLTSPKETNLFLQQM 176
Cdd:PRK08118 149 KDI-------VILKSRNEVRLFLEKI 167
PRK07261 PRK07261
DNA topology modulation protein;
1-103 3.29e-17

DNA topology modulation protein;


Pssm-ID: 180911 [Multi-domain]  Cd Length: 171  Bit Score: 74.75  E-value: 3.29e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490374875   1 MKINIIGTSGSGKSTLCQQLSLLLNVPSIELDSLYWLANWQGSSDDALNQKLTAALDKavSGWVLDGNYTRT-QPIKWKE 79
Cdd:PRK07261   1 MKIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQPNWQERDDDDMIADISNFLLK--HDWIIDGNYSWClYEERMQE 78

                         90       100
                 ....*....|....*....|....
gi 490374875  80 VDMVVWLDYSLPRTLYQSITRTLS 103
Cdd:PRK07261  79 ADQIIFLNFSRFNCLYRAFKRYLK 102
PRK06217 PRK06217
hypothetical protein; Validated
 1-108 3.30e-06

hypothetical protein; Validated


Pssm-ID: 168472  Cd Length: 183  Bit Score: 45.43  E-value: 3.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490374875   1 MKINIIGTSGSGKSTLCQQLSLLLNVPSIELDSLYWLanwqgSSDDALNQKLTAA-----LDKAVS---GWVLDGNytrt 72
Cdd:PRK06217   2 MRIHITGASGSGTTTLGAALAERLDIPHLDTDDYFWL-----PTDPPFTTKRPPEerlrlLLEDLRpreGWVLSGS---- 72

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 490374875  73 qPIKWKE-----VDMVVWL----DYSLPRTLYQSITRTLSRIRSG 108
Cdd:PRK06217  73 -ALGWGDpleplFDLVVFLtippELRLERLRLREFQRYGNRILPG 116
UMPK cd02023
Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or ...
 3-35 3.58e-04

Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.


Pssm-ID: 238981 [Multi-domain]  Cd Length: 198  Bit Score: 39.46  E-value: 3.58e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 490374875   3 INIIGTSGSGKSTLCQQLSLLLNVPS---IELDSLY 35
Cdd:cd02023    2 IGIAGGSGSGKTTVAEEIIEQLGNPKvviISQDSYY 37
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 1-30 8.48e-04

Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase is part of the Pathway/BioSystem: NAD biosynthesis


Pssm-ID: 442405 [Multi-domain]  Cd Length: 178  Bit Score: 38.26  E-value: 8.48e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 490374875   1 MKINIIGTSGSGKSTLCQQLSLLLNVPSIE 30
Cdd:COG3172    9 KKIVLLGAESTGKTTLARALAAHYNTPWVP 38
Udk COG0572
Uridine kinase [Nucleotide transport and metabolism]; Uridine kinase is part of the Pathway ...
 3-35 1.44e-03

Uridine kinase [Nucleotide transport and metabolism]; Uridine kinase is part of the Pathway/BioSystem: Pyrimidine salvage


Pssm-ID: 440337 [Multi-domain]  Cd Length: 206  Bit Score: 37.90  E-value: 1.44e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 490374875   3 INIIGTSGSGKSTLCQQLSLLL---NVPSIELDSLY 35
Cdd:COG0572   10 IGIAGPSGSGKTTFARRLAEQLgadKVVVISLDDYY 45
Fap7 COG1936
Broad-specificity NMP kinase [Nucleotide transport and metabolism];
1-34 1.80e-03

Broad-specificity NMP kinase [Nucleotide transport and metabolism];


Pssm-ID: 441539 [Multi-domain]  Cd Length: 173  Bit Score: 37.49  E-value: 1.80e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 490374875   1 MKINIIGTSGSGKSTLCQQLSLLLNVPSIELDSL 34
Cdd:COG1936    1 MRIAITGTPGTGKTTVAKLLAERLGLEVIHLNDL 34
GntK cd02021
Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting ...
 5-39 2.94e-03

Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.


Pssm-ID: 238979 [Multi-domain]  Cd Length: 150  Bit Score: 36.46  E-value: 2.94e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 490374875   5 IIGTSGSGKSTLCQQLSLLLNVPSIELDSLYWLAN 39
Cdd:cd02021    4 VMGVSGSGKSTVGKALAERLGAPFIDGDDLHPPAN 38
PRK13951 PRK13951
bifunctional shikimate kinase AroK/3-dehydroquinate synthase AroB;
1-32 4.79e-03

bifunctional shikimate kinase AroK/3-dehydroquinate synthase AroB;


Pssm-ID: 172457 [Multi-domain]  Cd Length: 488  Bit Score: 36.81  E-value: 4.79e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 490374875   1 MKINIIGTSGSGKSTLCQQLSLLLNVPSIELD 32
Cdd:PRK13951   1 MRIFLVGMMGSGKSTIGKRVSEVLDLQFIDMD 32
AroK COG0703
Shikimate kinase [Amino acid transport and metabolism]; Shikimate kinase is part of the ...
 3-34 4.83e-03

Shikimate kinase [Amino acid transport and metabolism]; Shikimate kinase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis


Pssm-ID: 440467 [Multi-domain]  Cd Length: 165  Bit Score: 35.87  E-value: 4.83e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 490374875   3 INIIGTSGSGKSTLCQQLSLLLNVPSIELDSL 34
Cdd:COG0703    1 IVLIGMMGAGKSTVGRLLAKRLGLPFVDTDAE 32
ABC_ATPase cd00267
ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large ...
 5-31 5.16e-03

ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213179 [Multi-domain]  Cd Length: 157  Bit Score: 35.68  E-value: 5.16e-03
                         10        20
                 ....*....|....*....|....*..
gi 490374875   5 IIGTSGSGKSTLCQQLSLLLNVPSIEL 31
Cdd:cd00267   30 LVGPNGSGKSTLLRAIAGLLKPTSGEI 56
YbbA COG4181
Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase ...
 5-28 5.24e-03

Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 443338 [Multi-domain]  Cd Length: 233  Bit Score: 36.26  E-value: 5.24e-03
                         10        20
                 ....*....|....*....|....*.
gi 490374875   5 IIGTSGSGKSTLcqqLSLL--LNVPS 28
Cdd:COG4181   43 IVGASGSGKSTL---LGLLagLDRPT 65
GntK COG3265
Gluconate kinase [Carbohydrate transport and metabolism]; Gluconate kinase is part of the ...
 1-34 6.44e-03

Gluconate kinase [Carbohydrate transport and metabolism]; Gluconate kinase is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway


Pssm-ID: 442496 [Multi-domain]  Cd Length: 164  Bit Score: 35.49  E-value: 6.44e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 490374875   1 MKINIIGTSGSGKSTLCQQLSLLLNVPSIELDSL 34
Cdd:COG3265    2 MVIVVMGVSGSGKSTVGQALAERLGWPFIDGDDF 35
SK cd00464
Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic ...
 5-34 6.60e-03

Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.


Pssm-ID: 238260 [Multi-domain]  Cd Length: 154  Bit Score: 35.61  E-value: 6.60e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 490374875   5 IIGTSGSGKSTLCQQLSLLLNVPSIELDSL 34
Cdd:cd00464    4 LIGMMGAGKTTVGRLLAKALGLPFVDLDEL 33
PduV-EutP pfam10662
Ethanolamine utilization - propanediol utilization; Members of this family function in ...
 2-21 6.88e-03

Ethanolamine utilization - propanediol utilization; Members of this family function in ethanolamine and propanediol degradation pathways. PduV may be involved in the association of the bacterial microcompartments (BMCs) to filaments.


Pssm-ID: 402341 [Multi-domain]  Cd Length: 137  Bit Score: 35.33  E-value: 6.88e-03
                          10        20
                  ....*....|....*....|
gi 490374875    2 KINIIGTSGSGKSTLCQQLS 21
Cdd:pfam10662   3 KIMLIGPTGCGKTTLCQALS 22
clpX PRK05342
ATP-dependent Clp protease ATP-binding subunit ClpX;
2-27 8.34e-03

ATP-dependent Clp protease ATP-binding subunit ClpX;


Pssm-ID: 235422 [Multi-domain]  Cd Length: 412  Bit Score: 35.90  E-value: 8.34e-03
                         10        20
                 ....*....|....*....|....*...
gi 490374875   2 KINI--IGTSGSGKSTLCQQLSLLLNVP 27
Cdd:PRK05342 108 KSNIllIGPTGSGKTLLAQTLARILDVP 135
 
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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