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Conserved domains on  [gi|940128223|gb|KPX44894|]
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Uncharacterized protein ALO37_02630 [Pseudomonas savastanoi pv. glycinea]

Protein Classification

ATP-dependent endonuclease( domain architecture ID 10099095)

OLD (overcoming lysogenization defect)-family ATP-dependent endonuclease may have DNAse as well as RNAse activity

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TOPRIM_OLD cd01026
TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 42-125 2.03e-28

TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


:

Pssm-ID: 173776  Cd Length: 97  Bit Score: 104.67  E-value: 2.03e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940128223  42 YFARFVLLVEGDSERIVLPILAEALDLLIDPAFVAIVPLGGHHVQYFWRLLKHLGIPHATLLDLDLGR----DGGGFGRI 117
Cdd:cd01026    1 FFADKVILVEGDSEEILLPALAKKLGLDLDEAGISIIPVGGKNFKPFIKLLNALGIPVAVLTDLDAKRnekkDDAGKGRN 80


                 ....*...
gi 940128223 118 KTAIQKLI 125
Cdd:cd01026   81 KKLDSKDD 88
 
Name Accession Description Interval E-value
TOPRIM_OLD cd01026
TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 42-125 2.03e-28

TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173776  Cd Length: 97  Bit Score: 104.67  E-value: 2.03e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940128223  42 YFARFVLLVEGDSERIVLPILAEALDLLIDPAFVAIVPLGGHHVQYFWRLLKHLGIPHATLLDLDLGR----DGGGFGRI 117
Cdd:cd01026    1 FFADKVILVEGDSEEILLPALAKKLGLDLDEAGISIIPVGGKNFKPFIKLLNALGIPVAVLTDLDAKRnekkDDAGKGRN 80


                 ....*...
gi 940128223 118 KTAIQKLI 125
Cdd:cd01026   81 KKLDSKDD 88
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 4-118 4.01e-22

Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair];


Pssm-ID: 442812 [Multi-domain]  Cd Length: 359  Bit Score: 94.30  E-value: 4.01e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940128223   4 CRCEPKTRVSTVKKIrFPVNEVDASKFVRGAMLAYPELYFARFVLLVEGDSERIVLPILAEALDLLIDPAFVAIVPLGG- 82
Cdd:COG3593  241 RRLRRDSGGTTSTKL-IDLDDEDLRKLLRYLGVTRSELLFARKVILVEGDTEVILLPALARKLGKDLDEEGISIIPVGGk 319

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 940128223  83 HHVQYFWRLLKHLGIPHATLLDLDLGRDGGGFGRIK 118
Cdd:COG3593  320 SNLKPLAKLLKALGIPVAVLTDGDEAGKAETIEKLK 355
OLD-like_TOPRIM pfam20469
Overcoming lysogenization defect protein-like, TOPRIM domain; This entry represents the ...
 43-106 3.16e-18

Overcoming lysogenization defect protein-like, TOPRIM domain; This entry represents the topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain. The nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. The TOPRIM domain has two conserved motifs, one of which centres at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 466618  Cd Length: 67  Bit Score: 76.66  E-value: 3.16e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 940128223   43 FARFVLLVEGDSERIVLPILAEALDLL-IDPAFVAIVPLGG-HHVQYFWRLLKHLGIPHATLLDLD 106
Cdd:pfam20469   2 FADKVILVEGDTEEILLPALAEKLLGKdLDALGISIVSVGGkGNFKRFLKLLKALGIPVAVITDLD 67
 
Name Accession Description Interval E-value
TOPRIM_OLD cd01026
TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 42-125 2.03e-28

TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173776  Cd Length: 97  Bit Score: 104.67  E-value: 2.03e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940128223  42 YFARFVLLVEGDSERIVLPILAEALDLLIDPAFVAIVPLGGHHVQYFWRLLKHLGIPHATLLDLDLGR----DGGGFGRI 117
Cdd:cd01026    1 FFADKVILVEGDSEEILLPALAKKLGLDLDEAGISIIPVGGKNFKPFIKLLNALGIPVAVLTDLDAKRnekkDDAGKGRN 80


                 ....*...
gi 940128223 118 KTAIQKLI 125
Cdd:cd01026   81 KKLDSKDD 88
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 4-118 4.01e-22

Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair];


Pssm-ID: 442812 [Multi-domain]  Cd Length: 359  Bit Score: 94.30  E-value: 4.01e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 940128223   4 CRCEPKTRVSTVKKIrFPVNEVDASKFVRGAMLAYPELYFARFVLLVEGDSERIVLPILAEALDLLIDPAFVAIVPLGG- 82
Cdd:COG3593  241 RRLRRDSGGTTSTKL-IDLDDEDLRKLLRYLGVTRSELLFARKVILVEGDTEVILLPALARKLGKDLDEEGISIIPVGGk 319

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 940128223  83 HHVQYFWRLLKHLGIPHATLLDLDLGRDGGGFGRIK 118
Cdd:COG3593  320 SNLKPLAKLLKALGIPVAVLTDGDEAGKAETIEKLK 355
OLD-like_TOPRIM pfam20469
Overcoming lysogenization defect protein-like, TOPRIM domain; This entry represents the ...
 43-106 3.16e-18

Overcoming lysogenization defect protein-like, TOPRIM domain; This entry represents the topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain. The nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. The TOPRIM domain has two conserved motifs, one of which centres at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 466618  Cd Length: 67  Bit Score: 76.66  E-value: 3.16e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 940128223   43 FARFVLLVEGDSERIVLPILAEALDLL-IDPAFVAIVPLGG-HHVQYFWRLLKHLGIPHATLLDLD 106
Cdd:pfam20469   2 FADKVILVEGDTEEILLPALAEKLLGKdLDALGISIVSVGGkGNFKRFLKLLKALGIPVAVITDLD 67
 
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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