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Conserved domains on  [gi|737287937|ref|WP_035271110|]
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AAA family ATPase, partial [Acinetobacter sp. Ver3]

Protein Classification

OLD family protein( domain architecture ID 1003243)

OLD (overcome lysogenization defect) family protein may function as an ATP-dependent endonuclease, similar to Bacteriophage P2 Old nuclease that acts preferentially on linear dsDNA, processively degrading it from 5'-3', releasing 5'-phosphomononucleotides

EC:  3.1.-.-
Gene Ontology:  GO:0005524|GO:0004527
PubMed:  2695400

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YbjD super family cl34639
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 3-111 3.64e-16

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


The actual alignment was detected with superfamily member COG3593:

Pssm-ID: 442812 [Multi-domain]  Cd Length: 359  Bit Score: 73.50  E-value: 3.64e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737287937   3 MHLKNLIIKNFRNFEAIDIPLSSNV-VLLGENRIGKSNLLFALRLVIDqslPDSARNLRISDFWDGCDlSKKPQIEIHLD 81
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLtVLVGENNSGKSSILEALRLLLG---PSSSRKFDEEDFYLGDD-PDLPEIEIELT 76

                         90       100       110
                 ....*....|....*....|....*....|
gi 737287937  82 ITDfendpYLTALLTDYRLAHDYKTIRLSY 111
Cdd:COG3593   77 FGS-----LLSRLLRLLLKEEDKEELEEAL 101
 
Name Accession Description Interval E-value
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 3-111 3.64e-16

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: 73.50  E-value: 3.64e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737287937   3 MHLKNLIIKNFRNFEAIDIPLSSNV-VLLGENRIGKSNLLFALRLVIDqslPDSARNLRISDFWDGCDlSKKPQIEIHLD 81
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLtVLVGENNSGKSSILEALRLLLG---PSSSRKFDEEDFYLGDD-PDLPEIEIELT 76

                         90       100       110
                 ....*....|....*....|....*....|
gi 737287937  82 ITDfendpYLTALLTDYRLAHDYKTIRLSY 111
Cdd:COG3593   77 FGS-----LLSRLLRLLLKEEDKEELEEAL 101
recF PRK00064
recombination protein F; Reviewed
 3-44 1.86e-10

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 57.48  E-value: 1.86e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 737287937   3 MHLKNLIIKNFRNFEAIDIPLSSN-VVLLGENRIGKSNLLFAL 44
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGvNVLVGENGQGKTNLLEAI 43
DUF2813 pfam11398
Protein of unknown function (DUF2813); This entry contains YjbD from Escherichia coli, which ...
 3-89 6.07e-08

Protein of unknown function (DUF2813); This entry contains YjbD from Escherichia coli, which is annotated as a nucleotide triphosphate hydrolase.


Pssm-ID: 431868 [Multi-domain]  Cd Length: 372  Bit Score: 50.43  E-value: 6.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737287937    3 MHLKNLIIKNFRNFEAIDIPLSSNVVLLGENRIGKSNLLFALRLVIDQSLPdsARNLRISDFWDGCDLSKKPQIEIHLDI 82
Cdd:pfam11398   1 MHLERIEVVGFRGINRLSLHFDQLTVLIGENAWGKSSLLDALSLLLNPTKE--LYQFTLDDFHQPYAIENEPTRHLQIIF 78


                  ....*..
gi 737287937   83 TDFENDP 89
Cdd:pfam11398  79 TFKESAP 85
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 5-44 3.05e-06

ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters involved in the transport of a wide variety of different compounds including 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 with 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: 213209 [Multi-domain]  Cd Length: 270  Bit Score: 44.98  E-value: 3.05e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 737287937   5 LKNLIIKNFRNFEAIDIPLSSNV-VLLGENRIGKSNLLFAL 44
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVtVLVGENAQGKTNLLEAI 41
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 5-60 2.65e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 36.96  E-value: 2.65e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 737287937     5 LKNLIIKNFRNF-EAIDIPLSSNVV-LLGENRIGKSNLLFALRLVIDQSlpdSARNLR 60
Cdd:TIGR02168    2 LKKLELAGFKSFaDPTTINFDKGITgIVGPNGCGKSNIVDAIRWVLGEQ---SAKALR 56
 
Name Accession Description Interval E-value
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 3-111 3.64e-16

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: 73.50  E-value: 3.64e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737287937   3 MHLKNLIIKNFRNFEAIDIPLSSNV-VLLGENRIGKSNLLFALRLVIDqslPDSARNLRISDFWDGCDlSKKPQIEIHLD 81
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLtVLVGENNSGKSSILEALRLLLG---PSSSRKFDEEDFYLGDD-PDLPEIEIELT 76

                         90       100       110
                 ....*....|....*....|....*....|
gi 737287937  82 ITDfendpYLTALLTDYRLAHDYKTIRLSY 111
Cdd:COG3593   77 FGS-----LLSRLLRLLLKEEDKEELEEAL 101
recF PRK00064
recombination protein F; Reviewed
 3-44 1.86e-10

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 57.48  E-value: 1.86e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 737287937   3 MHLKNLIIKNFRNFEAIDIPLSSN-VVLLGENRIGKSNLLFAL 44
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGvNVLVGENGQGKTNLLEAI 43
COG4637 COG4637
Predicted ATPase [General function prediction only];
5-101 9.53e-09

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 52.63  E-value: 9.53e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737287937   5 LKNLIIKNFRNFEAIDIPLSSNVVLLGENRIGKSNLLFALRL---VIDQSLPDS-ARNLRISD-FWDGCDlSKKPQIEIH 79
Cdd:COG4637    2 ITRIRIKNFKSLRDLELPLGPLTVLIGANGSGKSNLLDALRFlsdAARGGLQDAlARRGGLEElLWRGPR-TITEPIRLE 80

                         90       100
                 ....*....|....*....|..
gi 737287937  80 LDITDFENDPYltalltDYRLA 101
Cdd:COG4637   81 LEFAEEDERDL------RYELE 96
DUF2813 pfam11398
Protein of unknown function (DUF2813); This entry contains YjbD from Escherichia coli, which ...
 3-89 6.07e-08

Protein of unknown function (DUF2813); This entry contains YjbD from Escherichia coli, which is annotated as a nucleotide triphosphate hydrolase.


Pssm-ID: 431868 [Multi-domain]  Cd Length: 372  Bit Score: 50.43  E-value: 6.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737287937    3 MHLKNLIIKNFRNFEAIDIPLSSNVVLLGENRIGKSNLLFALRLVIDQSLPdsARNLRISDFWDGCDLSKKPQIEIHLDI 82
Cdd:pfam11398   1 MHLERIEVVGFRGINRLSLHFDQLTVLIGENAWGKSSLLDALSLLLNPTKE--LYQFTLDDFHQPYAIENEPTRHLQIIF 78


                  ....*..
gi 737287937   83 TDFENDP 89
Cdd:pfam11398  79 TFKESAP 85
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
4-41 3.45e-07

Recombinational DNA repair ATPase RecF [Replication, recombination and repair];


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 47.84  E-value: 3.45e-07
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 737287937   4 HLKNLIIKNFRNFEAIDIPLSSNVVLL-GENRIGKSNLL 41
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLvGPNGQGKTNLL 39
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 3-82 3.65e-07

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 433011 [Multi-domain]  Cd Length: 392  Bit Score: 47.98  E-value: 3.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737287937    3 MHLKNLIIKNFRNFEAIDIPLSSNV-VLLGENRIGKSNLLFALRLVIDQSLPDSArNLRISDFWDGCDLSKKPQIEIHLD 81
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLtVLIGKNNSGKSSILEALDIFLNNKEKFFE-DDFLVLYLKDVIKIDKEDLNIFEN 79


                  .
gi 737287937   82 I 82
Cdd:pfam13175  80 I 80
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
3-103 4.21e-07

Predicted ATP-binding protein involved in virulence [General function prediction only];


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 47.69  E-value: 4.21e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737287937   3 MHLKNLIIKNFRNFEAIDIPLSSN---VVLLGENRIGKSNLLFALRLVidqslpdsarnlrISDFWDGCDLSKKPQIEIH 79
Cdd:COG3950    1 MRIKSLTIENFRGFEDLEIDFDNPprlTVLVGENGSGKTTLLEAIALA-------------LSGLLSRLDDVKFRKLLIR 67

                         90       100
                 ....*....|....*....|....
gi 737287937  80 LDitDFENDPYLTALLTDYRLAHD 103
Cdd:COG3950   68 NG--EFGDSAKLILYYGTSRLLLD 89
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 4-99 6.63e-07

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 47.66  E-value: 6.63e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737287937     4 HLKNLIIKNFRNF-EAIDIPLSSNV-VLLGENRIGKSNLLFALRLVIDQSlpdSARNLR---ISD--FWDGCDLSKKPQI 76
Cdd:pfam02463    1 YLKRIEIEGFKSYaKTVILPFSPGFtAIVGPNGSGKSNILDAILFVLGER---SAKSLRserLSDliHSKSGAFVNSAEV 77

                           90       100
                   ....*....|....*....|....*.
gi 737287937    77 EIHLDITD---FENDPYLTALLTDYR 99
Cdd:pfam02463   78 EITFDNEDhelPIDKEEVSIRRRVYR 103
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 5-44 3.05e-06

ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters involved in the transport of a wide variety of different compounds including 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 with 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: 213209 [Multi-domain]  Cd Length: 270  Bit Score: 44.98  E-value: 3.05e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 737287937   5 LKNLIIKNFRNFEAIDIPLSSNV-VLLGENRIGKSNLLFAL 44
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVtVLVGENAQGKTNLLEAI 41
AAA_23 pfam13476
AAA domain;
8-92 9.20e-05

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 40.56  E-value: 9.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737287937    8 LIIKNFRNFEAIDIPLSSNVVLL-GENRIGKSNLLFALRLV----IDQSLPDSARNLRISDFWDGCDLSKKPQIEIHLDI 82
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLItGPNGSGKTTILDAIKLAlygkTSRLKRKSGGGFVKGDIRIGLEGKGKAYVEITFEN 80

                          90
                  ....*....|
gi 737287937   83 TDFENDPYLT 92
Cdd:pfam13476  81 NDGRYTYAIE 90
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
3-59 1.49e-04

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 40.52  E-value: 1.49e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 737287937   3 MHLKNLIIKNFRNFEAIDIPLSSNV-VLLGENRIGKSNLLFALRLVIDQSLPDSARNL 59
Cdd:COG4717    1 MKIKELEIYGFGKFRDRTIEFSPGLnVIYGPNEAGKSTLLAFIRAMLLERLEKEADEL 58
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
4-63 1.74e-04

ATPase/GTPase, AAA15 family [General function prediction only];


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 40.03  E-value: 1.74e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 737287937   4 HLKNLIIKNFR--------NFEAIDIPLSSNVVLLGENRIGKSNLLFALRLVIDQSLPDSARNLRISD 63
Cdd:COG1106    1 MLISFSIENFRsfkdeltlSMVASGLRLLRVNLIYGANASGKSNLLEALYFLRNLVLNSSQPGDKLVE 68
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 5-66 5.52e-04

ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).


Pssm-ID: 213245 [Multi-domain]  Cd Length: 197  Bit Score: 38.21  E-value: 5.52e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 737287937   5 LKNLIIKNFRNF-EAIDIPLSSNV-VLLGENRIGKSNLLFALRLVIDQSlpdSARNLRISDFWD 66
Cdd:cd03278    1 LKKLELKGFKSFaDKTTIPFPPGLtAIVGPNGSGKSNIIDAIRWVLGEQ---SAKSLRGEKMSD 61
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 5-60 2.65e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 36.96  E-value: 2.65e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 737287937     5 LKNLIIKNFRNF-EAIDIPLSSNVV-LLGENRIGKSNLLFALRLVIDQSlpdSARNLR 60
Cdd:TIGR02168    2 LKKLELAGFKSFaDPTTINFDKGITgIVGPNGCGKSNIVDAIRWVLGEQ---SAKALR 56
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 3-60 5.06e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 36.07  E-value: 5.06e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 737287937   3 MHLKNLIIKNFRNF-EAIDIPLSSN---VVllGENRIGKSNLLFALRLVI-DQslpdSARNLR 60
Cdd:COG1196    1 MRLKRLELAGFKSFaDPTTIPFEPGitaIV--GPNGSGKSNIVDAIRWVLgEQ----SAKSLR 57
COG4938 COG4938
Predicted ATPase [General function prediction only];
5-45 9.05e-03

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 34.94  E-value: 9.05e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 737287937   5 LKNLIIKNFRNFEAIDIPLSSNVVLLGENRIGKS---NLLFALR 45
Cdd:COG4938    1 IKSISIKNFGPFKEAELELKPLTLLIGPNGSGKStliQALLLLL 44
 
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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