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Conserved domains on  [gi|488043836|ref|WP_002115233|]
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MULTISPECIES: ATP-dependent endonuclease [Acinetobacter]

Protein Classification

ATP-dependent nuclease( domain architecture ID 11466458)

ATP-dependent nuclease is an OLD (overcoming lysogenization defect) family ATP-dependent nuclease which may have DNAse as well as RNAse activity; similar to Bacillus cereus endonuclease GajA and bacteriophage P2 OLD nuclease, which displays exonuclease activity

CATH:  3.40.50.300
EC:  3.1.-.-
Gene Ontology:  GO:0004519|GO:0004527|GO:0016887|GO:0005524|GO:0046872
PubMed:  18466635|32009148|31400118|37840731

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-527 5.20e-59

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: 201.00  E-value: 5.20e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836   1 MRIEKVRVEGYRLLEDIEIVLEKNSTVIVGRNNSGKTSFTSIFDCFCG-ESGARFRLEDFSSLSREKflnarklkeegas 79
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRLLLGpSSSRKFDEEDFYLGDDPD------------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  80 peqiyntLPIITLSLTFRydsdaptlgplspfiidldmdsttaiacieyrpvlakmhllfdipqppvgmepqihffkclr 159
Cdd:COG3593   68 -------LPEIEIELTFG-------------------------------------------------------------- 78

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 160 nnlskiyevhvsaidptdksnkrnfedtsafaallqcnfvqaqrtldktklgeaDVIGKLLSELFKTaaaptatESDQEL 239
Cdd:COG3593   79 ------------------------------------------------------SLLSRLLRLLLKE-------EDKEEL 97

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 240 AAKLKKsvedielnVQSDFDKMLKKLLPVMGVMGFPSLNDTELRPETSLNVEALLSGHTKVVYSgtDGVHLPEGYNGLGT 319
Cdd:COG3593   98 EEALEE--------LNEELKEALKALNELLSEYLKELLDGLDLELELSLDELEDLLKSLSLRIE--DGKELPLDRLGSGF 167

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 320 RNLIYMLLQLEsyhkiYRSQITRPSAHLIFIEEPEAHLHPQMQEVFINQLnvaiQKLSSaypaedvWNVQFIITTHSSHV 399
Cdd:COG3593  168 QRLILLALLSA-----LAELKRAPANPILLIEEPEAHLHPQAQRRLLKLL----KELSE-------KPNQVIITTHSPHL 231

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 400 ANAACFDAVRYFYNQKDAVKSirnTKVKDFKKGmqtisvtDKEFLHKYMTLTKCDLYFADKVIMVEGTTERLLMPRLREL 479
Cdd:COG3593  232 LSEVPLENIRRLRRDSGGTTS---TKLIDLDDE-------DLRKLLRYLGVTRSELLFARKVILVEGDTEVILLPALARK 301

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|....*....
gi 488043836 480 VDKSLPEHqklasqYVTCIEAGGAH-AHLFYPLLDFLELKTLVVTDLDS 527
Cdd:COG3593  302 LGKDLDEE------GISIIPVGGKSnLKPLAKLLKALGIPVAVLTDGDE 344
 
Name Accession Description Interval E-value
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-527 5.20e-59

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: 201.00  E-value: 5.20e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836   1 MRIEKVRVEGYRLLEDIEIVLEKNSTVIVGRNNSGKTSFTSIFDCFCG-ESGARFRLEDFSSLSREKflnarklkeegas 79
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRLLLGpSSSRKFDEEDFYLGDDPD------------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  80 peqiyntLPIITLSLTFRydsdaptlgplspfiidldmdsttaiacieyrpvlakmhllfdipqppvgmepqihffkclr 159
Cdd:COG3593   68 -------LPEIEIELTFG-------------------------------------------------------------- 78

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 160 nnlskiyevhvsaidptdksnkrnfedtsafaallqcnfvqaqrtldktklgeaDVIGKLLSELFKTaaaptatESDQEL 239
Cdd:COG3593   79 ------------------------------------------------------SLLSRLLRLLLKE-------EDKEEL 97

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 240 AAKLKKsvedielnVQSDFDKMLKKLLPVMGVMGFPSLNDTELRPETSLNVEALLSGHTKVVYSgtDGVHLPEGYNGLGT 319
Cdd:COG3593   98 EEALEE--------LNEELKEALKALNELLSEYLKELLDGLDLELELSLDELEDLLKSLSLRIE--DGKELPLDRLGSGF 167

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 320 RNLIYMLLQLEsyhkiYRSQITRPSAHLIFIEEPEAHLHPQMQEVFINQLnvaiQKLSSaypaedvWNVQFIITTHSSHV 399
Cdd:COG3593  168 QRLILLALLSA-----LAELKRAPANPILLIEEPEAHLHPQAQRRLLKLL----KELSE-------KPNQVIITTHSPHL 231

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 400 ANAACFDAVRYFYNQKDAVKSirnTKVKDFKKGmqtisvtDKEFLHKYMTLTKCDLYFADKVIMVEGTTERLLMPRLREL 479
Cdd:COG3593  232 LSEVPLENIRRLRRDSGGTTS---TKLIDLDDE-------DLRKLLRYLGVTRSELLFARKVILVEGDTEVILLPALARK 301

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|....*....
gi 488043836 480 VDKSLPEHqklasqYVTCIEAGGAH-AHLFYPLLDFLELKTLVVTDLDS 527
Cdd:COG3593  302 LGKDLDEE------GISIIPVGGKSnLKPLAKLLKALGIPVAVLTDGDE 344
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-400 4.86e-39

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: 147.75  E-value: 4.86e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836    1 MRIEKVRVEGYRLLEDIEIVLEKNSTVIVGRNNSGKTSFTSIFDCFCGESgARFRLEDFSSLSREKFLnarklKEEGASP 80
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDIFLNNK-EKFFEDDFLVLYLKDVI-----KIDKEDL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836   81 EQIYNTLPIITLSLTFRY-----------------------DSDAPTLGP---------LSPFIIDLDMDSTTAIACIEY 128
Cdd:pfam13175  75 NIFENISFSIDIEIDVEFllilfgyleikkkylclaskgkaKEYEKTLHPkgankadllLELKISDLKKYLKQFKIYIYN 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  129 RPVLAKMHLLFDIPQPPVGMEPQIHFFKCLRNNLSKIYEVHVSAIDPTDKSNKRNFEDTSAFAALLQcnFVQAQRTL-DK 207
Cdd:pfam13175 155 NYYLDEKKNVFDKKSKYELPSLKEEFLNSEKEEIKVDKEDLKKLINELEKSINYHENVLENLQIKKL--LISADRNAsDE 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  208 TKLGEADVIGKLLSELFKTAAAPTatESDQELAAKLKKSVEDIELNVQSDFDKMLKKLlpvmgvmgFPSLNDTELRPETS 287
Cdd:pfam13175 233 DSEKINSLLGALKQRIFEEALQEE--LELTEKLKETQNKLKEIDKTLAEELKNILFKK--------IDKLKDFGYPPFLN 302

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  288 LNVEALLsghtkvvysgtDGVHLPEGYNGLGTRNLIYMLLQLESYHKIYRSQITRPsaHLIFIEEPEAHLHPQMQEVFIN 367
Cdd:pfam13175 303 PEIEIKK-----------DDEDLPLNKNGSGVQRLILLIFFIAEAERKEDEIEEKN--VILAIEEPEAHLHPQAQRVLIK 369

                         410       420       430
                  ....*....|....*....|....*....|...
gi 488043836  368 qlnvAIQKLSsaypaeDVWNVQFIITTHSSHVA 400
Cdd:pfam13175 370 ----LLKELA------NDNKTQVIITTHSPHII 392
TOPRIM_OLD cd01026
TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 456-527 5.01e-18

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: 79.25  E-value: 5.01e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488043836 456 YFADKVIMVEGTTERLLMPRLRELVDKSLPEHqklasqYVTCIEAGGAHAHLFYPLLDFLELKTLVVTDLDS 527
Cdd:cd01026    1 FFADKVILVEGDSEEILLPALAKKLGLDLDEA------GISIIPVGGKNFKPFIKLLNALGIPVAVLTDLDA 66
retron_eff_Eco8 NF038234
retron Eco8 family effector endonuclease; This ATPase, found as the effector protein partner ...
 318-470 1.41e-09

retron Eco8 family effector endonuclease; This ATPase, found as the effector protein partner next to a reverse transcriptase in Eco8 type retron systems, is a predicted OLD family endonuclease.


Pssm-ID: 468422 [Multi-domain]  Cd Length: 679  Bit Score: 60.81  E-value: 1.41e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 318 GTRNLIYMLLQLESYHKIYRSQITRPsahLIFIEEPEAHLHPQMQEVFINQLNvaiQKLSSAYPAEDVWNVQFIITTHSS 397
Cdd:NF038234 249 GTNSFNFIKLFLNLLITLSRREYITP---FIFIDEPELGLHPKLNEQLINEIY---ESYSFKKKDNKTPYPKIILATHSP 322

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488043836 398 HVANaacfDAVRYFyNQKDAVKSIRNTKVKDFKKGMQTIsVTDKEFLHKYmTLTKCDLYFADKVIMVEGTTER 470
Cdd:NF038234 323 RIIK----NIIKLF-RDNHLIYHFSNENKYTKISRMNST-YDDERFLNIF-SDNEARLYFSKFILFVEGETEL 388
recF PRK00064
recombination protein F; Reviewed
 1-38 3.76e-03

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 39.76  E-value: 3.76e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 488043836   1 MRIEKVRVEGYRLLEDIEIVLEKNSTVIVGRNNSGKTS 38
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTN 38
 
Name Accession Description Interval E-value
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-527 5.20e-59

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: 201.00  E-value: 5.20e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836   1 MRIEKVRVEGYRLLEDIEIVLEKNSTVIVGRNNSGKTSFTSIFDCFCG-ESGARFRLEDFSSLSREKflnarklkeegas 79
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRLLLGpSSSRKFDEEDFYLGDDPD------------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  80 peqiyntLPIITLSLTFRydsdaptlgplspfiidldmdsttaiacieyrpvlakmhllfdipqppvgmepqihffkclr 159
Cdd:COG3593   68 -------LPEIEIELTFG-------------------------------------------------------------- 78

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 160 nnlskiyevhvsaidptdksnkrnfedtsafaallqcnfvqaqrtldktklgeaDVIGKLLSELFKTaaaptatESDQEL 239
Cdd:COG3593   79 ------------------------------------------------------SLLSRLLRLLLKE-------EDKEEL 97

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 240 AAKLKKsvedielnVQSDFDKMLKKLLPVMGVMGFPSLNDTELRPETSLNVEALLSGHTKVVYSgtDGVHLPEGYNGLGT 319
Cdd:COG3593   98 EEALEE--------LNEELKEALKALNELLSEYLKELLDGLDLELELSLDELEDLLKSLSLRIE--DGKELPLDRLGSGF 167

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 320 RNLIYMLLQLEsyhkiYRSQITRPSAHLIFIEEPEAHLHPQMQEVFINQLnvaiQKLSSaypaedvWNVQFIITTHSSHV 399
Cdd:COG3593  168 QRLILLALLSA-----LAELKRAPANPILLIEEPEAHLHPQAQRRLLKLL----KELSE-------KPNQVIITTHSPHL 231

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 400 ANAACFDAVRYFYNQKDAVKSirnTKVKDFKKGmqtisvtDKEFLHKYMTLTKCDLYFADKVIMVEGTTERLLMPRLREL 479
Cdd:COG3593  232 LSEVPLENIRRLRRDSGGTTS---TKLIDLDDE-------DLRKLLRYLGVTRSELLFARKVILVEGDTEVILLPALARK 301

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|....*....
gi 488043836 480 VDKSLPEHqklasqYVTCIEAGGAH-AHLFYPLLDFLELKTLVVTDLDS 527
Cdd:COG3593  302 LGKDLDEE------GISIIPVGGKSnLKPLAKLLKALGIPVAVLTDGDE 344
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-400 4.86e-39

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: 147.75  E-value: 4.86e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836    1 MRIEKVRVEGYRLLEDIEIVLEKNSTVIVGRNNSGKTSFTSIFDCFCGESgARFRLEDFSSLSREKFLnarklKEEGASP 80
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDIFLNNK-EKFFEDDFLVLYLKDVI-----KIDKEDL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836   81 EQIYNTLPIITLSLTFRY-----------------------DSDAPTLGP---------LSPFIIDLDMDSTTAIACIEY 128
Cdd:pfam13175  75 NIFENISFSIDIEIDVEFllilfgyleikkkylclaskgkaKEYEKTLHPkgankadllLELKISDLKKYLKQFKIYIYN 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  129 RPVLAKMHLLFDIPQPPVGMEPQIHFFKCLRNNLSKIYEVHVSAIDPTDKSNKRNFEDTSAFAALLQcnFVQAQRTL-DK 207
Cdd:pfam13175 155 NYYLDEKKNVFDKKSKYELPSLKEEFLNSEKEEIKVDKEDLKKLINELEKSINYHENVLENLQIKKL--LISADRNAsDE 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  208 TKLGEADVIGKLLSELFKTAAAPTatESDQELAAKLKKSVEDIELNVQSDFDKMLKKLlpvmgvmgFPSLNDTELRPETS 287
Cdd:pfam13175 233 DSEKINSLLGALKQRIFEEALQEE--LELTEKLKETQNKLKEIDKTLAEELKNILFKK--------IDKLKDFGYPPFLN 302

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  288 LNVEALLsghtkvvysgtDGVHLPEGYNGLGTRNLIYMLLQLESYHKIYRSQITRPsaHLIFIEEPEAHLHPQMQEVFIN 367
Cdd:pfam13175 303 PEIEIKK-----------DDEDLPLNKNGSGVQRLILLIFFIAEAERKEDEIEEKN--VILAIEEPEAHLHPQAQRVLIK 369

                         410       420       430
                  ....*....|....*....|....*....|...
gi 488043836  368 qlnvAIQKLSsaypaeDVWNVQFIITTHSSHVA 400
Cdd:pfam13175 370 ----LLKELA------NDNKTQVIITTHSPHII 392
TOPRIM_OLD cd01026
TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 456-527 5.01e-18

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: 79.25  E-value: 5.01e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488043836 456 YFADKVIMVEGTTERLLMPRLRELVDKSLPEHqklasqYVTCIEAGGAHAHLFYPLLDFLELKTLVVTDLDS 527
Cdd:cd01026    1 FFADKVILVEGDSEEILLPALAKKLGLDLDEA------GISIIPVGGKNFKPFIKLLNALGIPVAVLTDLDA 66
OLD-like_TOPRIM pfam20469
Overcoming lysogenization defect protein-like, TOPRIM domain; This entry represents the ...
 457-526 5.61e-17

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: 75.50  E-value: 5.61e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488043836  457 FADKVIMVEGTTERLLMPRLRELVDKSlpehqKLASQYVTCIEAGGA-HAHLFYPLLDFLELKTLVVTDLD 526
Cdd:pfam20469   2 FADKVILVEGDTEEILLPALAEKLLGK-----DLDALGISIVSVGGKgNFKRFLKLLKALGIPVAVITDLD 67
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-403 1.03e-12

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 68.87  E-value: 1.03e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836   1 MRIEKVRVEGYRLLEDIEIVLEKNS--TVIVGRNNSGKTSFtsifdcfcgesgarfrledfsslsrekfLNArklkeega 78
Cdd:COG3950    1 MRIKSLTIENFRGFEDLEIDFDNPPrlTVLVGENGSGKTTL----------------------------LEA-------- 44

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  79 speqiyntlpiITLSLTFRYDSDAPTLGPLSPFIIDLDMDSTTAIACIE-YRpvlakmhLLFDIPQPPvgmepqihfFKC 157
Cdd:COG3950   45 -----------IALALSGLLSRLDDVKFRKLLIRNGEFGDSAKLILYYGtSR-------LLLDGPLKK---------LER 97

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 158 LRNNLSKIYEVHVSAIDPtdKSNKRNFEDtsafaallqcnfvqaqrtldktklgeadvigkllselfktaaaptatesdq 237
Cdd:COG3950   98 LKEEYFSRLDGYDSLLDE--DSNLREFLE--------------------------------------------------- 124

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 238 elaaKLKKSVEDIELNVQSDFDKMLKKLLPVMGVMgFPSLNDTELRPEtslnveallsgHTKVVYSGTDGVHLPegYNGL 317
Cdd:COG3950  125 ----WLREYLEDLENKLSDELDEKLEAVREALNKL-LPDFKDIRIDRD-----------PGRLVILDKNGEELP--LNQL 186

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 318 --GTRNLIYMLLQLesyhkIYRSQITRPSAH-------LIFIEEPEAHLHPQMQEVFInqlnvaiQKLSSAYPaedvwNV 388
Cdd:COG3950  187 sdGERSLLALVGDL-----ARRLAELNPALEnplegegIVLIDEIDLHLHPKWQRRIL-------PDLRKIFP-----NI 249

                        410
                 ....*....|....*
gi 488043836 389 QFIITTHSSHVANAA 403
Cdd:COG3950  250 QFIVTTHSPLILSSL 264
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 26-399 5.40e-10

AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system.


Pssm-ID: 433102 [Multi-domain]  Cd Length: 303  Bit Score: 60.87  E-value: 5.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836   26 TVIVGRNNSGKTSFTSIFDCFCGESGARFRLEDFSSLSREKFLNARKLKEEGASPEQIYNTLPIITLSLTFRYdsdaptl 105
Cdd:pfam13304   2 NVLIGPNGSGKSNLLEALRFLADFDALVIGLTDERSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVRYRY------- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  106 gplspfIIDLDmDSTTAIACIEYRPVLAKMhlLFDIPQPPVGMEPQIHFFKCLRNNLSKIYEVHVSAIDPTDKSNKRNFE 185
Cdd:pfam13304  75 ------GLDLE-REDVEEKLSSKPTLLEKR--LLLREDSEEREPKFPPEAEELRLGLDVEERIELSLSELSDLISGLLLL 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  186 DTSAFAALLqcnfvqaqrtldktkLGEADVIGKLLSELFKTAAAPTATESDQELAAKLKKSVEDIELNVQsdfdkmlkkl 265
Cdd:pfam13304 146 SIISPLSFL---------------LLLDEGLLLEDWAVLDLAADLALFPDLKELLQRLVRGLKLADLNLS---------- 200

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  266 lpvmgvmgfpslnDTELRPETSLNVEALLSGHTKVVYSGTDGVHLPEGYNGLGTRNLIYMLLQLesyhkiyrsQITRPSA 345
Cdd:pfam13304 201 -------------DLGEGIEKSLLVDDRLRERGLILLENGGGGELPAFELSDGTKRLLALLAAL---------LSALPKG 258

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 488043836  346 HLIFIEEPEAHLHPQMQEVFINQLNVAIQKlssaypaedvwNVQFIITTHSSHV 399
Cdd:pfam13304 259 GLLLIDEPESGLHPKLLRRLLELLKELSRN-----------GAQLILTTHSPLL 301
retron_eff_Eco8 NF038234
retron Eco8 family effector endonuclease; This ATPase, found as the effector protein partner ...
 318-470 1.41e-09

retron Eco8 family effector endonuclease; This ATPase, found as the effector protein partner next to a reverse transcriptase in Eco8 type retron systems, is a predicted OLD family endonuclease.


Pssm-ID: 468422 [Multi-domain]  Cd Length: 679  Bit Score: 60.81  E-value: 1.41e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 318 GTRNLIYMLLQLESYHKIYRSQITRPsahLIFIEEPEAHLHPQMQEVFINQLNvaiQKLSSAYPAEDVWNVQFIITTHSS 397
Cdd:NF038234 249 GTNSFNFIKLFLNLLITLSRREYITP---FIFIDEPELGLHPKLNEQLINEIY---ESYSFKKKDNKTPYPKIILATHSP 322

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488043836 398 HVANaacfDAVRYFyNQKDAVKSIRNTKVKDFKKGMQTIsVTDKEFLHKYmTLTKCDLYFADKVIMVEGTTER 470
Cdd:NF038234 323 RIIK----NIIKLF-RDNHLIYHFSNENKYTKISRMNST-YDDERFLNIF-SDNEARLYFSKFILFVEGETEL 388
COG4938 COG4938
Predicted ATPase [General function prediction only];
347-402 2.98e-09

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 58.44  E-value: 2.98e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488043836 347 LIFIEEPEAHLHPQMQevfiNQLNVAIQKLSSAypaedvwNVQFIITTHSSHVANA 402
Cdd:COG4938  165 LLIIEEPEAHLHPKAQ----SALAELLAELANS-------GVQVIIETHSDYILNG 209
COG4637 COG4637
Predicted ATPase [General function prediction only];
2-402 3.63e-07

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 52.63  E-value: 3.63e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836   2 RIEKVRVEGYRLLEDIEIVLEkNSTVIVGRNNSGKTSFtsiFDCFcgesgaRFrledFSSLSREKFLNArkLKEEG---- 77
Cdd:COG4637    1 MITRIRIKNFKSLRDLELPLG-PLTVLIGANGSGKSNL---LDAL------RF----LSDAARGGLQDA--LARRGglee 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836  78 ---ASPEQIYntlPIITLSLTFRyDSDAPTLGplspFIIDLDMDSTTAiacieyRPVLAKMHLLFDIPQppvGMEPQIhf 154
Cdd:COG4637   65 llwRGPRTIT---EPIRLELEFA-EEDERDLR----YELELGLPEPGG------RPEVKEERLWLKRGS---GGRPFL-- 125

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 155 fkcLRNNLSKIYEVHVSAIDPTDK--SNKRNFEDTSAFAALLQcnFVQAQRTLDktklgeadvigkLLSELFKTAAAPTA 232
Cdd:COG4637  126 ---DFRPKGRAVGGEPERLDSPESllSQLGDPERFPELRALRE--ALRSWRFYD------------FHPAPLRQPQPAGR 188

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 233 TE---SD-QELAAKLKKsVEDIELNVQSDFDKMLKKLLPvmGVMGFpslnDTELRPETSLNVEALLSGHTKVVYSGtdgv 308
Cdd:COG4637  189 TPvlaPDgSNLAAVLAT-LRETHPERFERILEALRDAFP--GFEDI----EVEPDEDGRVLLEFREKGLDRPFPAR---- 257

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 309 HLPEgynglGTRNLIYMLLQLESYhkiyrsqitrPSAHLIFIEEPEAHLHPQMqevfINQLNVAIQKLSSaypaedvwNV 388
Cdd:COG4637  258 ELSD-----GTLRFLALLAALLSP----------RPPPLLCIEEPENGLHPDL----LPALAELLREASE--------RT 310

                        410
                 ....*....|....
gi 488043836 389 QFIITTHSSHVANA 402
Cdd:COG4637  311 QVIVTTHSPALLDA 324
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
316-403 4.17e-06

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 48.89  E-value: 4.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043836 316 GLGTRNLIYMLLQLesYHKIYRSQItrpsahlIFIEEPEAHLHPQMQEVFINQLNVAIQKLssaypaedvwNVQFIITTH 395
Cdd:COG1106  204 SDGTKRLLALAGAL--LDALAKGGV-------LLIDEIEASLHPSLLRKLLKLFLDLANKN----------NAQLIFTTH 264


                 ....*...
gi 488043836 396 SSHVANAA 403
Cdd:COG1106  265 STELLDAF 272
AAA_23 pfam13476
AAA domain;
6-47 1.42e-05

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 45.95  E-value: 1.42e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 488043836    6 VRVEGYRLLEDIEIVLEKNSTVIVGRNNSGKtsfTSIFDCFC 47
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGK---TTILDAIK 39
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
1-75 4.24e-05

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 46.30  E-value: 4.24e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488043836   1 MRIEKVRVEGYRLLEDIEIVLEKNSTVIVGRNNSGKTSFTSIFDCFCGESGARFRLEDFSSLSREKFLNARKLKE 75
Cdd:COG4717    1 MKIKELEIYGFGKFRDRTIEFSPGLNVIYGPNEAGKSTLLAFIRAMLLERLEKEADELFKPQGRKPELNLKELKE 75
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
2-58 6.00e-05

DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 44.23  E-value: 6.00e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488043836   2 RIEKVRVEGYRLLED-IEIVLEKNSTVIVGRNNSGKtsfTSIFDCFC----GESGARFRLED 58
Cdd:COG0419    1 KLLRLRLENFRSYRDtETIDFDDGLNLIVGPNGAGK---STILEAIRyalyGKARSRSKLRS 59
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 3-62 2.97e-03

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: 40.73  E-value: 2.97e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488043836     3 IEKVRVEGYR-LLEDIEIVLEKNSTVIVGRNNSGKtsfTSIFD--CFC-GESGAR-FRLEDFSSL 62
Cdd:pfam02463    2 LKRIEIEGFKsYAKTVILPFSPGFTAIVGPNGSGK---SNILDaiLFVlGERSAKsLRSERLSDL 63
recF PRK00064
recombination protein F; Reviewed
 1-38 3.76e-03

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 39.76  E-value: 3.76e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 488043836   1 MRIEKVRVEGYRLLEDIEIVLEKNSTVIVGRNNSGKTS 38
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTN 38
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
1-53 4.04e-03

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 40.02  E-value: 4.04e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488043836   1 MRIEKVRVEGYRLLEDIEIVLEKNSTVIVGRNNSGKTSFTSIfdCFCGESGAR 53
Cdd:PRK02224   1 MRFDRVRLENFKCYADADLRLEDGVTVIHGVNGSGKSSLLEA--CFFALYGSK 51
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 3-45 7.57e-03

ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.


Pssm-ID: 213207 [Multi-domain]  Cd Length: 204  Bit Score: 37.97  E-value: 7.57e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 488043836   3 IEKVRVEGYRLLEDIEIV-LEKNSTVIVGRNNSGKtsfTSIFDC 45
Cdd:cd03240    1 IDKLSIRNIRSFHERSEIeFFSPLTLIVGQNGAGK---TTIIEA 41
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-39 8.22e-03

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 38.60  E-value: 8.22e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 488043836   2 RIEKVRVEGYRLLEDIEIVLEKNSTVIVGRNNSGKTSF 39
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNL 38
 
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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