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Conserved domains on  [gi|1154315592|ref|WP_078630805|]
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ATP-dependent endonuclease [Streptomyces griseoaurantiacus]

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 ...
 29-507 3.64e-69

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: 229.89  E-value: 3.64e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRLAttpLNRRSTRWFDESDLSHGREGQEAQFRatydg 108
Cdd:COG3593     1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRLL---LGPSSSRKFDEEDFYLGDDPDLPEIE----- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 109 lsaaqrahyiaaldvetneaaytttykrdesrqqmrptVTAgpvdgpdaepdkrdqiahvylaplrdaqrELDSsdgnRL 188
Cdd:COG3593    73 --------------------------------------IEL-----------------------------TFGS----LL 81

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 189 LRIIRYLTEEDEQEEFRAQANDSFTKLKEhpVLTATTKEIQGHLGELTDsvrGQTVEVTFAEYELHRLARSLRVKMAEAg 268
Cdd:COG3593    82 SRLLRLLLKEEDKEELEEALEELNEELKE--ALKALNELLSEYLKELLD---GLDLELELSLDELEDLLKSLSLRIEDG- 155

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 269 iPPADLTESGLGYANLLFIATVILELRNAQHMELTLFLVEEPEAHLHPQLQAVLLDYLQEQAGASlkddthgpagrIQVV 348
Cdd:COG3593   156 -KELPLDRLGSGFQRLILLALLSALAELKRAPANPILLIEEPEAHLHPQAQRRLLKLLKELSEKP-----------NQVI 223

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 349 ASTHSPNLASSVGIENVValrtRVDKEavqDDQGKQKEVrrrktqalplakIALSEAERRKINQYLDATRAGLLFARRVI 428
Cdd:COG3593   224 ITTHSPHLLSEVPLENIR----RLRRD---SGGTTSTKL------------IDLDDEDLRKLLRYLGVTRSELLFARKVI 284

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1154315592 429 LVEGIAEAVLLPVIARHCvfgGDDQakqrrDFHGVTIINVGSVDFAPYITLLLSEVNgcrllDKLTVITDRDPDVPKEK 507
Cdd:COG3593   285 LVEGDTEVILLPALARKL---GKDL-----DEEGISIIPVGGKSNLKPLAKLLKALG-----IPVAVLTDGDEAGKAET 350
 
Name Accession Description Interval E-value
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 29-507 3.64e-69

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: 229.89  E-value: 3.64e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRLAttpLNRRSTRWFDESDLSHGREGQEAQFRatydg 108
Cdd:COG3593     1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRLL---LGPSSSRKFDEEDFYLGDDPDLPEIE----- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 109 lsaaqrahyiaaldvetneaaytttykrdesrqqmrptVTAgpvdgpdaepdkrdqiahvylaplrdaqrELDSsdgnRL 188
Cdd:COG3593    73 --------------------------------------IEL-----------------------------TFGS----LL 81

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 189 LRIIRYLTEEDEQEEFRAQANDSFTKLKEhpVLTATTKEIQGHLGELTDsvrGQTVEVTFAEYELHRLARSLRVKMAEAg 268
Cdd:COG3593    82 SRLLRLLLKEEDKEELEEALEELNEELKE--ALKALNELLSEYLKELLD---GLDLELELSLDELEDLLKSLSLRIEDG- 155

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 269 iPPADLTESGLGYANLLFIATVILELRNAQHMELTLFLVEEPEAHLHPQLQAVLLDYLQEQAGASlkddthgpagrIQVV 348
Cdd:COG3593   156 -KELPLDRLGSGFQRLILLALLSALAELKRAPANPILLIEEPEAHLHPQAQRRLLKLLKELSEKP-----------NQVI 223

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 349 ASTHSPNLASSVGIENVValrtRVDKEavqDDQGKQKEVrrrktqalplakIALSEAERRKINQYLDATRAGLLFARRVI 428
Cdd:COG3593   224 ITTHSPHLLSEVPLENIR----RLRRD---SGGTTSTKL------------IDLDDEDLRKLLRYLGVTRSELLFARKVI 284

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1154315592 429 LVEGIAEAVLLPVIARHCvfgGDDQakqrrDFHGVTIINVGSVDFAPYITLLLSEVNgcrllDKLTVITDRDPDVPKEK 507
Cdd:COG3593   285 LVEGDTEVILLPALARKL---GKDL-----DEEGISIIPVGGKSNLKPLAKLLKALG-----IPVAVLTDGDEAGKAET 350
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 29-357 2.08e-21

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: 96.90  E-value: 2.08e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRL----------ATTPLNRRSTRWFDESDLSHG---- 94
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDIflnnkekffeDDFLVLYLKDVIKIDKEDLNIfeni 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  95 ---------------REGQEAQFRATYDGLSAAQRAHYIAALDVETNEAA--------------------------YTTT 133
Cdd:pfam13175  81 sfsidieidveflliLFGYLEIKKKYLCLASKGKAKEYEKTLHPKGANKAdlllelkisdlkkylkqfkiyiynnyYLDE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 134 YKRDESRQQMRPTV-----------TAGPVDGPDAE------PDKRDQIAHVYLAPLRD-----AQRELDSSDGNR---- 187
Cdd:pfam13175 161 KKNVFDKKSKYELPslkeeflnsekEEIKVDKEDLKklinelEKSINYHENVLENLQIKkllisADRNASDEDSEKinsl 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 188 LLRIIRYLTEEDEQEEFRAQ--ANDSFTKLKEhpvltattkeIQGHLGELTDSVRGQTVEVTFAEYELHRLARSLRVKMA 265
Cdd:pfam13175 241 LGALKQRIFEEALQEELELTekLKETQNKLKE----------IDKTLAEELKNILFKKIDKLKDFGYPPFLNPEIEIKKD 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 266 EAGIPpadLTESGLGYANLLFIAT--VILELRNAQHMELTLFLV-EEPEAHLHPQLQAVLLDYLQEqagasLKDDTHGpa 342
Cdd:pfam13175 311 DEDLP---LNKNGSGVQRLILLIFfiAEAERKEDEIEEKNVILAiEEPEAHLHPQAQRVLIKLLKE-----LANDNKT-- 380

                         410
                  ....*....|....*
gi 1154315592 343 griQVVASTHSPNLA 357
Cdd:pfam13175 381 ---QVIITTHSPHII 392
TOPRIM_OLD cd01026
TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 422-509 1.50e-15

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: 72.31  E-value: 1.50e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 422 LFARRVILVEGIAEAVLLPVIARHCvfggddqaKQRRDFHGVTIINVGSVDFAPYITLLlsevngcRLLDKLT-VITDRD 500
Cdd:cd01026     1 FFADKVILVEGDSEEILLPALAKKL--------GLDLDEAGISIIPVGGKNFKPFIKLL-------NALGIPVaVLTDLD 65


                  ....*....
gi 1154315592 501 PDVPKEKKA 509
Cdd:cd01026    66 AKRNEKKDD 74
recF PRK00064
recombination protein F; Reviewed
 29-71 5.69e-09

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 58.25  E-value: 5.69e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEAL 71
Cdd:PRK00064    1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAI 43
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 29-71 4.24e-07

recF protein; All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273173 [Multi-domain]  Cd Length: 365  Bit Score: 52.74  E-value: 4.24e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEAL 71
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAI 43
retron_eff_Eco8 NF038234
retron Eco8 family effector endonuclease; This ATPase, found as the effector protein partner ...
 29-360 1.68e-04

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: 45.02  E-value: 1.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRLATTPLNRRSTrwfDESDLsHGREGQEAQFRATYDg 108
Cdd:NF038234    1 MPIKSIKIKNLLSFDDLEIDDLKDINCIIGKNNVGKSNLLKALKFFYKNLTGEKV---IPPIL-DSNYSSKGEISITYD- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 109 LSaaqRAHYIAALDVETNE---AAYTTTYKRD----ESRQQMRPTVTA-------GPVDGPDAEPDKRDQIAHVYlaPLR 174
Cdd:NF038234   76 TS---RLKRIARSNTNKNEyfkHIYNPFFKKIifsfKKYLDKNTLFTLtlkiyknGSISWSIKDYETRKLLSYLF--PFF 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 175 DAQ-RELDSSDGNRLLRIIRYLTEEDEQEEFRAQANDSFTKLKEhpvlTATTKEIQGHLGELTDSVRgqTVEVTFAEYEL 253
Cdd:NF038234  151 FIEsRHINLYDWDELWDLIGRLKKFNLSGLSNEEIIDFFDEKIS----SNYSNSYKDIIEEIKKSIE--TKPYSYKEKIL 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 254 HRLarSLRVKMAEAGIPPADLTESGLGYANLLFIAT---VILELRNAQHMELTLFlVEEPEAHLHPQLQAVLLDYLQEQA 330
Cdd:NF038234  225 SYI--KLGLGGYKFNIDGEELKTQSDGTNSFNFIKLflnLLITLSRREYITPFIF-IDEPELGLHPKLNEQLINEIYESY 301

                         330       340       350
                  ....*....|....*....|....*....|
gi 1154315592 331 gASLKDDTHGPagRIQVVASTHSPNLASSV 360
Cdd:NF038234  302 -SFKKKDNKTP--YPKIILATHSPRIIKNI 328
 
Name Accession Description Interval E-value
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 29-507 3.64e-69

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: 229.89  E-value: 3.64e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRLAttpLNRRSTRWFDESDLSHGREGQEAQFRatydg 108
Cdd:COG3593     1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRLL---LGPSSSRKFDEEDFYLGDDPDLPEIE----- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 109 lsaaqrahyiaaldvetneaaytttykrdesrqqmrptVTAgpvdgpdaepdkrdqiahvylaplrdaqrELDSsdgnRL 188
Cdd:COG3593    73 --------------------------------------IEL-----------------------------TFGS----LL 81

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 189 LRIIRYLTEEDEQEEFRAQANDSFTKLKEhpVLTATTKEIQGHLGELTDsvrGQTVEVTFAEYELHRLARSLRVKMAEAg 268
Cdd:COG3593    82 SRLLRLLLKEEDKEELEEALEELNEELKE--ALKALNELLSEYLKELLD---GLDLELELSLDELEDLLKSLSLRIEDG- 155

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 269 iPPADLTESGLGYANLLFIATVILELRNAQHMELTLFLVEEPEAHLHPQLQAVLLDYLQEQAGASlkddthgpagrIQVV 348
Cdd:COG3593   156 -KELPLDRLGSGFQRLILLALLSALAELKRAPANPILLIEEPEAHLHPQAQRRLLKLLKELSEKP-----------NQVI 223

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 349 ASTHSPNLASSVGIENVValrtRVDKEavqDDQGKQKEVrrrktqalplakIALSEAERRKINQYLDATRAGLLFARRVI 428
Cdd:COG3593   224 ITTHSPHLLSEVPLENIR----RLRRD---SGGTTSTKL------------IDLDDEDLRKLLRYLGVTRSELLFARKVI 284

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1154315592 429 LVEGIAEAVLLPVIARHCvfgGDDQakqrrDFHGVTIINVGSVDFAPYITLLLSEVNgcrllDKLTVITDRDPDVPKEK 507
Cdd:COG3593   285 LVEGDTEVILLPALARKL---GKDL-----DEEGISIIPVGGKSNLKPLAKLLKALG-----IPVAVLTDGDEAGKAET 350
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
29-369 1.49e-23

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 100.84  E-value: 1.49e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEF--RSGITLLVGENNSGKSNVIEALRLA-TTPLNRRSTRWFDESDLSHGREGQEAQFRAT 105
Cdd:COG3950     1 MRIKSLTIENFRGFEDLEIDFdnPPRLTVLVGENGSGKTTLLEAIALAlSGLLSRLDDVKFRKLLIRNGEFGDSAKLILY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 106 YDglsaAQRAHyiaaldvetneaaytttykrdesrqqmrptvtagpvdgPDAEPDKRDQIAHVYLAPLRDAQRELDSSDg 185
Cdd:COG3950    81 YG----TSRLL--------------------------------------LDGPLKKLERLKEEYFSRLDGYDSLLDEDS- 117

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 186 nRLLRIIRYL--TEEDEQEEFRAQANDSFTKLKEhpVLTATTKEIqghlgeltdsvrgQTVEVTFaeyelhRLARSLRVK 263
Cdd:COG3950   118 -NLREFLEWLreYLEDLENKLSDELDEKLEAVRE--ALNKLLPDF-------------KDIRIDR------DPGRLVILD 175

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 264 MAEAGIPPADLTEsglGYANLLFIATVIL--------ELRNAQHMElTLFLVEEPEAHLHPQLQAVLLDYLQEqagaslk 335
Cdd:COG3950   176 KNGEELPLNQLSD---GERSLLALVGDLArrlaelnpALENPLEGE-GIVLIDEIDLHLHPKWQRRILPDLRK------- 244

                         330       340       350
                  ....*....|....*....|....*....|....
gi 1154315592 336 ddtHGPagRIQVVASTHSPNLASSVGIENVVALR 369
Cdd:COG3950   245 ---IFP--NIQFIVTTHSPLILSSLEDEEVIVLE 273
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 29-357 2.08e-21

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: 96.90  E-value: 2.08e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRL----------ATTPLNRRSTRWFDESDLSHG---- 94
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDIflnnkekffeDDFLVLYLKDVIKIDKEDLNIfeni 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  95 ---------------REGQEAQFRATYDGLSAAQRAHYIAALDVETNEAA--------------------------YTTT 133
Cdd:pfam13175  81 sfsidieidveflliLFGYLEIKKKYLCLASKGKAKEYEKTLHPKGANKAdlllelkisdlkkylkqfkiyiynnyYLDE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 134 YKRDESRQQMRPTV-----------TAGPVDGPDAE------PDKRDQIAHVYLAPLRD-----AQRELDSSDGNR---- 187
Cdd:pfam13175 161 KKNVFDKKSKYELPslkeeflnsekEEIKVDKEDLKklinelEKSINYHENVLENLQIKkllisADRNASDEDSEKinsl 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 188 LLRIIRYLTEEDEQEEFRAQ--ANDSFTKLKEhpvltattkeIQGHLGELTDSVRGQTVEVTFAEYELHRLARSLRVKMA 265
Cdd:pfam13175 241 LGALKQRIFEEALQEELELTekLKETQNKLKE----------IDKTLAEELKNILFKKIDKLKDFGYPPFLNPEIEIKKD 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 266 EAGIPpadLTESGLGYANLLFIAT--VILELRNAQHMELTLFLV-EEPEAHLHPQLQAVLLDYLQEqagasLKDDTHGpa 342
Cdd:pfam13175 311 DEDLP---LNKNGSGVQRLILLIFfiAEAERKEDEIEEKNVILAiEEPEAHLHPQAQRVLIKLLKE-----LANDNKT-- 380

                         410
                  ....*....|....*
gi 1154315592 343 griQVVASTHSPNLA 357
Cdd:pfam13175 381 ---QVIITTHSPHII 392
COG4637 COG4637
Predicted ATPase [General function prediction only];
31-378 3.35e-17

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 83.83  E-value: 3.35e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  31 LRQLGIKNFRSCYDIEVEFrSGITLLVGENNSGKSNVIEALRL----ATTPLNR--------RSTRWFDESDLShgregQ 98
Cdd:COG4637     2 ITRIRIKNFKSLRDLELPL-GPLTVLIGANGSGKSNLLDALRFlsdaARGGLQDalarrgglEELLWRGPRTIT-----E 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  99 EAQFRATYDGlSAAQRAHYIAALDVETNEAAY-----TTTYKRDE-SRQQMRPTVTAGPVDGPDAEPDKRD--------- 163
Cdd:COG4637    76 PIRLELEFAE-EDERDLRYELELGLPEPGGRPevkeeRLWLKRGSgGRPFLDFRPKGRAVGGEPERLDSPEsllsqlgdp 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 164 ----------------QIAHVYLAPLRDAQRELD----SSDGNRLLRIIRYLTEEDEQEEfraqandsftklkehpvlta 223
Cdd:COG4637   155 erfpelralrealrswRFYDFHPAPLRQPQPAGRtpvlAPDGSNLAAVLATLRETHPERF-------------------- 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 224 ttKEIQGHLGELTDSVRGQTVEVTFAEYelhrlarsLRVKMAEAG----IPPADLTEsGLgyanLLFIATVILELRNAQH 299
Cdd:COG4637   215 --ERILEALRDAFPGFEDIEVEPDEDGR--------VLLEFREKGldrpFPARELSD-GT----LRFLALLAALLSPRPP 279

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1154315592 300 melTLFLVEEPEAHLHPQLQAVLLDYLQEQagaslkddthgpAGRIQVVASTHSPNLASSVGIENVVALRtRVDKEAVQ 378
Cdd:COG4637   280 ---PLLCIEEPENGLHPDLLPALAELLREA------------SERTQVIVTTHSPALLDALEPEEVLVLE-REDDGETR 342
TOPRIM_OLD cd01026
TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 422-509 1.50e-15

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: 72.31  E-value: 1.50e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 422 LFARRVILVEGIAEAVLLPVIARHCvfggddqaKQRRDFHGVTIINVGSVDFAPYITLLlsevngcRLLDKLT-VITDRD 500
Cdd:cd01026     1 FFADKVILVEGDSEEILLPALAKKL--------GLDLDEAGISIIPVGGKNFKPFIKLL-------NALGIPVaVLTDLD 65


                  ....*....
gi 1154315592 501 PDVPKEKKA 509
Cdd:cd01026    66 AKRNEKKDD 74
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 53-356 1.78e-14

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: 74.73  E-value: 1.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  53 ITLLVGENNSGKSNVIEALRLATTPLN----------RRSTRWFDESDLSHGREGQEAQFRaTYDGLSAAQRAHYIAALD 122
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDAlvigltdersRNGGIGGIPSLLNGIDPKEPIEFE-ISEFLEDGVRYRYGLDLE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 123 VETNEAAYTTTYKRDESRQQMRPTVTAGPVDGPDAEPDKRDQIAHVYLAPLRDAQRELDSSDGNRLLRIIRYLTEEDEQE 202
Cdd:pfam13304  80 REDVEEKLSSKPTLLEKRLLLREDSEEREPKFPPEAEELRLGLDVEERIELSLSELSDLISGLLLLSIISPLSFLLLLDE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 203 EFRAQANDSFTKLKEHpvltATTKEIQGHLGELTDSVRGQTVEVTFAEYEL-------HRLARSLRVKMAEAGIPPADLT 275
Cdd:pfam13304 160 GLLLEDWAVLDLAADL----ALFPDLKELLQRLVRGLKLADLNLSDLGEGIeksllvdDRLRERGLILLENGGGGELPAF 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 276 ESGLGYANLLFIATVILELRnaqhMELTLFLVEEPEAHLHPQLQAVLLDYLQEQAgaslkddthgpAGRIQVVASTHSPN 355
Cdd:pfam13304 236 ELSDGTKRLLALLAALLSAL----PKGGLLLIDEPESGLHPKLLRRLLELLKELS-----------RNGAQLILTTHSPL 300


                  .
gi 1154315592 356 L 356
Cdd:pfam13304 301 L 301
COG4938 COG4938
Predicted ATPase [General function prediction only];
31-389 5.96e-13

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 69.61  E-value: 5.96e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  31 LRQLGIKNFRSCYDIEVEFrSGITLLVGENNSGKSNVIEALRLattplnrrstrwfdesdlshgregqeaqFRATydgls 110
Cdd:COG4938     1 IKSISIKNFGPFKEAELEL-KPLTLLIGPNGSGKSTLIQALLL----------------------------LLQS----- 46

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 111 aaqRAHYIAAldvetneaaytttykrdeSRqqMRPTVTAGPVDGPDAEPDKRDQiahvYLAPLrdaqreldssdgnrLLR 190
Cdd:COG4938    47 ---NFIYLPA------------------ER--SGPARLYPSLVRELSDLGSRGE----YTADF--------------LAE 85

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 191 IIRYLTEEDEQEEFRAQANDsftklkehpvltattkeiqgHLGELTDsvrgqtvevTFAEYELHRLARSLRVKMAEAGIP 270
Cdd:COG4938    86 LENLEILDDKSKELLEQVEE--------------------WLEKIFP---------GKVEVDASSDLVRLVFRPSGNGKR 136

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 271 pADLTESGLGYANLLFIATVILELRNaqhmELTLFLVEEPEAHLHPQLQAVLLDYLQEQAgaslkddthgpAGRIQVVAS 350
Cdd:COG4938   137 -IPLSNVGSGVSELLPILLALLSAAK----PGSLLIIEEPEAHLHPKAQSALAELLAELA-----------NSGVQVIIE 200

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 1154315592 351 THSPNLASsvGIENVVALRTRVDKEAVQ----DDQGKQKEVRR 389
Cdd:COG4938   201 THSDYILN--GLRNLIKEGKLLDPDDVAvyffERDGGGSELRR 241
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
31-356 6.53e-13

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 70.46  E-value: 6.53e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  31 LRQLGIKNFRSCYD-IEVEFRSG------ITLLVGENNSGKSNVIEALRLATTPLNRRSTR---WFDESDLSHGREGQEA 100
Cdd:COG1106     2 LISFSIENFRSFKDeLTLSMVASglrllrVNLIYGANASGKSNLLEALYFLRNLVLNSSQPgdkLVEPFLLDSESKNEPS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 101 QFRATYdgLSAAQRAHYIAALDvetneaaytttykrdesrqqmrptvtagpvdgpdaepdkRDQIAH---VYLAPLRDAQ 177
Cdd:COG1106    82 EFEILF--LLDGVRYEYGFELD---------------------------------------KERIISewlYFLSTAAQLN 120

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 178 RELDSSDGNRLLRIIRYLTEEDeqeefraqanDSFTKLKEHPVLtatTKEIQGHLGELTDSVRGQTVEVTFAEYELHRLA 257
Cdd:COG1106   121 VPLLSPLYDWFDNNISLDTSSD----------GLTLLLKEDESL---KEELLELLKIADPGIEDIEVEEEEIEDLVERKL 187

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 258 RSLRVKMAEagipPADLTESGLGYANLLFIATVILELRNAQHmeltLFLVEEPEAHLHPQLQAVLLDYLQEQAgaslkdd 337
Cdd:COG1106   188 IFKHKGGNV----PLPLSEESDGTKRLLALAGALLDALAKGG----VLLIDEIEASLHPSLLRKLLKLFLDLA------- 252

                         330
                  ....*....|....*....
gi 1154315592 338 thgPAGRIQVVASTHSPNL 356
Cdd:COG1106   253 ---NKNNAQLIFTTHSTEL 268
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 31-84 7.41e-12

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: 64.94  E-value: 7.41e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1154315592  31 LRQLGIKNFRSCYDI-EVEFRSGITLLVGENNSGKSNVIEALRLATTPLNRRSTR 84
Cdd:cd03240     1 IDKLSIRNIRSFHERsEIEFFSPLTLIVGQNGAGKTTIIEALKYALTGELPPNSK 55
OLD-like_TOPRIM pfam20469
Overcoming lysogenization defect protein-like, TOPRIM domain; This entry represents the ...
 422-500 2.10e-11

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: 59.71  E-value: 2.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 422 LFARRVILVEGIAEAVLLPVIARHcVFGGDdqakqrRDFHGVTIINVGSVD-FAPYITLLlsevngcRLLDKLT-VITDR 499
Cdd:pfam20469   1 FFADKVILVEGDTEEILLPALAEK-LLGKD------LDALGISIVSVGGKGnFKRFLKLL-------KALGIPVaVITDL 66


                  .
gi 1154315592 500 D 500
Cdd:pfam20469  67 D 67
AAA_23 pfam13476
AAA domain;
34-210 4.46e-11

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 62.51  E-value: 4.46e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  34 LGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRLATT----PLNRRSTRWFDESDLSHGREGQ-EAQFRATYDG 108
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAIKLALYgktsRLKRKSGGGFVKGDIRIGLEGKgKAYVEITFEN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 109 lsaaQRAHYIAALDVETNEAAYTTTYKRDESRQQMRptvTAGPVDGPDAEPDKRDQIAHVYLA-PLRDAQRELDSSDGNR 187
Cdd:pfam13476  81 ----NDGRYTYAIERSRELSKKKGKTKKKEILEILE---IDELQQFISELLKSDKIILPLLVFlGQEREEEFERKEKKER 153

                         170       180
                  ....*....|....*....|....
gi 1154315592 188 LLRIIRYL-TEEDEQEEFRAQAND 210
Cdd:pfam13476 154 LEELEKALeEKEDEKKLLEKLLQL 177
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 31-129 4.16e-09

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: 58.08  E-value: 4.16e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  31 LRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRLATTPLNRRSTRwfdesDLSHGREGQ-EAQFRATydgl 109
Cdd:cd03242     1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSR-----DKELIRWGAeEAKISAV---- 71

                          90       100
                  ....*....|....*....|
gi 1154315592 110 saAQRAHYIAALDVETNEAA 129
Cdd:cd03242    72 --LERQGGELALELTIRSGG 89
recF PRK00064
recombination protein F; Reviewed
 29-71 5.69e-09

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 58.25  E-value: 5.69e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEAL 71
Cdd:PRK00064    1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAI 43
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
31-74 1.56e-08

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 55.40  E-value: 1.56e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1154315592  31 LRQLGIKNFRSCYD-IEVEFRSGITLLVGENNSGKSNVIEALRLA 74
Cdd:COG0419     2 LLRLRLENFRSYRDtETIDFDDGLNLIVGPNGAGKSTILEAIRYA 46
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
30-76 3.59e-08

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 55.93  E-value: 3.59e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1154315592  30 YLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRLATT 76
Cdd:COG1195     1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLAT 47
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
29-71 1.60e-07

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 54.68  E-value: 1.60e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEAL 71
Cdd:PRK03918    1 MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAI 43
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 31-72 3.32e-07

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: 51.31  E-value: 3.32e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1154315592  31 LRQLGIKNFRSCYD-IEVEFRSGITLLVGENNSGKSNVIEALR 72
Cdd:cd03278     1 LKKLELKGFKSFADkTTIPFPPGLTAIVGPNGSGKSNIIDAIR 43
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 29-71 4.24e-07

recF protein; All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273173 [Multi-domain]  Cd Length: 365  Bit Score: 52.74  E-value: 4.24e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEAL 71
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAI 43
DUF2813 pfam11398
Protein of unknown function (DUF2813); This entry contains YjbD from Escherichia coli, which ...
 29-410 1.70e-05

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: 47.73  E-value: 1.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSgITLLVGENNSGKSNVIEALRLATTPLNR-----RSTRWFDESDlSHGREgQEAQ-- 101
Cdd:pfam11398   1 MHLERIEVVGFRGINRLSLHFDQ-LTVLIGENAWGKSSLLDALSLLLNPTKElyqftLDDFHQPYAI-ENEPT-RHLQii 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 102 --FRATYDGLSAAQRAHYIAALDVETNEAAYTTTYKRD-ESRQQMRPTVTAGPVDGpDAEPDKRDQIAH-----VYLAP- 172
Cdd:pfam11398  78 ftFKESAPGEHKARRYRSLSALWVPHKDGYQRIYYRVEgEINEDGDVTTTRSFLDE-DGEPIPLDDIEElvrelISLHPv 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 173 --LRDAQRELDSSDGN----------------RLLRIIRYLTEEDEQEEFRAqandsFTKLKEHpVLTATTKEIQGHLGE 234
Cdd:pfam11398 157 lrLRDARRLRNGTLDVeycnsrlerridnlarRLITTPQQLSEGELKSGLQA-----MVQLLDH-YFSFQNHRRHNHRNM 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 235 LTDSVRGQTVE--VTFAEYELHR-LARSLRVKMaeagippadltesgLGYANLLFIATVILELRNAQHmelTLFLVEEPE 311
Cdd:pfam11398 231 REILTYGQKLWnkLKSLNQLLKQdESKSLRLLL--------------LGLLATLLQAKGPVELRRGAR---PILLLEDPE 293

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 312 AHLHPQLQAV---LLDYLqeqagaslkddthgPagrIQVVASTHSPNLASSVGIENVvalrtrvdkeavqddqgkQKEVR 388
Cdd:pfam11398 294 GRLHPTMLAIaweLLSLL--------------P---MQKILTTNSSELLSQVPLSSI------------------CRLVR 338

                         410       420
                  ....*....|....*....|...
gi 1154315592 389 RR-KTQALPLAKIALSEAERRKI 410
Cdd:pfam11398 339 ESdRTQSYQLGRKSLSREDLRRI 361
PRK01156 PRK01156
chromosome segregation protein; Provisional
 29-74 1.70e-05

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 48.36  E-value: 1.70e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRLA 74
Cdd:PRK01156    1 MIIKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAIRFA 46
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 29-72 3.07e-05

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 47.24  E-value: 3.07e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1154315592  29 MYLRQLGIKNFRSCYD-IEVEFRSGITLLVGENNSGKSNVIEALR 72
Cdd:COG1196     1 MRLKRLELAGFKSFADpTTIPFEPGITAIVGPNGSGKSNIVDAIR 45
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 30-72 5.02e-05

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: 46.89  E-value: 5.02e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1154315592   30 YLRQLGIKNFRSCYD-IEVEFRSGITLLVGENNSGKSNVIEALR 72
Cdd:pfam02463    1 YLKRIEIEGFKSYAKtVILPFSPGFTAIVGPNGSGKSNILDAIL 44
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 30-72 7.54e-05

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: 46.20  E-value: 7.54e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1154315592   30 YLRQLGIKNFRSCYD-IEVEFRSGITLLVGENNSGKSNVIEALR 72
Cdd:TIGR02168    1 RLKKLELAGFKSFADpTTINFDKGITGIVGPNGCGKSNIVDAIR 44
retron_eff_Eco8 NF038234
retron Eco8 family effector endonuclease; This ATPase, found as the effector protein partner ...
 29-360 1.68e-04

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: 45.02  E-value: 1.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRLATTPLNRRSTrwfDESDLsHGREGQEAQFRATYDg 108
Cdd:NF038234    1 MPIKSIKIKNLLSFDDLEIDDLKDINCIIGKNNVGKSNLLKALKFFYKNLTGEKV---IPPIL-DSNYSSKGEISITYD- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 109 LSaaqRAHYIAALDVETNE---AAYTTTYKRD----ESRQQMRPTVTA-------GPVDGPDAEPDKRDQIAHVYlaPLR 174
Cdd:NF038234   76 TS---RLKRIARSNTNKNEyfkHIYNPFFKKIifsfKKYLDKNTLFTLtlkiyknGSISWSIKDYETRKLLSYLF--PFF 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 175 DAQ-RELDSSDGNRLLRIIRYLTEEDEQEEFRAQANDSFTKLKEhpvlTATTKEIQGHLGELTDSVRgqTVEVTFAEYEL 253
Cdd:NF038234  151 FIEsRHINLYDWDELWDLIGRLKKFNLSGLSNEEIIDFFDEKIS----SNYSNSYKDIIEEIKKSIE--TKPYSYKEKIL 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 254 HRLarSLRVKMAEAGIPPADLTESGLGYANLLFIAT---VILELRNAQHMELTLFlVEEPEAHLHPQLQAVLLDYLQEQA 330
Cdd:NF038234  225 SYI--KLGLGGYKFNIDGEELKTQSDGTNSFNFIKLflnLLITLSRREYITPFIF-IDEPELGLHPKLNEQLINEIYESY 301

                         330       340       350
                  ....*....|....*....|....*....|
gi 1154315592 331 gASLKDDTHGPagRIQVVASTHSPNLASSV 360
Cdd:NF038234  302 -SFKKKDNKTP--YPKIILATHSPRIIKNI 328
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
29-413 2.15e-04

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 44.37  E-value: 2.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALR-LATTPLNRRSTRWFDESDLSHGREGQE-AQFRATY 106
Cdd:COG4717     1 MKIKELEIYGFGKFRDRTIEFSPGLNVIYGPNEAGKSTLLAFIRaMLLERLEKEADELFKPQGRKPELNLKElKELEEEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 107 DGLSAAQRAHYIAALDVETNEAAYTTTYKRDESRQQMRPTVtagpvdgpdaepdKRDQIAHVYLAPLRDAQRELDSSDG- 185
Cdd:COG4717    81 KEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKL-------------EKLLQLLPLYQELEALEAELAELPEr 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 186 -NRLLRIIRYLTE-EDEQEEFRAQANDSFTKLKEHpvLTATTKEIQGHLGELTDSVRGQTVEVTFAEYELHRLARSL--- 260
Cdd:COG4717   148 lEELEERLEELRElEEELEELEAELAELQEELEEL--LEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELeel 225

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 261 --RVKMAEAGIPPADLTESGLGYANLLFIATVILELRNAQHMELTLFLVEEPEAHLHPQLQAVLLDYLQEQAGASLKD-D 337
Cdd:COG4717   226 eeELEQLENELEAAALEERLKEARLLLLIAAALLALLGLGGSLLSLILTIAGVLFLVLGLLALLFLLLAREKASLGKEaE 305

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592 338 THGPAGRIQVVASTHSPNLASSVGI-------------ENVVALRTRVDKEAVQDDQGKQKEVRRRKTQALPLAKIALSE 404
Cdd:COG4717   306 ELQALPALEELEEEELEELLAALGLppdlspeellellDRIEELQELLREAEELEEELQLEELEQEIAALLAEAGVEDEE 385


                  ....*....
gi 1154315592 405 AERRKINQY 413
Cdd:COG4717   386 ELRAALEQA 394
ABC_RecN cd03241
ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC ...
 31-74 5.49e-04

ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC (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 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 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: 213208 [Multi-domain]  Cd Length: 276  Bit Score: 42.19  E-value: 5.49e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1154315592  31 LRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRLA 74
Cdd:cd03241     1 LLELSIKNFALIEELELDFEEGLTVLTGETGAGKSILLDALSLL 44
COG3910 COG3910
Predicted ATPase [General function prediction only];
46-71 9.60e-04

Predicted ATPase [General function prediction only];


Pssm-ID: 443116 [Multi-domain]  Cd Length: 239  Bit Score: 41.29  E-value: 9.60e-04
                          10        20
                  ....*....|....*....|....*.
gi 1154315592  46 EVEFRSGITLLVGENNSGKSNVIEAL 71
Cdd:COG3910    32 GLEFHPPVTFFVGENGSGKSTLLEAI 57
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 33-114 1.03e-03

ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterized by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.


Pssm-ID: 213194 [Multi-domain]  Cd Length: 162  Bit Score: 40.42  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154315592  33 QLGIKNFRS-CYDIEVEF-RSGITLLVGENNSGKSNVIEALRLATTplnRRSTRWFDESDLSHGREG--QEAQFRATYDG 108
Cdd:cd03227     1 KIVLGRFPSyFVPNDVTFgEGSLTIITGPNGSGKSTILDAIGLALG---GAQSATRRRSGVKAGCIVaaVSAELIFTRLQ 77


                  ....*.
gi 1154315592 109 LSAAQR 114
Cdd:cd03227    78 LSGGEK 83
recF PRK14079
recombination protein F; Provisional
 29-76 3.62e-03

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 40.15  E-value: 3.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1154315592  29 MYLRQLGIKNFRSCYDIEVEFRSGITLLVGENNSGKSNVIEALRLATT 76
Cdd:PRK14079    1 MRLLSLRQLNYRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAIYLALT 48
ABC_SMC4_euk cd03274
ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of ...
 29-71 3.88e-03

ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of chromosomes (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: 213241 [Multi-domain]  Cd Length: 212  Bit Score: 39.20  E-value: 3.88e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1154315592  29 MYLRQLGIKNFRSCYDIEV--EFRSGITLLVGENNSGKSNVIEAL 71
Cdd:cd03274     1 LIITKLVLENFKSYAGEQVigPFHKSFSAIVGPNGSGKSNVIDSM 45
ABC_SMC6_euk cd03276
ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of ...
 37-74 4.44e-03

ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of chromosomes (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: 213243 [Multi-domain]  Cd Length: 198  Bit Score: 38.73  E-value: 4.44e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1154315592  37 KNFRsCYD-IEVEFRSGITLLVGENNSGKSNVIEALRLA 74
Cdd:cd03276     7 KNFM-CHRhLQIEFGPRVNFIVGNNGSGKSAILTALTIG 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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