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Conserved domains on  [gi|491899495|ref|WP_005660010|]
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AAA family ATPase [Dethiosulfovibrio peptidovorans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-330 1.09e-80

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


:

Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 250.69  E-value: 1.09e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   1 MLIN-LTLNNFRRYEKAHFCFH--PKMTILVGENGKGKTTILDAIAVMLGTYFQGskiktgqstVKKDDARLLSVELGgq 77
Cdd:COG3950    1 MRIKsLTIENFRGFEDLEIDFDnpPRLTVLVGENGSGKTTLLEAIALALSGLLSR---------LDDVKFRKLLIRNG-- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  78 fnlepqddvfiqarstirnetidwirEMGDRGgkakdivsigtqdrkkavkgepidlPLYLYYGSGRLWDIHRNVKTGK- 156
Cdd:COG3950   70 --------------------------EFGDSA-------------------------KLILYYGTSRLLLDGPLKKLERl 98

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 157 ---PGSRLDAYRFCLDPKSDQKAFEEWFKKlTLAELQKKNSFKG---LQTVRNTVLRCIPNSSDFYHDVERDELIIVTDE 230
Cdd:COG3950   99 keeYFSRLDGYDSLLDEDSNLREFLEWLRE-YLEDLENKLSDELdekLEAVREALNKLLPDFKDIRIDRDPGRLVILDKN 177

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 231 G-PMPFDHLSDGYRNMVAMVADIAHRASRLNPHLEekAATRTKGIVLIDEIDLHLHPKWQRRVVSDLQEAFPEIQFIATT 309
Cdd:COG3950  178 GeELPLNQLSDGERSLLALVGDLARRLAELNPALE--NPLEGEGIVLIDEIDLHLHPKWQRRILPDLRKIFPNIQFIVTT 255

                        330       340
                 ....*....|....*....|.
gi 491899495 310 HSPFIIQSLEPGQVIDLEATE 330
Cdd:COG3950  256 HSPLILSSLEDEEVIVLERDE 276
restrict_AAA_1 super family cl26249
restriction system-associated AAA family ATPase; Members of this family are AAA family ATPases ...
 271-410 1.87e-06

restriction system-associated AAA family ATPase; Members of this family are AAA family ATPases by homology. They occur regularly in a conserved gene neighborhood with the restriction (R), modification (M), and specificity (S) proteins of an apparent type I restriction enzyme system, plus one additional uncharacterized protein. It is not clear whether members of this family contribute to restriction per se, or to another process such as transfer of mobile elements.


The actual alignment was detected with superfamily member TIGR04435:

Pssm-ID: 275228 [Multi-domain]  Cd Length: 555  Bit Score: 50.05  E-value: 1.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  271 TKGIVLIDEIDLHLHPKWQRRVVSDLQEAFPEI-------QFIATTHSPFIIQSLEPGQVIDLEATEEKAERTCDTGEQA 343
Cdd:TIGR04435 406 TNSLFLLDEPETHFNPKWRASFISRLRQCLEAGntknvmqEMLITTHSPFLISDCKPENVLVFKKNKENGKVEISLPKFN 485

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491899495  344 SPGTtapysnrSIEDIVEDIMGvdipqrseRYQKMYDVAKEYYKTLREARDADETRKKELKEKLDRL 410
Cdd:TIGR04435 486 TFGA-------SINKITMETFG--------KRETIGDYAQKQLKELRERFEEGEDDDELIKKILRNL 537
 
Name Accession Description Interval E-value
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-330 1.09e-80

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 250.69  E-value: 1.09e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   1 MLIN-LTLNNFRRYEKAHFCFH--PKMTILVGENGKGKTTILDAIAVMLGTYFQGskiktgqstVKKDDARLLSVELGgq 77
Cdd:COG3950    1 MRIKsLTIENFRGFEDLEIDFDnpPRLTVLVGENGSGKTTLLEAIALALSGLLSR---------LDDVKFRKLLIRNG-- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  78 fnlepqddvfiqarstirnetidwirEMGDRGgkakdivsigtqdrkkavkgepidlPLYLYYGSGRLWDIHRNVKTGK- 156
Cdd:COG3950   70 --------------------------EFGDSA-------------------------KLILYYGTSRLLLDGPLKKLERl 98

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 157 ---PGSRLDAYRFCLDPKSDQKAFEEWFKKlTLAELQKKNSFKG---LQTVRNTVLRCIPNSSDFYHDVERDELIIVTDE 230
Cdd:COG3950   99 keeYFSRLDGYDSLLDEDSNLREFLEWLRE-YLEDLENKLSDELdekLEAVREALNKLLPDFKDIRIDRDPGRLVILDKN 177

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 231 G-PMPFDHLSDGYRNMVAMVADIAHRASRLNPHLEekAATRTKGIVLIDEIDLHLHPKWQRRVVSDLQEAFPEIQFIATT 309
Cdd:COG3950  178 GeELPLNQLSDGERSLLALVGDLARRLAELNPALE--NPLEGEGIVLIDEIDLHLHPKWQRRILPDLRKIFPNIQFIVTT 255

                        330       340
                 ....*....|....*....|.
gi 491899495 310 HSPFIIQSLEPGQVIDLEATE 330
Cdd:COG3950  256 HSPLILSSLEDEEVIVLERDE 276
AAA_23 pfam13476
AAA domain;
5-203 9.12e-19

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 84.08  E-value: 9.12e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495    5 LTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVMLGTYFQGSKIKTGQSTVKKDdarllsVELGGQFNLEPQD 84
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAIKLALYGKTSRLKRKSGGGFVKGD------IRIGLEGKGKAYV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   85 DVFIQARSTIRNETIDWIREMGDRGGKAKD-------IVSIGTQDRKKAVKGEPIDLPLYLYYGSGRLWdihrNVKTGKP 157
Cdd:pfam13476  75 EITFENNDGRYTYAIERSRELSKKKGKTKKkeileilEIDELQQFISELLKSDKIILPLLVFLGQEREE----EFERKEK 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 491899495  158 GSRLDAYRFCLDPKSDqkafeewFKKLTLAELQKKNSFKGLQTVRN 203
Cdd:pfam13476 151 KERLEELEKALEEKED-------EKKLLEKLLQLKEKKKELEELKE 189
recF PRK00064
recombination protein F; Reviewed
 4-42 3.18e-09

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 58.25  E-value: 3.18e-09
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 491899495   4 NLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAI 42
Cdd:PRK00064   5 RLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAI 43
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 2-42 1.51e-08

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: 55.38  E-value: 1.51e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 491899495   2 LINLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAI 42
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAI 41
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 2-123 1.66e-08

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: 56.21  E-value: 1.66e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495    2 LINLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIavmlgtYFQGskikTGQSTVKKDDARLLSVElggqfnle 81
Cdd:TIGR00611   3 LSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAI------YYLA----LGRSHRTSRDKPLIRFG-------- 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 491899495   82 pQDDVFIQAR--STIRNETIDWIREMGDRGGKAKdiVSIGTQDR 123
Cdd:TIGR00611  65 -AEAFVIEGRvsKGDREVTIPLEGLLKKKGKKAK--VNIDGQDK 105
restrict_AAA_1 TIGR04435
restriction system-associated AAA family ATPase; Members of this family are AAA family ATPases ...
 271-410 1.87e-06

restriction system-associated AAA family ATPase; Members of this family are AAA family ATPases by homology. They occur regularly in a conserved gene neighborhood with the restriction (R), modification (M), and specificity (S) proteins of an apparent type I restriction enzyme system, plus one additional uncharacterized protein. It is not clear whether members of this family contribute to restriction per se, or to another process such as transfer of mobile elements.


Pssm-ID: 275228 [Multi-domain]  Cd Length: 555  Bit Score: 50.05  E-value: 1.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  271 TKGIVLIDEIDLHLHPKWQRRVVSDLQEAFPEI-------QFIATTHSPFIIQSLEPGQVIDLEATEEKAERTCDTGEQA 343
Cdd:TIGR04435 406 TNSLFLLDEPETHFNPKWRASFISRLRQCLEAGntknvmqEMLITTHSPFLISDCKPENVLVFKKNKENGKVEISLPKFN 485

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491899495  344 SPGTtapysnrSIEDIVEDIMGvdipqrseRYQKMYDVAKEYYKTLREARDADETRKKELKEKLDRL 410
Cdd:TIGR04435 486 TFGA-------SINKITMETFG--------KRETIGDYAQKQLKELRERFEEGEDDDELIKKILRNL 537
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 21-102 2.63e-04

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 41.20  E-value: 2.63e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495    21 HPKMTILVGENGKGKTTILDAIAVMLGTYFQGSKIKTGQSTVKKDDARLLSVELGGQFNLEPQDDVFIQARSTIRNETID 100
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPD 80


                   ..
gi 491899495   101 WI 102
Cdd:smart00382  81 VL 82
retron_eff_Eco8 NF038234
retron Eco8 family effector endonuclease; This ATPase, found as the effector protein partner ...
 274-318 3.44e-03

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: 39.63  E-value: 3.44e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 491899495 274 IVLIDEIDLHLHPKWQRRVVSDLQE---------AFPEIQFIATTHSPFIIQSL 318
Cdd:NF038234 275 FIFIDEPELGLHPKLNEQLINEIYEsysfkkkdnKTPYPKIILATHSPRIIKNI 328
 
Name Accession Description Interval E-value
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-330 1.09e-80

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 250.69  E-value: 1.09e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   1 MLIN-LTLNNFRRYEKAHFCFH--PKMTILVGENGKGKTTILDAIAVMLGTYFQGskiktgqstVKKDDARLLSVELGgq 77
Cdd:COG3950    1 MRIKsLTIENFRGFEDLEIDFDnpPRLTVLVGENGSGKTTLLEAIALALSGLLSR---------LDDVKFRKLLIRNG-- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  78 fnlepqddvfiqarstirnetidwirEMGDRGgkakdivsigtqdrkkavkgepidlPLYLYYGSGRLWDIHRNVKTGK- 156
Cdd:COG3950   70 --------------------------EFGDSA-------------------------KLILYYGTSRLLLDGPLKKLERl 98

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 157 ---PGSRLDAYRFCLDPKSDQKAFEEWFKKlTLAELQKKNSFKG---LQTVRNTVLRCIPNSSDFYHDVERDELIIVTDE 230
Cdd:COG3950   99 keeYFSRLDGYDSLLDEDSNLREFLEWLRE-YLEDLENKLSDELdekLEAVREALNKLLPDFKDIRIDRDPGRLVILDKN 177

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 231 G-PMPFDHLSDGYRNMVAMVADIAHRASRLNPHLEekAATRTKGIVLIDEIDLHLHPKWQRRVVSDLQEAFPEIQFIATT 309
Cdd:COG3950  178 GeELPLNQLSDGERSLLALVGDLARRLAELNPALE--NPLEGEGIVLIDEIDLHLHPKWQRRILPDLRKIFPNIQFIVTT 255

                        330       340
                 ....*....|....*....|.
gi 491899495 310 HSPFIIQSLEPGQVIDLEATE 330
Cdd:COG3950  256 HSPLILSSLEDEEVIVLERDE 276
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 2-324 7.89e-23

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: 99.31  E-value: 7.89e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   2 LINLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVMLGTyfqgskikTGQSTVKKDDarllsvelggqFNLE 81
Cdd:COG3593    3 LEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRLLLGP--------SSSRKFDEED-----------FYLG 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  82 PQDDvfiqarstirnetidwiremgdrggkakdivsigtqdrkkavkgePIDLPLYLYYGSgRLWDIHRNVKTGKPGSRL 161
Cdd:COG3593   64 DDPD---------------------------------------------LPEIEIELTFGS-LLSRLLRLLLKEEDKEEL 97

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 162 DAyrfclDPKSDQKAFEEWFKKLTlAELqkKNSFKGLQTVRNTVLRCIPNSSDfyhDVERDELIIVTDEGPMPFDHLSDG 241
Cdd:COG3593   98 EE-----ALEELNEELKEALKALN-ELL--SEYLKELLDGLDLELELSLDELE---DLLKSLSLRIEDGKELPLDRLGSG 166

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 242 YRNMVAMVadiahrasrLNPHLEEKAATRTKGIVLIDEIDLHLHPKWQRRVVSDLQE-AFPEIQFIATTHSPFIIQSLEP 320
Cdd:COG3593  167 FQRLILLA---------LLSALAELKRAPANPILLIEEPEAHLHPQAQRRLLKLLKElSEKPNQVIITTHSPHLLSEVPL 237


                 ....
gi 491899495 321 GQVI 324
Cdd:COG3593  238 ENIR 241
AAA_23 pfam13476
AAA domain;
5-203 9.12e-19

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 84.08  E-value: 9.12e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495    5 LTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVMLGTYFQGSKIKTGQSTVKKDdarllsVELGGQFNLEPQD 84
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAIKLALYGKTSRLKRKSGGGFVKGD------IRIGLEGKGKAYV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   85 DVFIQARSTIRNETIDWIREMGDRGGKAKD-------IVSIGTQDRKKAVKGEPIDLPLYLYYGSGRLWdihrNVKTGKP 157
Cdd:pfam13476  75 EITFENNDGRYTYAIERSRELSKKKGKTKKkeileilEIDELQQFISELLKSDKIILPLLVFLGQEREE----EFERKEK 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 491899495  158 GSRLDAYRFCLDPKSDqkafeewFKKLTLAELQKKNSFKGLQTVRN 203
Cdd:pfam13476 151 KERLEELEKALEEKED-------EKKLLEKLLQLKEKKKELEELKE 189
COG4637 COG4637
Predicted ATPase [General function prediction only];
1-331 1.47e-18

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 86.91  E-value: 1.47e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   1 MLINLTLNNFRRYEKAHFCFHPkMTILVGENGKGKTTILDAIAVM-------LGTYF-----------QGSKIKTGQ--- 59
Cdd:COG4637    1 MITRIRIKNFKSLRDLELPLGP-LTVLIGANGSGKSNLLDALRFLsdaarggLQDALarrggleellwRGPRTITEPirl 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  60 -STVKKDDARLLSVELggQFNLEPQDDVFIqarstIRNETIDWIREMGDRGgkakdivSIGTQDRKKAVKGEPIDLPLY- 137
Cdd:COG4637   80 eLEFAEEDERDLRYEL--ELGLPEPGGRPE-----VKEERLWLKRGSGGRP-------FLDFRPKGRAVGGEPERLDSPe 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 138 --LyygsGRLWDIHRNVKTGKPGSRLDAYRF-CLDP---KSDQKAFEEWFKKLT-------LAELQKKNSfKGLQTVRNT 204
Cdd:COG4637  146 slL----SQLGDPERFPELRALREALRSWRFyDFHPaplRQPQPAGRTPVLAPDgsnlaavLATLRETHP-ERFERILEA 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 205 VLRCIPNSSDFYHDVERDELIIV--TDEG---PMPFDHLSDGYRNMVAMVAdIAHrasrlnphleekaATRTKGIVLIDE 279
Cdd:COG4637  221 LRDAFPGFEDIEVEPDEDGRVLLefREKGldrPFPARELSDGTLRFLALLA-ALL-------------SPRPPPLLCIEE 286

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
gi 491899495 280 IDLHLHPKWQRRVVSDLQEAFPEIQFIATTHSPFIIQSLEPGQVIDLEATEE 331
Cdd:COG4637  287 PENGLHPDLLPALAELLREASERTQVIVTTHSPALLDALEPEEVLVLEREDD 338
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 24-315 3.37e-17

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: 82.05  E-value: 3.37e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   24 MTILVGENGKGKTTILDAIAVMLG--TYFQGSKIKtGQSTVKKDDARLLSVELGGQFNLEPQDDVFIQARSTIRNETI-- 99
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADfdALVIGLTDE-RSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVRYRYGLDle 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  100 -DWIREMGDRGGKAKDIvsigTQDRKKAVKGEPIDLPLYLYYGSGRLWDIHRNVKTGKPGSRLDAYRFCLDPKSDQKAFE 178
Cdd:pfam13304  80 rEDVEEKLSSKPTLLEK----RLLLREDSEEREPKFPPEAEELRLGLDVEERIELSLSELSDLISGLLLLSIISPLSFLL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  179 EWFKKLTLAELQKKNSFK--GLQTVRNTVLRCIPNSSDFYHDVERDELIIV--------------------TDEGPMPFD 236
Cdd:pfam13304 156 LLDEGLLLEDWAVLDLAAdlALFPDLKELLQRLVRGLKLADLNLSDLGEGIeksllvddrlrerglillenGGGGELPAF 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  237 HLSDGYRNMVAMVADIAHRASrlnphleekaatrTKGIVLIDEIDLHLHPKWQRRVVSDLQE-AFPEIQFIATTHSPFII 315
Cdd:pfam13304 236 ELSDGTKRLLALLAALLSALP-------------KGGLLLIDEPESGLHPKLLRRLLELLKElSRNGAQLILTTHSPLLL 302
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
1-333 4.07e-17

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 82.01  E-value: 4.07e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   1 MLINLTLNNFRRYEK-------AHFCFHPKMTILVGENGKGKTTILDAIAVMLGTYFQGSKIKTG--QSTVKKDDARLLS 71
Cdd:COG1106    1 MLISFSIENFRSFKDeltlsmvASGLRLLRVNLIYGANASGKSNLLEALYFLRNLVLNSSQPGDKlvEPFLLDSESKNEP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  72 VELGGQFNlepQDDVFIQARSTIRNETIdwIREmgdrggkAKDIVSIGTQdrkkavKGEPIDLPLYLYYGSgrlwDIHRN 151
Cdd:COG1106   81 SEFEILFL---LDGVRYEYGFELDKERI--ISE-------WLYFLSTAAQ------LNVPLLSPLYDWFDN----NISLD 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 152 VKTGKPGSRLDayrfclDPKSDQKAFEEWFKKLTLaelqkknSFKGLQTVRNTVLRCIPNSSDFYHDverdeliivTDEG 231
Cdd:COG1106  139 TSSDGLTLLLK------EDESLKEELLELLKIADP-------GIEDIEVEEEEIEDLVERKLIFKHK---------GGNV 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 232 PMPFDHLSDGYRNMVAMVADIAHrasrlnphleekaATRTKGIVLIDEIDLHLHPKWQRRVVSDLQEAFPE--IQFIATT 309
Cdd:COG1106  197 PLPLSEESDGTKRLLALAGALLD-------------ALAKGGVLLIDEIEASLHPSLLRKLLKLFLDLANKnnAQLIFTT 263

                        330       340
                 ....*....|....*....|....*...
gi 491899495 310 HSPFIIQS----LEPGQVIDLEATEEKA 333
Cdd:COG1106  264 HSTELLDAflelLRRDQIWFVEKDKDGA 291
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-315 1.29e-12

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: 69.16  E-value: 1.29e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495    1 MLIN-LTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVMLGT-----------YFQGSKIKTGQST--VKKDD 66
Cdd:pfam13175   1 MKIKsIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDIFLNNkekffeddflvLYLKDVIKIDKEDlnIFENI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   67 ARLLSVELGGQFNL---EPQDDVFIQARSTIRNETIDWIREMGDRGGKAKDIVSIGTQDRKKAVKGEPI----------- 132
Cdd:pfam13175  81 SFSIDIEIDVEFLLilfGYLEIKKKYLCLASKGKAKEYEKTLHPKGANKADLLLELKISDLKKYLKQFKiyiynnyylde 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  133 -----------DLPLYLYYGSG--------------RLWDIHRNVKTGKPG---SRLDAYRFCLDPKSDQKAFEEWFKKL 184
Cdd:pfam13175 161 kknvfdkkskyELPSLKEEFLNsekeeikvdkedlkKLINELEKSINYHENvleNLQIKKLLISADRNASDEDSEKINSL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  185 TLAELQKKNS------------FKGLQTV------------RNTVLRCIPNSSDFYHDVERDELI-IVTDEGPMPFDHLS 239
Cdd:pfam13175 241 LGALKQRIFEealqeeleltekLKETQNKlkeidktlaeelKNILFKKIDKLKDFGYPPFLNPEIeIKKDDEDLPLNKNG 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  240 DGYRNMVAMVADIAhrasrlnpHLEEKAATRTK--GIVLIDEIDLHLHPKWQRRVVSDLQEAF--PEIQFIATTHSPFII 315
Cdd:pfam13175 321 SGVQRLILLIFFIA--------EAERKEDEIEEknVILAIEEPEAHLHPQAQRVLIKLLKELAndNKTQVIITTHSPHII 392
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-42 4.36e-10

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 60.94  E-value: 4.36e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 491899495   2 LINLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAI 42
Cdd:COG1195    2 LKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAI 42
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
1-100 1.36e-09

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 57.71  E-value: 1.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   1 MLINLTLNNFRRYEKAH-FCFHPKMTILVGENGKGKTTILDAIAVMLgtYFQGSKIKTGQSTVKKDDARLLSVEL----- 74
Cdd:COG0419    1 KLLRLRLENFRSYRDTEtIDFDDGLNLIVGPNGAGKSTILEAIRYAL--YGKARSRSKLRSDLINVGSEEASVELefehg 78

                         90       100
                 ....*....|....*....|....*....
gi 491899495  75 GGQFNLE-PQDDV--FIQARSTIRNETID 100
Cdd:COG0419   79 GKRYRIErRQGEFaeFLEAKPSERKEALK 107
recF PRK00064
recombination protein F; Reviewed
 4-42 3.18e-09

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 58.25  E-value: 3.18e-09
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 491899495   4 NLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAI 42
Cdd:PRK00064   5 RLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAI 43
COG4938 COG4938
Predicted ATPase [General function prediction only];
5-318 1.26e-08

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 55.74  E-value: 1.26e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   5 LTLNNFRRYEKAHFCFHPkMTILVGENGKGKTTILDAIAVMLGTYFQgskiktgqstvkkddarllsvelggqfnlepqd 84
Cdd:COG4938    4 ISIKNFGPFKEAELELKP-LTLLIGPNGSGKSTLIQALLLLLQSNFI--------------------------------- 49

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  85 dvFIQA-RSTIRN---ETIDWIREMGDRGGKAKDIvsigtqdrkkavkgepidlplylyygsgrLWDIHRNVKTGKpgsr 160
Cdd:COG4938   50 --YLPAeRSGPARlypSLVRELSDLGSRGEYTADF-----------------------------LAELENLEILDD---- 94

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 161 ldayrfclDPKSDQKAFEEWFKKLtlaelqkknsFKGLQTVRntvlrcipnssdfyHDVERDELII--VTDEGPMPFDHL 238
Cdd:COG4938   95 --------KSKELLEQVEEWLEKI----------FPGKVEVD--------------ASSDLVRLVFrpSGNGKRIPLSNV 142

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 239 SDGYRNMVAMVADIAHrasrlnphleekaATRTKGIVLIDEIDLHLHPKWQRRVVSDLQEAFPE-IQFIATTHSPFIIQS 317
Cdd:COG4938  143 GSGVSELLPILLALLS-------------AAKPGSLLIIEEPEAHLHPKAQSALAELLAELANSgVQVIIETHSDYILNG 209


                 .
gi 491899495 318 L 318
Cdd:COG4938  210 L 210
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 2-42 1.51e-08

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: 55.38  E-value: 1.51e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 491899495   2 LINLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAI 42
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAI 41
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 2-123 1.66e-08

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: 56.21  E-value: 1.66e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495    2 LINLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIavmlgtYFQGskikTGQSTVKKDDARLLSVElggqfnle 81
Cdd:TIGR00611   3 LSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAI------YYLA----LGRSHRTSRDKPLIRFG-------- 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 491899495   82 pQDDVFIQAR--STIRNETIDWIREMGDRGGKAKdiVSIGTQDR 123
Cdd:TIGR00611  65 -AEAFVIEGRvsKGDREVTIPLEGLLKKKGKKAK--VNIDGQDK 105
COG3910 COG3910
Predicted ATPase [General function prediction only];
20-47 4.72e-07

Predicted ATPase [General function prediction only];


Pssm-ID: 443116 [Multi-domain]  Cd Length: 239  Bit Score: 50.53  E-value: 4.72e-07
                         10        20
                 ....*....|....*....|....*...
gi 491899495  20 FHPKMTILVGENGKGKTTILDAIAVMLG 47
Cdd:COG3910   35 FHPPVTFFVGENGSGKSTLLEAIAVAAG 62
restrict_AAA_1 TIGR04435
restriction system-associated AAA family ATPase; Members of this family are AAA family ATPases ...
 271-410 1.87e-06

restriction system-associated AAA family ATPase; Members of this family are AAA family ATPases by homology. They occur regularly in a conserved gene neighborhood with the restriction (R), modification (M), and specificity (S) proteins of an apparent type I restriction enzyme system, plus one additional uncharacterized protein. It is not clear whether members of this family contribute to restriction per se, or to another process such as transfer of mobile elements.


Pssm-ID: 275228 [Multi-domain]  Cd Length: 555  Bit Score: 50.05  E-value: 1.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495  271 TKGIVLIDEIDLHLHPKWQRRVVSDLQEAFPEI-------QFIATTHSPFIIQSLEPGQVIDLEATEEKAERTCDTGEQA 343
Cdd:TIGR04435 406 TNSLFLLDEPETHFNPKWRASFISRLRQCLEAGntknvmqEMLITTHSPFLISDCKPENVLVFKKNKENGKVEISLPKFN 485

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491899495  344 SPGTtapysnrSIEDIVEDIMGvdipqrseRYQKMYDVAKEYYKTLREARDADETRKKELKEKLDRL 410
Cdd:TIGR04435 486 TFGA-------SINKITMETFG--------KRETIGDYAQKQLKELRERFEEGEDDDELIKKILRNL 537
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 4-102 2.57e-06

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: 47.99  E-value: 2.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   4 NLTLNNFR-RYEKAHFCFHPKMTILVGENGKGKTTILDAIAVML-GTYFQGSKIKTGQSTVKKDDARLLSVELggQFNLE 81
Cdd:cd03240    3 KLSIRNIRsFHERSEIEFFSPLTLIVGQNGAGKTTIIEALKYALtGELPPNSKGGAHDPKLIREGEVRAQVKL--AFENA 80

                         90       100
                 ....*....|....*....|....*...
gi 491899495  82 PQDDVFI-----QARSTI--RNETIDWI 102
Cdd:cd03240   81 NGKKYTItrslaILENVIfcHQGESNWP 108
ABC_RecN cd03241
ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC ...
 2-88 1.51e-05

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: 46.43  E-value: 1.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   2 LINLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVMLGTYFQGSKIKTGqstvkKDDARLLsvelgGQFNLE 81
Cdd:cd03241    1 LLELSIKNFALIEELELDFEEGLTVLTGETGAGKSILLDALSLLLGGRASADLIRSG-----AEKAVVE-----GVFDIS 70


                 ....*..
gi 491899495  82 PQDDVFI 88
Cdd:cd03241   71 DEEEAKA 77
ABC_SMC6_euk cd03276
ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of ...
 5-63 1.89e-05

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: 45.28  E-value: 1.89e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491899495   5 LTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVMLGTYFQ----GSK----IKTGQSTVK 63
Cdd:cd03276    4 ITLKNFMCHRHLQIEFGPRVNFIVGNNGSGKSAILTALTIGLGGKASdtnrGSSlkdlIKDGESSAK 70
ABC_SMC4_euk cd03274
ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of ...
 1-58 4.14e-05

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: 44.59  E-value: 4.14e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   1 MLINLTLNNFRRYEKAHFC--FHPKMTILVGENGKGKTTILDAIAVMLGtyFQGSKIKTG 58
Cdd:cd03274    2 IITKLVLENFKSYAGEQVIgpFHKSFSAIVGPNGSGKSNVIDSMLFVFG--FRASKMRQK 59
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 5-47 4.63e-05

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: 43.50  E-value: 4.63e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 491899495   5 LTLNNFRRY---EKAHFcFHPKMTILVGENGKGKTTILDAIAVMLG 47
Cdd:cd03227    2 IVLGRFPSYfvpNDVTF-GEGSLTIITGPNGSGKSTILDAIGLALG 46
PRK01156 PRK01156
chromosome segregation protein; Provisional
 1-74 7.31e-05

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 45.28  E-value: 7.31e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491899495   1 MLIN-LTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVMLgtyFQGSKIKTGQSTVKKdDARLLSVEL 74
Cdd:PRK01156   1 MIIKrIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAIRFAL---FTDKRTEKIEDMIKK-GKNNLEVEL 71
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
2-46 1.15e-04

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 44.37  E-value: 1.15e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 491899495   2 LINLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVML 46
Cdd:COG4717    3 IKELEIYGFGKFRDRTIEFSPGLNVIYGPNEAGKSTLLAFIRAML 47
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
1-66 1.64e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 44.28  E-value: 1.64e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491899495   1 MLIN-LTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVMLgTYFQGSKIKtgqsTVKKDD 66
Cdd:PRK03918   1 MKIEeLKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAILVGL-YWGHGSKPK----GLKKDD 62
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 21-102 2.63e-04

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 41.20  E-value: 2.63e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495    21 HPKMTILVGENGKGKTTILDAIAVMLGTYFQGSKIKTGQSTVKKDDARLLSVELGGQFNLEPQDDVFIQARSTIRNETID 100
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPD 80


                   ..
gi 491899495   101 WI 102
Cdd:smart00382  81 VL 82
AAA_29 pfam13555
P-loop containing region of AAA domain;
18-46 2.64e-04

P-loop containing region of AAA domain;


Pssm-ID: 433304 [Multi-domain]  Cd Length: 61  Bit Score: 38.74  E-value: 2.64e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 491899495   18 FCFHPK-MTILVGENGKGKTTILDAIAVML 46
Cdd:pfam13555  17 IPIDPRgNTLLTGPSGSGKSTLLDAIQTLL 46
MK0520 COG2401
ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction ...
 234-324 3.27e-04

ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only];


Pssm-ID: 441957 [Multi-domain]  Cd Length: 222  Bit Score: 41.87  E-value: 3.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495 234 PFDHLSDG--YRNMVAMVadiahrasrlnphLEEKAATrtkgiVLIDEIDLHLHPKWQRRVVSDLQEAFPE--IQFIATT 309
Cdd:COG2401  133 RFKELSTGqkFRFRLALL-------------LAERPKL-----LVIDEFCSHLDRQTAKRVARNLQKLARRagITLVVAT 194

                         90
                 ....*....|....*
gi 491899495 310 HSPFIIQSLEPGQVI 324
Cdd:COG2401  195 HHYDVIDDLQPDLLI 209
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 1-47 3.89e-04

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: 43.04  E-value: 3.89e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 491899495     1 MLINLTLNNFRRY-EKAHFCFHPKMTILVGENGKGKTTILDAIAVMLG 47
Cdd:pfam02463    1 YLKRIEIEGFKSYaKTVILPFSPGFTAIVGPNGSGKSNILDAILFVLG 48
RecN COG0497
DNA repair ATPase RecN [Replication, recombination and repair];
1-47 7.42e-04

DNA repair ATPase RecN [Replication, recombination and repair];


Pssm-ID: 440263 [Multi-domain]  Cd Length: 555  Bit Score: 41.98  E-value: 7.42e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 491899495   1 MLINLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVMLG 47
Cdd:COG0497    1 MLTELSIRNFALIDELELEFGPGLTVLTGETGAGKSILLDALGLLLG 47
ABC_SMC5_euk cd03277
ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of ...
 2-47 9.52e-04

ATP-binding cassette domain of eukaryotic SMC5 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: 213244 [Multi-domain]  Cd Length: 213  Bit Score: 40.27  E-value: 9.52e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 491899495   2 LINLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVMLG 47
Cdd:cd03277    3 IVRIKLENFVTYDETEFRPGPSLNMIIGPNGSGKSSIVCAICLGLG 48
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 2-54 1.61e-03

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: 39.37  E-value: 1.61e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 491899495   2 LINLTLNNFRRY-EKAHFCFHPKMTILVGENGKGKTTILDAIAVMLGTyfQGSK 54
Cdd:cd03278    1 LKKLELKGFKSFaDKTTIPFPPGLTAIVGPNGSGKSNIIDAIRWVLGE--QSAK 52
ABCF_EF-3 cd03221
ATP-binding cassette domain of elongation factor 3, subfamily F; Elongation factor 3 (EF-3) is ...
 3-58 2.64e-03

ATP-binding cassette domain of elongation factor 3, subfamily F; Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.


Pssm-ID: 213188 [Multi-domain]  Cd Length: 144  Bit Score: 38.20  E-value: 2.64e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   3 INLTLNNFRRYekahfcfhpkmtILVGENGKGKTTILDAIAVML----GTYFQGSKIKTG 58
Cdd:cd03221   19 ISLTINPGDRI------------GLVGRNGAGKSTLLKLIAGELepdeGIVTWGSTVKIG 66
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 5-77 3.21e-03

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. 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: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 39.95  E-value: 3.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495     5 LTLNNFRRYEKAH---FCFHPKMTILVGENGKGKTTILDAIAVML----GTYFQGSKIKTGQSTVKKDDARL-LSVELGG 76
Cdd:TIGR00618    6 LTLKNFGSYKGTHtidFTALGPIFLICGKTGAGKTTLLDAITYALygklPRRSEVIRSLNSLYAAPSEAAFAeLEFSLGT 85


                   .
gi 491899495    77 Q 77
Cdd:TIGR00618   86 K 86
recF PRK14079
recombination protein F; Provisional
 2-47 3.23e-03

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 39.38  E-value: 3.23e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 491899495   2 LINLTLNNFRRYEKAHFCFHPKMTILVGENGKGKTTILDAIAVMLG 47
Cdd:PRK14079   3 LLSLRQLNYRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAIYLALT 48
ABC_SMC_head cd03239
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ...
 5-47 3.37e-03

The SMC head domain belongs to the ATP-binding cassette superfamily; The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.


Pssm-ID: 213206 [Multi-domain]  Cd Length: 178  Bit Score: 38.44  E-value: 3.37e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 491899495   5 LTLNNFR--RYEKAHFCFHPkMTILVGENGKGKTTILDAIAVMLG 47
Cdd:cd03239    4 ITLKNFKsyRDETVVGGSNS-FNAIVGPNGSGKSNIVDAICFVLG 47
retron_eff_Eco8 NF038234
retron Eco8 family effector endonuclease; This ATPase, found as the effector protein partner ...
 274-318 3.44e-03

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: 39.63  E-value: 3.44e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 491899495 274 IVLIDEIDLHLHPKWQRRVVSDLQE---------AFPEIQFIATTHSPFIIQSL 318
Cdd:NF038234 275 FIFIDEPELGLHPKLNEQLINEIYEsysfkkkdnKTPYPKIILATHSPRIIKNI 328
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 265-315 5.13e-03

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 37.65  E-value: 5.13e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491899495 265 EKAATRTKGIVLIDEIDL-------HLHPKWQRRVVS------DLQEAFPEIQFIATTHSPFII 315
Cdd:cd19481   79 ERARRLAPCILFIDEIDAigrkrdsSGESGELRRVLNqlltelDGVNSRSKVLVIAATNRPDLL 142
ABC_tran pfam00005
ABC transporter; ABC transporters for a large family of proteins responsible for translocation ...
 17-114 5.30e-03

ABC transporter; ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain pfam00664. These four domains may belong to a single polypeptide or belong in different polypeptide chains.


Pssm-ID: 394964 [Multi-domain]  Cd Length: 150  Bit Score: 37.24  E-value: 5.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491899495   17 HFCFHP-KMTILVGENGKGKTTILDAIAVMLgTYFQGSkIKTGQSTVKKDDARLLSVELGgqfnLEPQDDVFIQaRSTIR 95
Cdd:pfam00005   5 SLTLNPgEILALVGPNGAGKSTLLKLIAGLL-SPTEGT-ILLDGQDLTDDERKSLRKEIG----YVFQDPQLFP-RLTVR 77

                          90
                  ....*....|....*....
gi 491899495   96 nETIDWIREMGDRGGKAKD 114
Cdd:pfam00005  78 -ENLRLGLLLKGLSKREKD 95
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
20-47 6.13e-03

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 39.13  E-value: 6.13e-03
                          10        20
                  ....*....|....*....|....*....
gi 491899495   20 FHPKMTILVGENGKGKTTILDAI-AVMLG 47
Cdd:COG4913    22 FDGRGTLLTGDNGSGKSTLLDAIqTLLVP 50
 
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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