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Conserved domains on  [gi|495028647|ref|WP_007754208|]
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DNA replication/repair protein RecF [Cronobacter dublinensis]

Protein Classification

DNA replication/repair protein RecF( domain architecture ID 11489442)

DNA replication/repair protein RecF is required for DNA replication and normal SOS inducibility; it binds preferentially to single-stranded, linear DNA

Gene Ontology:  GO:0003697|GO:0005524|GO:0006260|GO:0009432
PubMed:  26874520|30657965

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-355 1.77e-173

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: 486.48  E-value: 1.77e-173
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647    1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQDAFILHGRLQGDERE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   81 V---SVGLTKDRNGDSTVRIDGSDghKVAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGFFVAWSNLKRL 157
Cdd:TIGR00611  81 VtipLEGLLKKKGKKAKVNIDGQD--KLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  158 LKQRNAALRQVTRY----EQLRPWDRELVPLAEQISQWRASYSEAIASDMADTCAQFLPEFTLTFSFQRG--WEKESDYA 231
Cdd:TIGR00611 159 LKQRNAALKQAQRQygdrTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGelWDKETDYA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  232 DVLERGFERDRMLTYTAHGPHKADFRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDA 311
Cdd:TIGR00611 239 EALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDVASELDDQ 318

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 495028647  312 RRGLLAQRLKATQSQVFVSAISAEHILDMTDKNSK---MFAVDQGKI 355
Cdd:TIGR00611 319 RRRLLAELLQSLGVQVFVTAISLDHLKEMWDPNRVtiaLVSVDRGTI 365
 
Name Accession Description Interval E-value
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-355 1.77e-173

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: 486.48  E-value: 1.77e-173
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647    1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQDAFILHGRLQGDERE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   81 V---SVGLTKDRNGDSTVRIDGSDghKVAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGFFVAWSNLKRL 157
Cdd:TIGR00611  81 VtipLEGLLKKKGKKAKVNIDGQD--KLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  158 LKQRNAALRQVTRY----EQLRPWDRELVPLAEQISQWRASYSEAIASDMADTCAQFLPEFTLTFSFQRG--WEKESDYA 231
Cdd:TIGR00611 159 LKQRNAALKQAQRQygdrTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGelWDKETDYA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  232 DVLERGFERDRMLTYTAHGPHKADFRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDA 311
Cdd:TIGR00611 239 EALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDVASELDDQ 318

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 495028647  312 RRGLLAQRLKATQSQVFVSAISAEHILDMTDKNSK---MFAVDQGKI 355
Cdd:TIGR00611 319 RRRLLAELLQSLGVQVFVTAISLDHLKEMWDPNRVtiaLVSVDRGTI 365
recF PRK00064
recombination protein F; Reviewed
 1-357 4.04e-159

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 449.99  E-value: 4.04e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQDAFILHGRLQGDERE 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  81 VSVGLTKDRNGDSTVRIDGSDGHKVAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGFFVAWSNLKRLLKQ 160
Cdd:PRK00064  81 LPLGLEIDKKGGRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 161 RNAALRQvTRYEQLRPWDRELVPLAEQISQWRASYSEAIASDMADTCAQFLPEF-TLTFSFQRGWEK-----ESDYADVL 234
Cdd:PRK00064 161 RNALLKQ-ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFeLASLSYQSSVEDdaekiEEDLLEAL 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 235 ERGFERDRMLTYTAHGPHKADFRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDARRG 314
Cdd:PRK00064 240 AKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDVASELDDGRRA 319

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|...
gi 495028647 315 LLAQRLKATQSQVFVSAISAEHILDMTDkNSKMFAVDQGKITD 357
Cdd:PRK00064 320 ALLERLKGLGAQVFITTTDLEDLADLLE-NAKIFHVEQGKITD 361
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
3-343 8.18e-134

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 385.66  E-value: 8.18e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   3 LSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQDAFILHGRLQGDEREVS 82
Cdd:COG1195    2 LKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREVR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  83 VGLTKDRNGDSTVRIDGSDGHKVAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGFFVAWSNLKRLLKQRN 162
Cdd:COG1195   82 LGLGLSRGGKKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQRN 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 163 AALRQ--VTRYEQLRPWDRELVPLAEQISQWRASYSEAIASDMADTCAQF-LPEFTLTFSFQRGWEKES-----DYADVL 234
Cdd:COG1195  162 ALLKQgrEADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALsGGKEELELRYRSGWLYESaeleeALLEAL 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 235 ERGFERDRMLTYTAHGPHKADFRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDARRG 314
Cdd:COG1195  242 AENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVFAELDEERRE 321

                        330       340
                 ....*....|....*....|....*....
gi 495028647 315 LLAQRLKATQSQVFVSAISAEHILDMTDK 343
Cdd:COG1195  322 ALLELLADLGGQVFITTTDPEDFPALLER 350
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 3-194 4.22e-41

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: 153.97  E-value: 4.22e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647     3 LSRLLIKDFRNI-ENADLALSPGFNFLVGANGSGKTSVLEAI-YTLG--HGRAFRSLQIGRVIRHEQDAFILHGRLQG-- 76
Cdd:pfam02463    2 LKRIEIEGFKSYaKTVILPFSPGFTAIVGPNGSGKSNILDAIlFVLGerSAKSLRSERLSDLIHSKSGAFVNSAEVEItf 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647    77 ---------DEREVSVGLTKDRNGDSTVRIDGSDGHKvAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGF 147
Cdd:pfam02463   82 dnedhelpiDKEEVSIRRRVYRGGDSEYYINGKNVTK-KEVAELLESQGISPEAYNFLVQGGKIEIIAMMKPERRLEIEE 160

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 495028647   148 FVAWSNLKRLLKQRNAALRQVTRYEQLRPWDRELVPLAEQISQWRAS 194
Cdd:pfam02463  161 EAAGSRLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQAK 207
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-356 7.62e-39

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: 139.35  E-value: 7.62e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   3 LSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQDAFILHGRLQGDEREVS 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  83 VGLTKDRNGDSTVRIDGSDGHKVAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGFFVAWSNLKRLLKQRN 162
Cdd:cd03242   81 LELTIRSGGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 163 AALRqvtryeqlrpwdrelvplaeqisqwrasyseaiasdmadtcaqflpeftltfsfqrgwekesdyadvlergferdr 242
Cdd:cd03242  161 ALLK---------------------------------------------------------------------------- 164

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 243 mltytahGPHKADFRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDARRGLLAQRLKA 322
Cdd:cd03242  165 -------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLAELDLGRQAALLDAIEG 237

                        330       340       350
                 ....*....|....*....|....*....|....
gi 495028647 323 TQsQVFVSAISAEHILDMTDKNSKMFAVDQGKIT 356
Cdd:cd03242  238 RV-QTFVTTTDLADFDALWLRRAQIFRVDAGTLS 270
 
Name Accession Description Interval E-value
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-355 1.77e-173

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: 486.48  E-value: 1.77e-173
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647    1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQDAFILHGRLQGDERE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   81 V---SVGLTKDRNGDSTVRIDGSDghKVAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGFFVAWSNLKRL 157
Cdd:TIGR00611  81 VtipLEGLLKKKGKKAKVNIDGQD--KLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  158 LKQRNAALRQVTRY----EQLRPWDRELVPLAEQISQWRASYSEAIASDMADTCAQFLPEFTLTFSFQRG--WEKESDYA 231
Cdd:TIGR00611 159 LKQRNAALKQAQRQygdrTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGelWDKETDYA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  232 DVLERGFERDRMLTYTAHGPHKADFRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDA 311
Cdd:TIGR00611 239 EALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDVASELDDQ 318

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 495028647  312 RRGLLAQRLKATQSQVFVSAISAEHILDMTDKNSK---MFAVDQGKI 355
Cdd:TIGR00611 319 RRRLLAELLQSLGVQVFVTAISLDHLKEMWDPNRVtiaLVSVDRGTI 365
recF PRK00064
recombination protein F; Reviewed
 1-357 4.04e-159

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 449.99  E-value: 4.04e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQDAFILHGRLQGDERE 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  81 VSVGLTKDRNGDSTVRIDGSDGHKVAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGFFVAWSNLKRLLKQ 160
Cdd:PRK00064  81 LPLGLEIDKKGGRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 161 RNAALRQvTRYEQLRPWDRELVPLAEQISQWRASYSEAIASDMADTCAQFLPEF-TLTFSFQRGWEK-----ESDYADVL 234
Cdd:PRK00064 161 RNALLKQ-ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFeLASLSYQSSVEDdaekiEEDLLEAL 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 235 ERGFERDRMLTYTAHGPHKADFRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDARRG 314
Cdd:PRK00064 240 AKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDVASELDDGRRA 319

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|...
gi 495028647 315 LLAQRLKATQSQVFVSAISAEHILDMTDkNSKMFAVDQGKITD 357
Cdd:PRK00064 320 ALLERLKGLGAQVFITTTDLEDLADLLE-NAKIFHVEQGKITD 361
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
3-343 8.18e-134

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 385.66  E-value: 8.18e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   3 LSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQDAFILHGRLQGDEREVS 82
Cdd:COG1195    2 LKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREVR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  83 VGLTKDRNGDSTVRIDGSDGHKVAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGFFVAWSNLKRLLKQRN 162
Cdd:COG1195   82 LGLGLSRGGKKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQRN 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 163 AALRQ--VTRYEQLRPWDRELVPLAEQISQWRASYSEAIASDMADTCAQF-LPEFTLTFSFQRGWEKES-----DYADVL 234
Cdd:COG1195  162 ALLKQgrEADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALsGGKEELELRYRSGWLYESaeleeALLEAL 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 235 ERGFERDRMLTYTAHGPHKADFRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDARRG 314
Cdd:COG1195  242 AENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVFAELDEERRE 321

                        330       340
                 ....*....|....*....|....*....
gi 495028647 315 LLAQRLKATQSQVFVSAISAEHILDMTDK 343
Cdd:COG1195  322 ALLELLADLGGQVFITTTDPEDFPALLER 350
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 3-194 4.22e-41

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: 153.97  E-value: 4.22e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647     3 LSRLLIKDFRNI-ENADLALSPGFNFLVGANGSGKTSVLEAI-YTLG--HGRAFRSLQIGRVIRHEQDAFILHGRLQG-- 76
Cdd:pfam02463    2 LKRIEIEGFKSYaKTVILPFSPGFTAIVGPNGSGKSNILDAIlFVLGerSAKSLRSERLSDLIHSKSGAFVNSAEVEItf 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647    77 ---------DEREVSVGLTKDRNGDSTVRIDGSDGHKvAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGF 147
Cdd:pfam02463   82 dnedhelpiDKEEVSIRRRVYRGGDSEYYINGKNVTK-KEVAELLESQGISPEAYNFLVQGGKIEIIAMMKPERRLEIEE 160

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 495028647   148 FVAWSNLKRLLKQRNAALRQVTRYEQLRPWDRELVPLAEQISQWRAS 194
Cdd:pfam02463  161 EAAGSRLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQAK 207
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-356 7.62e-39

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: 139.35  E-value: 7.62e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   3 LSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQDAFILHGRLQGDEREVS 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  83 VGLTKDRNGDSTVRIDGSDGHKVAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGFFVAWSNLKRLLKQRN 162
Cdd:cd03242   81 LELTIRSGGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 163 AALRqvtryeqlrpwdrelvplaeqisqwrasyseaiasdmadtcaqflpeftltfsfqrgwekesdyadvlergferdr 242
Cdd:cd03242  161 ALLK---------------------------------------------------------------------------- 164

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 243 mltytahGPHKADFRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDARRGLLAQRLKA 322
Cdd:cd03242  165 -------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLAELDLGRQAALLDAIEG 237

                        330       340       350
                 ....*....|....*....|....*....|....
gi 495028647 323 TQsQVFVSAISAEHILDMTDKNSKMFAVDQGKIT 356
Cdd:cd03242  238 RV-QTFVTTTDLADFDALWLRRAQIFRVDAGTLS 270
recF PRK14079
recombination protein F; Provisional
 1-334 6.16e-36

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 133.37  E-value: 6.16e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYtLGHGRAFRSLQIGRVIRHEQDAFILHGRLQ--GDE 78
Cdd:PRK14079   1 MRLLSLRQLNYRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAIY-LALTGELPNGRLADLVRFGEGEAWVHAEVEtgGGL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  79 REVSVGLTKDRNgdsTVRIDGSDGhKVAELAQLMPMQLITPEGFTLLGGGPKYRRAFLDWGCFHNEPGFFVAWSNLKRLL 158
Cdd:PRK14079  80 SRLEVGLGPGRR---ELKLDGVRV-SLRELARLPGAVLIRPEDLELVLGPPEGRRAYLDRLLSRLSARYAALLSAYERAV 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 159 KQRNAALRQVTRyEQLRPWDRELVPLAEQISQWRASYSEAIASDMADTCAQFLPEFTLTFSFQRGWEKESdYADVLERGF 238
Cdd:PRK14079 156 QQRNAALKSGGG-WGLHVWDDELVKLGDEIMALRRRALTRLSELAREAYAELGSRKPLRLELSESTAPEG-YLAALEARR 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 239 ERDRMLTYTAHGPHKADFRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDARRGLLAQ 318
Cdd:PRK14079 234 AEELARGATVVGPHRDDLVLTLEGRPAHRYASRGEARTVALALRLAEHRLLWEHFGEAPVLLVDDFTAELDPRRRGALLA 313

                        330
                 ....*....|....*.
gi 495028647 319 rLKATQSQVFVSAISA 334
Cdd:PRK14079 314 -LAASLPQAIVAGTEA 328
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 193-356 1.77e-22

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: 98.89  E-value: 1.77e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   193 ASYSEAIASDMADTCAQFLPEFTLTFSFQRGWEKESDYADVLERGFERDRMLTYTAHGPHKADFRIRADGAPVEDTLSRG 272
Cdd:pfam02463 1002 EEKKKLIRAIIEETCQRLKEFLELFVSINKGWNKVFFYLELGGSAELRLEDPDDPFSGGIEISARPPGKGVKNLDLLSGG 1081

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   273 QLKLLMCALRLAqgeflTRESGRRCLYLIDDFASELDDARRGLLAQRLKA--TQSQVFVSAISAEHILDMtDKNSKMFAV 350
Cdd:pfam02463 1082 EKTLVALALIFA-----IQKYKPAPFYLLDEIDAALDDQNVSRVANLLKElsKNAQFIVISLREEMLEKA-DKLVGVTMV 1155


                   ....*.
gi 495028647   351 DQGKIT 356
Cdd:pfam02463 1156 ENGVST 1161
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-46 1.29e-12

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: 68.11  E-value: 1.29e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 495028647   1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYTL 46
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRLL 46
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-72 1.28e-11

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 64.25  E-value: 1.28e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   1 MSLSRLLIKDFRNIENADLALS--PGFNFLVGANGSGKTSVLEAIYTLGHG-------RAFRSLQIgRVIRHEQDAFILH 71
Cdd:COG3950    1 MRIKSLTIENFRGFEDLEIDFDnpPRLTVLVGENGSGKTTLLEAIALALSGllsrlddVKFRKLLI-RNGEFGDSAKLIL 79


                 .
gi 495028647  72 G 72
Cdd:COG3950   80 Y 80
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-44 3.55e-10

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: 60.69  E-value: 3.55e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 495028647    1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIY 44
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALD 44
COG4637 COG4637
Predicted ATPase [General function prediction only];
3-338 5.34e-10

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 60.33  E-value: 5.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   3 LSRLLIKDFRNIENADLALSPgFNFLVGANGSGKTSVLEAIYTLghgRAFRSLQIGRVIRHE---QDAFILHGRLQGDER 79
Cdd:COG4637    2 ITRIRIKNFKSLRDLELPLGP-LTVLIGANGSGKSNLLDALRFL---SDAARGGLQDALARRgglEELLWRGPRTITEPI 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  80 EVSVGLTKDRNGDSTVRIdgsdghkvaELAQLMPMQ--LITPEGFTLLGGGpkYRRAFLDwgcfhnEPGFFVAWSNLKRL 157
Cdd:COG4637   78 RLELEFAEEDERDLRYEL---------ELGLPEPGGrpEVKEERLWLKRGS--GGRPFLD------FRPKGRAVGGEPER 140

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 158 LKQRNAALRQVTRYEQLrpwdRELVPLAEQISQWR--------------ASYSEAIASDMADtcaqfLPEFTLTFSFQRg 223
Cdd:COG4637  141 LDSPESLLSQLGDPERF----PELRALREALRSWRfydfhpaplrqpqpAGRTPVLAPDGSN-----LAAVLATLRETH- 210

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647 224 wekESDYADVLER------GFERDR---------MLTYTAHGphkADFRIRADGapvedtLSRGQLKLLMCALRLaqgef 288
Cdd:COG4637  211 ---PERFERILEAlrdafpGFEDIEvepdedgrvLLEFREKG---LDRPFPARE------LSDGTLRFLALLAAL----- 273

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 495028647 289 LTRESGRrcLYLIDdfasE----LDDARRGLLAQRLK----------ATQSQVFVSAISAEHIL 338
Cdd:COG4637  274 LSPRPPP--LLCIE----EpengLHPDLLPALAELLReasertqvivTTHSPALLDALEPEEVL 331
ABC_RecN cd03241
ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC ...
 3-158 1.47e-08

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: 55.29  E-value: 1.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   3 LSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLqigrvIRHEQD---------------- 66
Cdd:cd03241    1 LLELSIKNFALIEELELDFEEGLTVLTGETGAGKSILLDALSLLLGGRASADL-----IRSGAEkavvegvfdisdeeea 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  67 AFILHGRLQGDEREVSVGLTKDRNGDSTVRIDGsdghKVAELAQLmpmQLITPEGFTLLG-------GGPKYRRAFLDWG 139
Cdd:cd03241   76 KALLLELGIEDDDDLIIRREISRKGRSRYFING----QSVTLKLL---RELGSLLVDIHGqhdhqnlLNPERQLDLLDGG 148

                        170
                 ....*....|....*....
gi 495028647 140 CFHNEpgFFVAWSNLKRLL 158
Cdd:cd03241  149 LDDVE--FLFSTNPGEPLK 165
AAA_23 pfam13476
AAA domain;
6-110 1.60e-08

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 54.04  E-value: 1.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647    6 LLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAI-YTLGH--GRAFRSLQIGRVIR-------HEQDAFI-LHGRL 74
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAIkLALYGktSRLKRKSGGGFVKGdirigleGKGKAYVeITFEN 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 495028647   75 QGDEREVSVGLTKDRNGDSTVRIDGSDGHKVAELAQ 110
Cdd:pfam13476  81 NDGRYTYAIERSRELSKKKGKTKKKEILEILEIDEL 116
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
1-62 4.39e-08

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 55.07  E-value: 4.39e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 495028647   1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAIYT---LGHGRAFRSLQIGRVIR 62
Cdd:PRK03918   1 MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAILVglyWGHGSKPKGLKKDDFTR 65
COG4938 COG4938
Predicted ATPase [General function prediction only];
3-46 3.87e-06

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 47.66  E-value: 3.87e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 495028647   3 LSRLLIKDFRNIENADLALSPgFNFLVGANGSGKTSVLEAIYTL 46
Cdd:COG4938    1 IKSISIKNFGPFKEAELELKP-LTLLIGPNGSGKSTLIQALLLL 43
ABC_SMC5_euk cd03277
ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of ...
 2-116 8.40e-06

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: 46.05  E-value: 8.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   2 SLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAI-YTLGHGRAF--RSLQIGRVIRH-EQDAFIlHGRLQGD 77
Cdd:cd03277    2 SIVRIKLENFVTYDETEFRPGPSLNMIIGPNGSGKSSIVCAIcLGLGGKPKLlgRAKKVGEFVKRgCDEGTI-EIELYGN 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 495028647  78 EREVSVG-----LTKDRngdstvridgsdghkVAELAQLMPMQL 116
Cdd:cd03277   81 PGNIQVDnlcqfLPQDR---------------VGEFAKLSPIEL 109
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
3-62 1.47e-05

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 46.19  E-value: 1.47e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 495028647   3 LSRLLIKDFRNIENaDLALS--------PGFNFLVGANGSGKTSVLEAIYTLgHGRAFRSLQIGRVIR 62
Cdd:COG1106    2 LISFSIENFRSFKD-ELTLSmvasglrlLRVNLIYGANASGKSNLLEALYFL-RNLVLNSSQPGDKLV 67
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-330 2.29e-05

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: 45.46  E-value: 2.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647   25 FNFLVGANGSGKTSVLEAIYTLGHG-RAFRSLQIGRVIRHEQDAFILHGRLQGDEREVSVGLTKDRNGDSTVRIDGSDGh 103
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFdALVIGLTDERSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVRYRYGLDLE- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  104 kvAELAQLMPMQLITPEGFTLL---GGGPKYRRAFLDWGCFH-NEPGFFVAWSNLKRLLKQRNAALRQ--VTRYEQLRPW 177
Cdd:pfam13304  80 --REDVEEKLSSKPTLLEKRLLlreDSEEREPKFPPEAEELRlGLDVEERIELSLSELSDLISGLLLLsiISPLSFLLLL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  178 DRELVPLAEQISQWRASYseAIASDMADTCAQFLPEF-TLTFSFQRGWEKESDYADVLERGFERDRMltytahgphkadF 256
Cdd:pfam13304 158 DEGLLLEDWAVLDLAADL--ALFPDLKELLQRLVRGLkLADLNLSDLGEGIEKSLLVDDRLRERGLI------------L 223

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 495028647  257 RIRADGAPVE-DTLSRGQLKLLmcALRLAQgeFLTRESGRrcLYLIDDFASELDDARRGLLAQRLKAT---QSQVFVS 330
Cdd:pfam13304 224 LENGGGGELPaFELSDGTKRLL--ALLAAL--LSALPKGG--LLLIDEPESGLHPKLLRRLLELLKELsrnGAQLILT 295
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
3-43 3.82e-05

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 44.23  E-value: 3.82e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 495028647   3 LSRLLIKDFRNIENAD-LALSPGFNFLVGANGSGKTSVLEAI 43
Cdd:COG0419    2 LLRLRLENFRSYRDTEtIDFDDGLNLIVGPNGAGKSTILEAI 43
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 3-43 6.08e-05

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: 43.36  E-value: 6.08e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 495028647   3 LSRLLIKDFRNI-ENADLALSPGFNFLVGANGSGKTSVLEAI 43
Cdd:cd03240    1 IDKLSIRNIRSFhERSEIEFFSPLTLIVGQNGAGKTTIIEAL 42
PRK01156 PRK01156
chromosome segregation protein; Provisional
 1-43 1.43e-04

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 43.74  E-value: 1.43e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 495028647   1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAI 43
Cdd:PRK01156   1 MIIKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAI 43
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
1-42 3.76e-04

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 42.33  E-value: 3.76e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 495028647   1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEA 42
Cdd:PRK02224   1 MRFDRVRLENFKCYADADLRLEDGVTVIHGVNGSGKSSLLEA 42
ABC_SMC_head cd03239
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ...
 25-125 4.85e-04

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: 40.37  E-value: 4.85e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495028647  25 FNFLVGANGSGKTSVLEAI-YTLGhgraFRSLQIGRvirhEQDAFILHGRLQGDEREVSVGLTKDrNGDSTV---RIDG- 99
Cdd:cd03239   24 FNAIVGPNGSGKSNIVDAIcFVLG----GKAAKLRR----GSLLFLAGGGVKAGINSASVEITFD-KSYFLVlqgKVEQi 94

                         90       100
                 ....*....|....*....|....*...
gi 495028647 100 -SDGHK-VAELAQLMPMQLITPEGFTLL 125
Cdd:cd03239   95 lSGGEKsLSALALIFALQEIKPSPFYVL 122
ABC_SMC6_euk cd03276
ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of ...
 15-49 6.53e-04

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: 40.27  E-value: 6.53e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 495028647  15 ENADLALSPGFNFLVGANGSGKTSVLEAIyTLGHG 49
Cdd:cd03276   13 RHLQIEFGPRVNFIVGNNGSGKSAILTAL-TIGLG 46
RecN COG0497
DNA repair ATPase RecN [Replication, recombination and repair];
3-73 8.77e-04

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


Pssm-ID: 440263 [Multi-domain]  Cd Length: 555  Bit Score: 41.21  E-value: 8.77e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495028647   3 LSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAI-YTLGhGRAFRSLqigrvIRHEQDAFILHGR 73
Cdd:COG0497    2 LTELSIRNFALIDELELEFGPGLTVLTGETGAGKSILLDALgLLLG-GRADASL-----VRHGADKAEVEAV 67
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
1-43 2.99e-03

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 39.37  E-value: 2.99e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 495028647   1 MSLSRLLIKDFRNIENADLALSPGFNFLVGANGSGKTSVLEAI 43
Cdd:COG4717    1 MKIKELEIYGFGKFRDRTIEFSPGLNVIYGPNEAGKSTLLAFI 43
COG3910 COG3910
Predicted ATPase [General function prediction only];
11-43 4.47e-03

Predicted ATPase [General function prediction only];


Pssm-ID: 443116 [Multi-domain]  Cd Length: 239  Bit Score: 38.21  E-value: 4.47e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 495028647  11 FRNIEnaDLALSPGFNFLVGANGSGKTSVLEAI 43
Cdd:COG3910   27 VRNLE--GLEFHPPVTFFVGENGSGKSTLLEAI 57
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 3-59 6.35e-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: 37.44  E-value: 6.35e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 495028647   3 LSRLLIKDFRN-IENADLALSPGFNFLVGANGSGKTSVLEAI-YTLGHGRAfRSLQIGR 59
Cdd:cd03278    1 LKKLELKGFKSfADKTTIPFPPGLTAIVGPNGSGKSNIIDAIrWVLGEQSA-KSLRGEK 58
ABC_ATPase cd00267
ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large ...
 8-43 9.33e-03

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, like 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: 213179 [Multi-domain]  Cd Length: 157  Bit Score: 36.45  E-value: 9.33e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 495028647   8 IKDFRNIENADLALSPG-FNFLVGANGSGKTSVLEAI 43
Cdd:cd00267    9 YGGRTALDNVSLTLKAGeIVALVGPNGSGKSTLLRAI 45
 
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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