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Conserved domains on  [gi|1790135|gb|AAC76723|]
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recombination mediator protein RecF [Escherichia coli str. K-12 substr. MG1655]

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 0e+00

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: 509.20  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135      1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQEAFVLHGRLQGEERE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135     81 TAI---GLTKDKQGDSKVRIDGTDghKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGFFTAWSNLKRL 157
Cdd:TIGR00611  81 VTIpleGLLKKKGKKAKVNIDGQD--KLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    158 LKQRNAALRQVTRY----EQLRPWDKELIPLAEQISTWRAEYSAGIAADMADTCKQFLPEFSLTFSFQRG--WEKETEYA 231
Cdd:TIGR00611 159 LKQRNAALKQAQRQygdrTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGelWDKETDYA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    232 EVLERNFERDRQLTYTAHGPHKADLRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDE 311
Cdd:TIGR00611 239 EALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDVASELDDQ 318

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 1790135    312 RRGLLASRLKATQSQVFVSAISAEHVIDMSDENSK---MFTVEKGKI 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 0e+00

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: 509.20  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135      1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQEAFVLHGRLQGEERE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135     81 TAI---GLTKDKQGDSKVRIDGTDghKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGFFTAWSNLKRL 157
Cdd:TIGR00611  81 VTIpleGLLKKKGKKAKVNIDGQD--KLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    158 LKQRNAALRQVTRY----EQLRPWDKELIPLAEQISTWRAEYSAGIAADMADTCKQFLPEFSLTFSFQRG--WEKETEYA 231
Cdd:TIGR00611 159 LKQRNAALKQAQRQygdrTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGelWDKETDYA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    232 EVLERNFERDRQLTYTAHGPHKADLRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDE 311
Cdd:TIGR00611 239 EALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDVASELDDQ 318

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 1790135    312 RRGLLASRLKATQSQVFVSAISAEHVIDMSDENSK---MFTVEKGKI 355
Cdd:TIGR00611 319 RRRLLAELLQSLGVQVFVTAISLDHLKEMWDPNRVtiaLVSVDRGTI 365
recF PRK00064
recombination protein F; Reviewed
 1-357 6.75e-159

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 449.61  E-value: 6.75e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135     1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQEAFVLHGRLQGEERE 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    81 TAIGLTKDKQGDSKVRIDGTDGHKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGFFTAWSNLKRLLKQ 160
Cdd:PRK00064  81 LPLGLEIDKKGGRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135   161 RNAALRQvTRYEQLRPWDKELIPLAEQISTWRAEYSAGIAADMADTCKQFLPEF-SLTFSFQRGWEK-----ETEYAEVL 234
Cdd:PRK00064 161 RNALLKQ-ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFeLASLSYQSSVEDdaekiEEDLLEAL 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135   235 ERNFERDRQLTYTAHGPHKADLRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDERRG 314
Cdd:PRK00064 240 AKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDVASELDDGRRA 319

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|...
gi 1790135   315 LLASRLKATQSQVFVSAISAEHVIDMSdENSKMFTVEKGKITD 357
Cdd:PRK00064 320 ALLERLKGLGAQVFITTTDLEDLADLL-ENAKIFHVEQGKITD 361
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
3-343 1.72e-133

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 384.51  E-value: 1.72e-133
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    3 LTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQEAFVLHGRLQGEERETA 82
Cdd:COG1195   2 LKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREVR 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135   83 IGLTKDKQGDSKVRIDGTDGHKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGFFTAWSNLKRLLKQRN 162
Cdd:COG1195  82 LGLGLSRGGKKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQRN 161

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135  163 AALRQ--VTRYEQLRPWDKELIPLAEQISTWRAEYSAGIAADMADTCKQF-LPEFSLTFSFQRGWEKET-----EYAEVL 234
Cdd:COG1195 162 ALLKQgrEADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALsGGKEELELRYRSGWLYESaeleeALLEAL 241

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135  235 ERNFERDRQLTYTAHGPHKADLRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDERRG 314
Cdd:COG1195 242 AENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVFAELDEERRE 321

                       330       340
                ....*....|....*....|....*....
gi 1790135  315 LLASRLKATQSQVFVSAISAEHVIDMSDE 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 6.71e-39

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: 147.43  E-value: 6.71e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135       3 LTRLLIRDFRNI-ETADLALSPGFNFLVGANGSGKTSVLEAI-YTLG--HGRAFRSLQIGRVIRHEQEAFVLHGRLQG-- 76
Cdd:pfam02463    2 LKRIEIEGFKSYaKTVILPFSPGFTAIVGPNGSGKSNILDAIlFVLGerSAKSLRSERLSDLIHSKSGAFVNSAEVEItf 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135      77 ---------EERETAIGLTKDKQGDSKVRIDGTDGHKvAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGF 147
Cdd:pfam02463   82 dnedhelpiDKEEVSIRRRVYRGGDSEYYINGKNVTK-KEVAELLESQGISPEAYNFLVQGGKIEIIAMMKPERRLEIEE 160

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1790135     148 FTAWSNLKRLLKQRNAALRQVTRYEQLRPWDKELIPLAEQISTWRAE 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 2.35e-38

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: 137.81  E-value: 2.35e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    3 LTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQEAFVLHGRLQGEERETA 82
Cdd:cd03242   1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135   83 IGLTKDKQGDSKVRIDGTDGHKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGFFTAWSNLKRLLKQRN 162
Cdd:cd03242  81 LELTIRSGGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135  163 AALRqvtryeqlrpwdkeliplaeqistwraeysagiaadmadtckqflpefsltfsfqrgweketeyaevlernferdr 242
Cdd:cd03242 161 ALLK---------------------------------------------------------------------------- 164

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135  243 qltytahGPHKADLRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDERRGLLASRLKA 322
Cdd:cd03242 165 -------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLAELDLGRQAALLDAIEG 237

                       330       340       350
                ....*....|....*....|....*....|....
gi 1790135  323 TQsQVFVSAISAEHVIDMSDENSKMFTVEKGKIT 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 0e+00

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: 509.20  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135      1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQEAFVLHGRLQGEERE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135     81 TAI---GLTKDKQGDSKVRIDGTDghKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGFFTAWSNLKRL 157
Cdd:TIGR00611  81 VTIpleGLLKKKGKKAKVNIDGQD--KLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    158 LKQRNAALRQVTRY----EQLRPWDKELIPLAEQISTWRAEYSAGIAADMADTCKQFLPEFSLTFSFQRG--WEKETEYA 231
Cdd:TIGR00611 159 LKQRNAALKQAQRQygdrTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGelWDKETDYA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    232 EVLERNFERDRQLTYTAHGPHKADLRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDE 311
Cdd:TIGR00611 239 EALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDVASELDDQ 318

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 1790135    312 RRGLLASRLKATQSQVFVSAISAEHVIDMSDENSK---MFTVEKGKI 355
Cdd:TIGR00611 319 RRRLLAELLQSLGVQVFVTAISLDHLKEMWDPNRVtiaLVSVDRGTI 365
recF PRK00064
recombination protein F; Reviewed
 1-357 6.75e-159

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 449.61  E-value: 6.75e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135     1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQEAFVLHGRLQGEERE 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    81 TAIGLTKDKQGDSKVRIDGTDGHKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGFFTAWSNLKRLLKQ 160
Cdd:PRK00064  81 LPLGLEIDKKGGRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135   161 RNAALRQvTRYEQLRPWDKELIPLAEQISTWRAEYSAGIAADMADTCKQFLPEF-SLTFSFQRGWEK-----ETEYAEVL 234
Cdd:PRK00064 161 RNALLKQ-ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFeLASLSYQSSVEDdaekiEEDLLEAL 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135   235 ERNFERDRQLTYTAHGPHKADLRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDERRG 314
Cdd:PRK00064 240 AKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDVASELDDGRRA 319

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|...
gi 1790135   315 LLASRLKATQSQVFVSAISAEHVIDMSdENSKMFTVEKGKITD 357
Cdd:PRK00064 320 ALLERLKGLGAQVFITTTDLEDLADLL-ENAKIFHVEQGKITD 361
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
3-343 1.72e-133

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 384.51  E-value: 1.72e-133
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    3 LTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQEAFVLHGRLQGEERETA 82
Cdd:COG1195   2 LKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREVR 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135   83 IGLTKDKQGDSKVRIDGTDGHKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGFFTAWSNLKRLLKQRN 162
Cdd:COG1195  82 LGLGLSRGGKKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQRN 161

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135  163 AALRQ--VTRYEQLRPWDKELIPLAEQISTWRAEYSAGIAADMADTCKQF-LPEFSLTFSFQRGWEKET-----EYAEVL 234
Cdd:COG1195 162 ALLKQgrEADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALsGGKEELELRYRSGWLYESaeleeALLEAL 241

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135  235 ERNFERDRQLTYTAHGPHKADLRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDERRG 314
Cdd:COG1195 242 AENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVFAELDEERRE 321

                       330       340
                ....*....|....*....|....*....
gi 1790135  315 LLASRLKATQSQVFVSAISAEHVIDMSDE 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 6.71e-39

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: 147.43  E-value: 6.71e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135       3 LTRLLIRDFRNI-ETADLALSPGFNFLVGANGSGKTSVLEAI-YTLG--HGRAFRSLQIGRVIRHEQEAFVLHGRLQG-- 76
Cdd:pfam02463    2 LKRIEIEGFKSYaKTVILPFSPGFTAIVGPNGSGKSNILDAIlFVLGerSAKSLRSERLSDLIHSKSGAFVNSAEVEItf 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135      77 ---------EERETAIGLTKDKQGDSKVRIDGTDGHKvAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGF 147
Cdd:pfam02463   82 dnedhelpiDKEEVSIRRRVYRGGDSEYYINGKNVTK-KEVAELLESQGISPEAYNFLVQGGKIEIIAMMKPERRLEIEE 160

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1790135     148 FTAWSNLKRLLKQRNAALRQVTRYEQLRPWDKELIPLAEQISTWRAE 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 2.35e-38

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: 137.81  E-value: 2.35e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    3 LTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQEAFVLHGRLQGEERETA 82
Cdd:cd03242   1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135   83 IGLTKDKQGDSKVRIDGTDGHKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGFFTAWSNLKRLLKQRN 162
Cdd:cd03242  81 LELTIRSGGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135  163 AALRqvtryeqlrpwdkeliplaeqistwraeysagiaadmadtckqflpefsltfsfqrgweketeyaevlernferdr 242
Cdd:cd03242 161 ALLK---------------------------------------------------------------------------- 164

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135  243 qltytahGPHKADLRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDERRGLLASRLKA 322
Cdd:cd03242 165 -------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLAELDLGRQAALLDAIEG 237

                       330       340       350
                ....*....|....*....|....*....|....
gi 1790135  323 TQsQVFVSAISAEHVIDMSDENSKMFTVEKGKIT 356
Cdd:cd03242 238 RV-QTFVTTTDLADFDALWLRRAQIFRVDAGTLS 270
recF PRK14079
recombination protein F; Provisional
 1-334 1.15e-36

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 135.68  E-value: 1.15e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135     1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIY-----TLGHGRAFRSLQIGrvirhEQEAFVlhgrlq 75
Cdd:PRK14079   1 MRLLSLRQLNYRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAIYlaltgELPNGRLADLVRFG-----EGEAWV------ 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    76 GEERETAIGLTKDK----QGDSKVRIDGTDGhKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGFFTAW 151
Cdd:PRK14079  70 HAEVETGGGLSRLEvglgPGRRELKLDGVRV-SLRELARLPGAVLIRPEDLELVLGPPEGRRAYLDRLLSRLSARYAALL 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135   152 SNLKRLLKQRNAALRQVTRyEQLRPWDKELIPLAEQISTWRAEYSAGIAADMADTCKQFLPEFSLTFSFQRGWEKETeYA 231
Cdd:PRK14079 149 SAYERAVQQRNAALKSGGG-WGLHVWDDELVKLGDEIMALRRRALTRLSELAREAYAELGSRKPLRLELSESTAPEG-YL 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135   232 EVLERNFERDRQLTYTAHGPHKADLRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDE 311
Cdd:PRK14079 227 AALEARRAEELARGATVVGPHRDDLVLTLEGRPAHRYASRGEARTVALALRLAEHRLLWEHFGEAPVLLVDDFTAELDPR 306

                        330       340
                 ....*....|....*....|...
gi 1790135   312 RRGLLASrLKATQSQVFVSAISA 334
Cdd:PRK14079 307 RRGALLA-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 1.44e-21

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: 96.19  E-value: 1.44e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135     193 AEYSAGIAADMADTCKQFLPEFSLTFSFQRGWEKETEYAEVLERNFERDRQLTYTAHGPHKADLRIRADGAPVEDTLSRG 272
Cdd:pfam02463 1002 EEKKKLIRAIIEETCQRLKEFLELFVSINKGWNKVFFYLELGGSAELRLEDPDDPFSGGIEISARPPGKGVKNLDLLSGG 1081

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135     273 QLKLLMCALRLAqgeflTRESGRRCLYLIDDFASELDDERRGLLASRLKA--TQSQVFVSAISAEHVIDMsDENSKMFTV 350
Cdd:pfam02463 1082 EKTLVALALIFA-----IQKYKPAPFYLLDEIDAALDDQNVSRVANLLKElsKNAQFIVISLREEMLEKA-DKLVGVTMV 1155


                   ....*.
gi 1790135     351 EKGKIT 356
Cdd:pfam02463 1156 ENGVST 1161
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-46 2.09e-11

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: 64.25  E-value: 2.09e-11
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 1790135    1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTL 46
Cdd:COG3593   1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRLL 46
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-100 1.92e-10

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 60.78  E-value: 1.92e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    1 MSLTRLLIRDFRNIETADLALS--PGFNFLVGANGSGKTSVLEAIYTLGHG-------RAFRSLQIgRVIRHEQEAFVLH 71
Cdd:COG3950   1 MRIKSLTIENFRGFEDLEIDFDnpPRLTVLVGENGSGKTTLLEAIALALSGllsrlddVKFRKLLI-RNGEFGDSAKLIL 79

                        90       100       110
                ....*....|....*....|....*....|...
gi 1790135   72 G----RLQGEERETAIGLTKDKQGDSKVRIDGT 100
Cdd:COG3950  80 YygtsRLLLDGPLKKLERLKEEYFSRLDGYDSL 112
COG4637 COG4637
Predicted ATPase [General function prediction only];
3-48 5.68e-09

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 56.86  E-value: 5.68e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 1790135    3 LTRLLIRDFRNIETADLALSPgFNFLVGANGSGKTSVLEAIYTLGH 48
Cdd:COG4637   2 ITRIRIKNFKSLRDLELPLGP-LTVLIGANGSGKSNLLDALRFLSD 46
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-44 7.63e-09

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: 56.84  E-value: 7.63e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1790135      1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIY 44
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALD 44
ABC_RecN cd03241
ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC ...
 3-93 6.76e-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: 52.97  E-value: 6.76e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    3 LTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLqigrvIRHEQEAFVLHGRLQGEERETA 82
Cdd:cd03241   1 LLELSIKNFALIEELELDFEEGLTVLTGETGAGKSILLDALSLLLGGRASADL-----IRSGAEKAVVEGVFDISDEEEA 75

                        90
                ....*....|.
gi 1790135   83 IGLTKDKQGDS 93
Cdd:cd03241  76 KALLLELGIED 86
AAA_23 pfam13476
AAA domain;
6-43 2.32e-06

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 47.49  E-value: 2.32e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1790135      6 LLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAI 43
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAI 38
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
1-62 3.08e-06

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 48.91  E-value: 3.08e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1790135     1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYT---LGHGRAFRSLQIGRVIR 62
Cdd:PRK03918   1 MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAILVglyWGHGSKPKGLKKDDFTR 65
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-330 1.03e-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: 46.61  E-value: 1.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135     25 FNFLVGANGSGKTSVLEAIYTLGHG-RAFRSLQIGRVIRHEQEAFVLHGRLQGEERETAIGLTKDKQGDSKVRIdgtdGH 103
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFdALVIGLTDERSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVRYRY----GL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    104 KVAELAHLMP-MQLITPEGFTLL---NGGPKYRRAFLDWGCFH-NEPGFFTAWSNLKRLLKQRNAALRQ--VTRYEQLRP 176
Cdd:pfam13304  77 DLEREDVEEKlSSKPTLLEKRLLlreDSEEREPKFPPEAEELRlGLDVEERIELSLSELSDLISGLLLLsiISPLSFLLL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    177 WDKELIPLAEQISTWRAEYSAGiaADMADTCKQFLPEFSLT-FSFQRGWEKETEYAEVLERNFERDrqlTYTAHGPHKAD 255
Cdd:pfam13304 157 LDEGLLLEDWAVLDLAADLALF--PDLKELLQRLVRGLKLAdLNLSDLGEGIEKSLLVDDRLRERG---LILLENGGGGE 231

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1790135    256 LRIRAdgapvedtLSRGQLKLLmcALRLAQgeFLTRESGRrcLYLIDDFASELDDERRGLLASRLKAT---QSQVFVS 330
Cdd:pfam13304 232 LPAFE--------LSDGTKRLL--ALLAAL--LSALPKGG--LLLIDEPESGLHPKLLRRLLELLKELsrnGAQLILT 295
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
3-70 2.51e-05

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 45.42  E-value: 2.51e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1790135    3 LTRLLIRDFRNI-ETADLALSPG------FNFLVGANGSGKTSVLEAIYTLgHGRAFRSLQIGRVIRheqEAFVL 70
Cdd:COG1106   2 LISFSIENFRSFkDELTLSMVASglrllrVNLIYGANASGKSNLLEALYFL-RNLVLNSSQPGDKLV---EPFLL 72
COG4938 COG4938
Predicted ATPase [General function prediction only];
3-46 7.14e-05

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 43.80  E-value: 7.14e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 1790135    3 LTRLLIRDFRNIETADLALSPgFNFLVGANGSGKTSVLEAIYTL 46
Cdd:COG4938   1 IKSISIKNFGPFKEAELELKP-LTLLIGPNGSGKSTLIQALLLL 43
ABC_SMC_head cd03239
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ...
 3-125 7.49e-05

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: 43.07  E-value: 7.49e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    3 LTRLLIRDFRNIETADL-ALSPGFNFLVGANGSGKTSVLEAI-YTLGhgraFRSLQIGRvirhEQEAFVLHGRLQGEERE 80
Cdd:cd03239   1 IKQITLKNFKSYRDETVvGGSNSFNAIVGPNGSGKSNIVDAIcFVLG----GKAAKLRR----GSLLFLAGGGVKAGINS 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 1790135   81 TAIGLTKDK------QGDSKVRIDGtdGHK-VAELAHLMPMQLITPEGFTLL 125
Cdd:cd03239  73 ASVEITFDKsyflvlQGKVEQILSG--GEKsLSALALIFALQEIKPSPFYVL 122
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
3-80 8.17e-05

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 43.08  E-value: 8.17e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135    3 LTRLLIRDFRNI-ETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGR--------------VIRHEQEA 67
Cdd:COG0419   2 LLRLRLENFRSYrDTETIDFDDGLNLIVGPNGAGKSTILEAIRYALYGKARSRSKLRSdlinvgseeasvelEFEHGGKR 81

                        90
                ....*....|...
gi 1790135   68 FVLHgRLQGEERE 80
Cdd:COG0419  82 YRIE-RRQGEFAE 93
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 3-43 1.73e-04

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: 42.21  E-value: 1.73e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 1790135    3 LTRLLIRDFRNI-ETADLALSPGFNFLVGANGSGKTSVLEAI 43
Cdd:cd03240   1 IDKLSIRNIRSFhERSEIEFFSPLTLIVGQNGAGKTTIIEAL 42
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
1-42 3.39e-04

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 42.72  E-value: 3.39e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 1790135     1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEA 42
Cdd:PRK02224   1 MRFDRVRLENFKCYADADLRLEDGVTVIHGVNGSGKSSLLEA 42
PRK01156 PRK01156
chromosome segregation protein; Provisional
 1-43 4.36e-04

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 42.20  E-value: 4.36e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 1790135     1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAI 43
Cdd:PRK01156   1 MIIKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAI 43
RecN COG0497
DNA repair ATPase RecN [Replication, recombination and repair];
3-73 4.47e-04

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


Pssm-ID: 440263 [Multi-domain]  Cd Length: 555  Bit Score: 41.98  E-value: 4.47e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1790135    3 LTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAI-YTLGhGRAFRSLqigrvIRHEQEAFVLHGR 73
Cdd:COG0497   2 LTELSIRNFALIDELELEFGPGLTVLTGETGAGKSILLDALgLLLG-GRADASL-----VRHGADKAEVEAV 67
ABC_SMC5_euk cd03277
ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of ...
 2-69 4.82e-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: 41.04  E-value: 4.82e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1790135    2 SLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAI-YTLGHGRAF--RSLQIGRVIRH-EQEAFV 69
Cdd:cd03277   2 SIVRIKLENFVTYDETEFRPGPSLNMIIGPNGSGKSSIVCAIcLGLGGKPKLlgRAKKVGEFVKRgCDEGTI 73
ABC_SMC6_euk cd03276
ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of ...
 19-49 1.25e-03

ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).


Pssm-ID: 213243 [Multi-domain]  Cd Length: 198  Bit Score: 39.50  E-value: 1.25e-03
                        10        20        30
                ....*....|....*....|....*....|.
gi 1790135   19 LALSPGFNFLVGANGSGKTSVLEAIyTLGHG 49
Cdd:cd03276  17 IEFGPRVNFIVGNNGSGKSAILTAL-TIGLG 46
COG3910 COG3910
Predicted ATPase [General function prediction only];
11-43 4.55e-03

Predicted ATPase [General function prediction only];


Pssm-ID: 443116 [Multi-domain]  Cd Length: 239  Bit Score: 38.21  E-value: 4.55e-03
                        10        20        30
                ....*....|....*....|....*....|...
gi 1790135   11 FRNIETadLALSPGFNFLVGANGSGKTSVLEAI 43
Cdd:COG3910  27 VRNLEG--LEFHPPVTFFVGENGSGKSTLLEAI 57
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 22-108 6.62e-03

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


Pssm-ID: 213194 [Multi-domain]  Cd Length: 162  Bit Score: 36.95  E-value: 6.62e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1790135   22 SPGFNFLVGANGSGKTSVLEAI-YTLGhGRAFRSLQIGRVIRHEQEA-------FVLHGRLQGEER--ETAIGLTKDKQG 91
Cdd:cd03227  20 EGSLTIITGPNGSGKSTILDAIgLALG-GAQSATRRRSGVKAGCIVAavsaeliFTRLQLSGGEKElsALALILALASLK 98

                        90       100
                ....*....|....*....|....*
gi 1790135   92 DSKVRI--------DGTDGHKVAEL 108
Cdd:cd03227  99 PRPLYIldeidrglDPRDGQALAEA 123
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
1-43 8.97e-03

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 37.82  E-value: 8.97e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 1790135    1 MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAI 43
Cdd:COG4717   1 MKIKELEIYGFGKFRDRTIEFSPGLNVIYGPNEAGKSTLLAFI 43
 
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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