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Conserved domains on  [gi|123369971|sp|Q1BG58|]
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RecName: Full=DNA replication and repair protein RecF

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 ...
 1-375 7.44e-156

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: 442.95  E-value: 7.44e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971    1 MFVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWYSATLGSHRVASDAPLIRVGAPRAVVSTIVVNEGRE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   81 LAVDLEITTGRANK-ARLNRSPVRSPREVLGVLRAVLFAPEDLALVRGDPGERRRYLDELATTRRPSIAGVRADYDRVIR 159
Cdd:TIGR00611  81 VTIPLEGLLKKKGKkAKVNIDGQDKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  160 QRTALLKSAagARYRGDRSvleTLDVWDGHLAAHGALLMAARADLVHHLAPEVEKAYQLLAPGSRPAAIRYRTSIdaedd 239
Cdd:TIGR00611 161 QRNAALKQA--QRQYGDRT---TLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGEL----- 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  240 vsaEYYEAALLDAMTRRRDAELERGVCLVGPHRDDLELRLGDQMAKGYASHGESWSMALSLRLAAYELLRTDGSD-PVLL 318
Cdd:TIGR00611 231 ---WDKETDYAEALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEyPILL 307

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 123369971  319 LDDVFAELDAARRRALAEVAASA-EQVLVTAAVAEDIPADWDARRIMIRMQDDDDGRV 375
Cdd:TIGR00611 308 LDDVASELDDQRRRLLAELLQSLgVQVFVTAISLDHLKEMWDPNRVTIALVSVDRGTI 365
 
Name Accession Description Interval E-value
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-375 7.44e-156

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: 442.95  E-value: 7.44e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971    1 MFVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWYSATLGSHRVASDAPLIRVGAPRAVVSTIVVNEGRE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   81 LAVDLEITTGRANK-ARLNRSPVRSPREVLGVLRAVLFAPEDLALVRGDPGERRRYLDELATTRRPSIAGVRADYDRVIR 159
Cdd:TIGR00611  81 VTIPLEGLLKKKGKkAKVNIDGQDKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  160 QRTALLKSAagARYRGDRSvleTLDVWDGHLAAHGALLMAARADLVHHLAPEVEKAYQLLAPGSRPAAIRYRTSIdaedd 239
Cdd:TIGR00611 161 QRNAALKQA--QRQYGDRT---TLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGEL----- 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  240 vsaEYYEAALLDAMTRRRDAELERGVCLVGPHRDDLELRLGDQMAKGYASHGESWSMALSLRLAAYELLRTDGSD-PVLL 318
Cdd:TIGR00611 231 ---WDKETDYAEALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEyPILL 307

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 123369971  319 LDDVFAELDAARRRALAEVAASA-EQVLVTAAVAEDIPADWDARRIMIRMQDDDDGRV 375
Cdd:TIGR00611 308 LDDVASELDDQRRRLLAELLQSLgVQVFVTAISLDHLKEMWDPNRVTIALVSVDRGTI 365
recF PRK00064
recombination protein F; Reviewed
 1-363 9.53e-156

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 442.29  E-value: 9.53e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   1 MFVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWYSATLGSHRVASDAPLIRVGAPRAVVSTIVVNEGRE 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  81 LAVDLEITTGRANKARLNRSPVRSPREVLGVLRAVLFAPEDLALVRGDPGERRRYLDELATTRRPSIAGVRADYDRVIRQ 160
Cdd:PRK00064  81 LPLGLEIDKKGGRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 161 RTALLKSAAGAryrgdrsvleTLDVWDGHLAAHGALLMAARADLVHHLAPEVEKAYQLLAPGSRPAAIRYRTSIDAeddv 240
Cdd:PRK00064 161 RNALLKQADYA----------WLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSVED---- 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 241 SAEYYEAALLDAMTRRRDAELERGVCLVGPHRDDLELRLGDQMAKGYASHGESWSMALSLRLAAYELL-RTDGSDPVLLL 319
Cdd:PRK00064 227 DAEKIEEDLLEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLkEETGEAPILLL 306

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*
gi 123369971 320 DDVFAELDAARRRALAE-VAASAEQVLVTAAVAEDIPADWDARRI 363
Cdd:PRK00064 307 DDVASELDDGRRAALLErLKGLGAQVFITTTDLEDLADLLENAKI 351
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-359 3.87e-140

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 402.61  E-value: 3.87e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   2 FVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWYSATLGSHRVASDAPLIRVGAPRAVVSTIVVNEGREL 81
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  82 AVDLEITTGRANKARLNRSPVRSPREVLGVLRAVLFAPEDLALVRGDPGERRRYLDELATTRRPSIAGVRADYDRVIRQR 161
Cdd:COG1195   81 RLGLGLSRGGKKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 162 TALLKSAAGARYrgdrsvlETLDVWDGHLAAHGALLMAARADLVHHLAPEVEKAYQLLAPGSRPAAIRYRTSIDAEDDVS 241
Cdd:COG1195  161 NALLKQGREADL-------ALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALSGGKEELELRYRSGWLYESAEL 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 242 aeyyEAALLDAMTRRRDAELERGVCLVGPHRDDLELRLGDQMAKGYASHGESWSMALSLRLAAYELLRTD-GSDPVLLLD 320
Cdd:COG1195  234 ----EEALLEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEEtGEAPILLLD 309

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 123369971 321 DVFAELDAARRRALAE-VAASAEQVLVTAAVAEDIPADWD 359
Cdd:COG1195  310 DVFAELDEERREALLElLADLGGQVFITTTDPEDFPALLE 349
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-369 9.20e-99

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: 294.20  E-value: 9.20e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   3 VRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWYSATLGSHRVASDAPLIRVGAPRAVVSTIVVNEGRELA 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  83 VDLEITTGRANKARLNRSPVRSPREVLGVLRAVLFAPEDLALVRGDPGERRRYLDELATTRRPSIAGVRADYDRVIRQRT 162
Cdd:cd03242   81 LELTIRSGGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 163 ALLKsaagaryrgdrsvletldvwdghlaahgallmaaradlvhhlapevekayqllapgsrpaairyrtsidaeddvsa 242
Cdd:cd03242  161 ALLK---------------------------------------------------------------------------- 164

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 243 eyyeaalldamtrrrdaelergvclvGPHRDDLELRLGDQMAKGYASHGESWSMALSLRLAAYELLRT-DGSDPVLLLDD 321
Cdd:cd03242  165 --------------------------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEvSGEYPVLLLDD 218

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 123369971 322 VFAELDAARRRALAEVAASAEQVLVTAAVAEDIPADWDARRIMIRMQD 369
Cdd:cd03242  219 VLAELDLGRQAALLDAIEGRVQTFVTTTDLADFDALWLRRAQIFRVDA 266
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 2-161 1.47e-12

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: 69.23  E-value: 1.47e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971     2 FVRHLTLTDFRSWA-RADLELEPGRTVFVGPNGFGKTNLVEA-LWY-----SATLGSHRVaSDapLIRVGAPRAV----V 70
Cdd:pfam02463    1 YLKRIEIEGFKSYAkTVILPFSPGFTAIVGPNGSGKSNILDAiLFVlgersAKSLRSERL-SD--LIHSKSGAFVnsaeV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971    71 STIVVNEGRELAVDL-EITTGR------ANKARLNRSPVRSpREVLGVLRAVLFAPEDLA-LVRGD--------PGERRR 134
Cdd:pfam02463   78 EITFDNEDHELPIDKeEVSIRRrvyrggDSEYYINGKNVTK-KEVAELLESQGISPEAYNfLVQGGkieiiammKPERRL 156

                          170       180
                   ....*....|....*....|....*..
gi 123369971   135 YLDELAttrrpsiagVRADYDRVIRQR 161
Cdd:pfam02463  157 EIEEEA---------AGSRLKRKKKEA 174
 
Name Accession Description Interval E-value
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-375 7.44e-156

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: 442.95  E-value: 7.44e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971    1 MFVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWYSATLGSHRVASDAPLIRVGAPRAVVSTIVVNEGRE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   81 LAVDLEITTGRANK-ARLNRSPVRSPREVLGVLRAVLFAPEDLALVRGDPGERRRYLDELATTRRPSIAGVRADYDRVIR 159
Cdd:TIGR00611  81 VTIPLEGLLKKKGKkAKVNIDGQDKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  160 QRTALLKSAagARYRGDRSvleTLDVWDGHLAAHGALLMAARADLVHHLAPEVEKAYQLLAPGSRPAAIRYRTSIdaedd 239
Cdd:TIGR00611 161 QRNAALKQA--QRQYGDRT---TLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGEL----- 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  240 vsaEYYEAALLDAMTRRRDAELERGVCLVGPHRDDLELRLGDQMAKGYASHGESWSMALSLRLAAYELLRTDGSD-PVLL 318
Cdd:TIGR00611 231 ---WDKETDYAEALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEyPILL 307

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 123369971  319 LDDVFAELDAARRRALAEVAASA-EQVLVTAAVAEDIPADWDARRIMIRMQDDDDGRV 375
Cdd:TIGR00611 308 LDDVASELDDQRRRLLAELLQSLgVQVFVTAISLDHLKEMWDPNRVTIALVSVDRGTI 365
recF PRK00064
recombination protein F; Reviewed
 1-363 9.53e-156

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 442.29  E-value: 9.53e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   1 MFVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWYSATLGSHRVASDAPLIRVGAPRAVVSTIVVNEGRE 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  81 LAVDLEITTGRANKARLNRSPVRSPREVLGVLRAVLFAPEDLALVRGDPGERRRYLDELATTRRPSIAGVRADYDRVIRQ 160
Cdd:PRK00064  81 LPLGLEIDKKGGRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 161 RTALLKSAAGAryrgdrsvleTLDVWDGHLAAHGALLMAARADLVHHLAPEVEKAYQLLAPGSRPAAIRYRTSIDAeddv 240
Cdd:PRK00064 161 RNALLKQADYA----------WLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSVED---- 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 241 SAEYYEAALLDAMTRRRDAELERGVCLVGPHRDDLELRLGDQMAKGYASHGESWSMALSLRLAAYELL-RTDGSDPVLLL 319
Cdd:PRK00064 227 DAEKIEEDLLEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLkEETGEAPILLL 306

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*
gi 123369971 320 DDVFAELDAARRRALAE-VAASAEQVLVTAAVAEDIPADWDARRI 363
Cdd:PRK00064 307 DDVASELDDGRRAALLErLKGLGAQVFITTTDLEDLADLLENAKI 351
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-359 3.87e-140

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 402.61  E-value: 3.87e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   2 FVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWYSATLGSHRVASDAPLIRVGAPRAVVSTIVVNEGREL 81
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  82 AVDLEITTGRANKARLNRSPVRSPREVLGVLRAVLFAPEDLALVRGDPGERRRYLDELATTRRPSIAGVRADYDRVIRQR 161
Cdd:COG1195   81 RLGLGLSRGGKKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 162 TALLKSAAGARYrgdrsvlETLDVWDGHLAAHGALLMAARADLVHHLAPEVEKAYQLLAPGSRPAAIRYRTSIDAEDDVS 241
Cdd:COG1195  161 NALLKQGREADL-------ALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALSGGKEELELRYRSGWLYESAEL 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 242 aeyyEAALLDAMTRRRDAELERGVCLVGPHRDDLELRLGDQMAKGYASHGESWSMALSLRLAAYELLRTD-GSDPVLLLD 320
Cdd:COG1195  234 ----EEALLEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEEtGEAPILLLD 309

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 123369971 321 DVFAELDAARRRALAE-VAASAEQVLVTAAVAEDIPADWD 359
Cdd:COG1195  310 DVFAELDEERREALLElLADLGGQVFITTTDPEDFPALLE 349
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-369 9.20e-99

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: 294.20  E-value: 9.20e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   3 VRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWYSATLGSHRVASDAPLIRVGAPRAVVSTIVVNEGRELA 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  83 VDLEITTGRANKARLNRSPVRSPREVLGVLRAVLFAPEDLALVRGDPGERRRYLDELATTRRPSIAGVRADYDRVIRQRT 162
Cdd:cd03242   81 LELTIRSGGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 163 ALLKsaagaryrgdrsvletldvwdghlaahgallmaaradlvhhlapevekayqllapgsrpaairyrtsidaeddvsa 242
Cdd:cd03242  161 ALLK---------------------------------------------------------------------------- 164

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 243 eyyeaalldamtrrrdaelergvclvGPHRDDLELRLGDQMAKGYASHGESWSMALSLRLAAYELLRT-DGSDPVLLLDD 321
Cdd:cd03242  165 --------------------------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEvSGEYPVLLLDD 218

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 123369971 322 VFAELDAARRRALAEVAASAEQVLVTAAVAEDIPADWDARRIMIRMQD 369
Cdd:cd03242  219 VLAELDLGRQAALLDAIEGRVQTFVTTTDLADFDALWLRRAQIFRVDA 266
recF PRK14079
recombination protein F; Provisional
 6-347 7.38e-51

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 173.82  E-value: 7.38e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   6 LTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALwYSATLGSHRVASDAPLIRVGAPRAVVSTIVVNEGRELAVDL 85
Cdd:PRK14079   6 LRQLNYRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAI-YLALTGELPNGRLADLVRFGEGEAWVHAEVETGGGLSRLEV 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  86 EITTGRaNKARLNRSPVRSpREVLGVLRAVLFAPEDLALVRGDPGERRRYLDELATTRRPSIAGVRADYDRVIRQRTALL 165
Cdd:PRK14079  85 GLGPGR-RELKLDGVRVSL-RELARLPGAVLIRPEDLELVLGPPEGRRAYLDRLLSRLSARYAALLSAYERAVQQRNAAL 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 166 KSAAGaryrgdrsvlETLDVWDGHLAAHGALLMAARADLVHHLAPEVEKAY-QLLAPGsrPAAIRYRTSIDAEddvsaey 244
Cdd:PRK14079 163 KSGGG----------WGLHVWDDELVKLGDEIMALRRRALTRLSELAREAYaELGSRK--PLRLELSESTAPE------- 223

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971 245 yeaALLDAMTRRRDAELERGVCLVGPHRDDLELRLGDQMAKGYASHGESWSMALSLRLAAYELLRTD-GSDPVLLLDDVF 323
Cdd:PRK14079 224 ---GYLAALEARRAEELARGATVVGPHRDDLVLTLEGRPAHRYASRGEARTVALALRLAEHRLLWEHfGEAPVLLVDDFT 300

                        330       340
                 ....*....|....*....|....
gi 123369971 324 AELDAARRRALAEVAASAEQVLVT 347
Cdd:PRK14079 301 AELDPRRRGALLALAASLPQAIVA 324
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 2-161 1.47e-12

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: 69.23  E-value: 1.47e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971     2 FVRHLTLTDFRSWA-RADLELEPGRTVFVGPNGFGKTNLVEA-LWY-----SATLGSHRVaSDapLIRVGAPRAV----V 70
Cdd:pfam02463    1 YLKRIEIEGFKSYAkTVILPFSPGFTAIVGPNGSGKSNILDAiLFVlgersAKSLRSERL-SD--LIHSKSGAFVnsaeV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971    71 STIVVNEGRELAVDL-EITTGR------ANKARLNRSPVRSpREVLGVLRAVLFAPEDLA-LVRGD--------PGERRR 134
Cdd:pfam02463   78 EITFDNEDHELPIDKeEVSIRRrvyrggDSEYYINGKNVTK-KEVAELLESQGISPEAYNfLVQGGkieiiammKPERRL 156

                          170       180
                   ....*....|....*....|....*..
gi 123369971   135 YLDELAttrrpsiagVRADYDRVIRQR 161
Cdd:pfam02463  157 EIEEEA---------AGSRLKRKKKEA 174
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-45 6.34e-09

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: 56.93  E-value: 6.34e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 123369971   1 MFVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWY 45
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRL 45
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-48 1.19e-08

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 55.39  E-value: 1.19e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 123369971   1 MFVRHLTLTDFRSWARADLELE--PGRTVFVGPNGFGKTNLVEALWYSAT 48
Cdd:COG3950    1 MRIKSLTIENFRGFEDLEIDFDnpPRLTVLVGENGSGKTTLLEAIALALS 50
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 3-83 2.10e-07

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: 51.07  E-value: 2.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   3 VRHLTLTDFRSWA-RADLELEPGRTVFVGPNGFGKTNLVEALWYSAT----LGSHRVASDAPLIRVGAPRAVVS-TIVVN 76
Cdd:cd03240    1 IDKLSIRNIRSFHeRSEIEFFSPLTLIVGQNGAGKTTIIEALKYALTgelpPNSKGGAHDPKLIREGEVRAQVKlAFENA 80


                 ....*..
gi 123369971  77 EGRELAV 83
Cdd:cd03240   81 NGKKYTI 87
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
4-83 3.00e-07

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 50.39  E-value: 3.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   4 RHLTLTDFRSWARAD-LELEPGRTVFVGPNGFGKTNLVEALW---YSATLGSHRVASDapLIRVGAPRAVVSTIVVNEGR 79
Cdd:COG0419    3 LRLRLENFRSYRDTEtIDFDDGLNLIVGPNGAGKSTILEAIRyalYGKARSRSKLRSD--LINVGSEEASVELEFEHGGK 80


                 ....
gi 123369971  80 ELAV 83
Cdd:COG0419   81 RYRI 84
AAA_23 pfam13476
AAA domain;
6-45 5.58e-07

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 49.42  E-value: 5.58e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 123369971    6 LTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWY 45
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAIKL 40
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 26-347 1.25e-06

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: 49.70  E-value: 1.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   26 TVFVGPNGFGKTNLVEALWY---SATLGSHRVASDAPLIRVGAPRAVVSTIVVNEGRELAVDLEITTGRANKARLNRSPv 102
Cdd:pfam13304   2 NVLIGPNGSGKSNLLEALRFladFDALVIGLTDERSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVRYRYGLDLER- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  103 rsprevlgvlRAVLFAPEDLALVRGDPGERRRYLDELATTRRPSIAGVRADYDRVIRQRTALLKSAAGARYRGDRSVLET 182
Cdd:pfam13304  81 ----------EDVEEKLSSKPTLLEKRLLLREDSEEREPKFPPEAEELRLGLDVEERIELSLSELSDLISGLLLLSIISP 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  183 LDVWDGHLAAHGALLMaARADLVHHLA--PEVEKAYQLLAPGSRPAAIRYRTSIDAEDDVsaeyyeaalldamtrRRDAE 260
Cdd:pfam13304 151 LSFLLLLDEGLLLEDW-AVLDLAADLAlfPDLKELLQRLVRGLKLADLNLSDLGEGIEKS---------------LLVDD 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  261 LERGVCLVGPHRDDLELRLGDQMAKGyashgeswsmALSLRLAAYELLRTDGSDPVLLLDDVFAELDAARRRALAEVAAS 340
Cdd:pfam13304 215 RLRERGLILLENGGGGELPAFELSDG----------TKRLLALLAALLSALPKGGLLLIDEPESGLHPKLLRRLLELLKE 284

                         330
                  ....*....|.
gi 123369971  341 AE----QVLVT 347
Cdd:pfam13304 285 LSrngaQLILT 295
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 5-83 2.48e-06

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: 47.46  E-value: 2.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   5 HLTLTDFRSWA-RADLELEPGRTVFVGPNGFGKTNLVEAL-WysaTLG-----SHRVASDAPLI------RVGAPRAVVS 71
Cdd:cd03278    3 KLELKGFKSFAdKTTIPFPPGLTAIVGPNGSGKSNIIDAIrW---VLGeqsakSLRGEKMSDVIfagsetRKPANFAEVT 79

                         90
                 ....*....|..
gi 123369971  72 TIVVNEGRELAV 83
Cdd:cd03278   80 LTFDNSDGRYSI 91
COG4637 COG4637
Predicted ATPase [General function prediction only];
4-43 3.03e-05

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 45.69  E-value: 3.03e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 123369971   4 RHLTLTDFRSWARADLELEPgRTVFVGPNGFGKTNLVEAL 43
Cdd:COG4637    3 TRIRIKNFKSLRDLELPLGP-LTVLIGANGSGKSNLLDAL 41
ABC_RecN cd03241
ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC ...
 17-137 6.42e-05

ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213208 [Multi-domain]  Cd Length: 276  Bit Score: 44.12  E-value: 6.42e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  17 ADLELEPGRTVFVGPNGFGKTNLVEALwySATLGShrvASDAPLIRVGAPRAVVSTIVVNEGRELAVDL----------- 85
Cdd:cd03241   15 LELDFEEGLTVLTGETGAGKSILLDAL--SLLLGG---RASADLIRSGAEKAVVEGVFDISDEEEAKALllelgiedddd 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 123369971  86 -----EITTGRANKARLNRSPVrsPREVLGVLRAVLFA----PEDLALvrGDPGERRRYLD 137
Cdd:cd03241   90 liirrEISRKGRSRYFINGQSV--TLKLLRELGSLLVDihgqHDHQNL--LNPERQLDLLD 146
PRK01156 PRK01156
chromosome segregation protein; Provisional
 1-139 8.40e-05

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 44.89  E-value: 8.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   1 MFVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWYsATLGSHRVASDAPLIRVGApravvstivvnegRE 80
Cdd:PRK01156   1 MIIKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAIRF-ALFTDKRTEKIEDMIKKGK-------------NN 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971  81 LAVDLEITTG------RANKARLNRSPVRSP---------------------REVLGVLRAVLFAP------EDLALVRG 127
Cdd:PRK01156  67 LEVELEFRIGghvyqiRRSIERRGKGSRREAyikkdgsiiaegfddttkyieKNILGISKDVFLNSifvgqgEMDSLISG 146

                        170
                 ....*....|..
gi 123369971 128 DPGERRRYLDEL 139
Cdd:PRK01156 147 DPAQRKKILDEI 158
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 6-160 9.16e-05

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 44.67  E-value: 9.16e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971     6 LTLTDFRSWA-RADLELEPGRTVFVGPNGFGKTNLVEALWYS-ATLGSHRVASD--APLI---RVGAPRAVVSTIVV--N 76
Cdd:TIGR02169    5 IELENFKSFGkKKVIPFSKGFTVISGPNGSGKSNIGDAILFAlGLSSSKAMRAErlSDLIsngKNGQSGNEAYVTVTfkN 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971    77 EGRELAVDLEIT-------TGRANKARLNRSPVRSpREVLGVLRAVLFAPEDLALV-RGD--------PGERRRYLDEla 140
Cdd:TIGR02169   85 DDGKFPDELEVVrrlkvtdDGKYSYYYLNGQRVRL-SEIHDFLAAAGIYPEGYNVVlQGDvtdfismsPVERRKIIDE-- 161

                          170       180
                   ....*....|....*....|
gi 123369971   141 ttrrpsIAGVrADYDRVIRQ 160
Cdd:TIGR02169  162 ------IAGV-AEFDRKKEK 174
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
1-61 1.13e-04

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 43.49  E-value: 1.13e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 123369971   1 MFVRhLTLTDFRSWA-RADLELEPGR------TVFVGPNGFGKTNLVEALWYSATLGSHRVASDAPLI 61
Cdd:COG1106    1 MLIS-FSIENFRSFKdELTLSMVASGlrllrvNLIYGANASGKSNLLEALYFLRNLVLNSSQPGDKLV 67
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-45 1.17e-04

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: 43.74  E-value: 1.17e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 123369971    1 MFVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWY 45
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDI 45
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
1-42 2.23e-04

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 43.49  E-value: 2.23e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 123369971   1 MFVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEA 42
Cdd:PRK02224   1 MRFDRVRLENFKCYADADLRLEDGVTVIHGVNGSGKSSLLEA 42
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 1-43 7.18e-04

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 41.85  E-value: 7.18e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 123369971   1 MFVRHLTLTDFRSWA-RADLELEPGRTVFVGPNGFGKTNLVEAL 43
Cdd:COG1196    1 MRLKRLELAGFKSFAdPTTIPFEPGITAIVGPNGSGKSNIVDAI 44
ABC_SMC4_euk cd03274
ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of ...
 1-43 4.94e-03

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


Pssm-ID: 213241 [Multi-domain]  Cd Length: 212  Bit Score: 38.05  E-value: 4.94e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 123369971   1 MFVRHLTLTDFRSWArADLELEPGRTVF---VGPNGFGKTNLVEAL 43
Cdd:cd03274    1 LIITKLVLENFKSYA-GEQVIGPFHKSFsaiVGPNGSGKSNVIDSM 45
COG3910 COG3910
Predicted ATPase [General function prediction only];
1-43 5.50e-03

Predicted ATPase [General function prediction only];


Pssm-ID: 443116 [Multi-domain]  Cd Length: 239  Bit Score: 37.82  E-value: 5.50e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 123369971   1 MFVRHLTL-----TDFRSW--------ARADLELEPGRTVFVGPNGFGKTNLVEAL 43
Cdd:COG3910    2 PYLRRVSLkrekvPDRDAYpfnlpavrNLEGLEFHPPVTFFVGENGSGKSTLLEAI 57
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
1-79 6.87e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 38.51  E-value: 6.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 123369971   1 MFVRHLTLTDFRSWARADLELEPGRTVFVGPNGFGKTNLVEALWYSATLGSHRVASD---APLIRVGAPRAVVSTIVVNE 77
Cdd:PRK03918   1 MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAILVGLYWGHGSKPKGlkkDDFTRIGGSGTEIELKFEKN 80


                 ..
gi 123369971  78 GR 79
Cdd:PRK03918  81 GR 82
 
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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