NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|226737819|sp|B4F0U7|]
View 

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 1-358 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: 508.05  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819    1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQANRVIQHDENAFILHGRLSGLDEE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   81 SRGYSIGLSKDREGNSTVRIDGSDghKIAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRFFAAWSDLKRV 160
Cdd:TIGR00611  81 VTIPLEGLLKKKGKKAKVNIDGQD--KLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  161 LKQRNAALRQASSYR----QLLPWDKELILLTEQISQWRAEYTEDIAKDIEETCQLFLPEFTLKVSFQRG--WDKETDYA 234
Cdd:TIGR00611 159 LKQRNAALKQAQRQYgdrtTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGelWDKETDYA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  235 QLLERQFERDKVLSYTSLGAHKADLRIRANGTPVEDMLSRGQLKLLMCALRLAQGEYFTRKNGQRCLYLLDDFASELDAN 314
Cdd:TIGR00611 239 EALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDVASELDDQ 318

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 226737819  315 RRQLLAERLKSTQAQVFVSAITSGQVKDMLDVNS---RLFSVEHGKI 358
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 ...
 1-358 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: 508.05  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819    1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQANRVIQHDENAFILHGRLSGLDEE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   81 SRGYSIGLSKDREGNSTVRIDGSDghKIAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRFFAAWSDLKRV 160
Cdd:TIGR00611  81 VTIPLEGLLKKKGKKAKVNIDGQD--KLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  161 LKQRNAALRQASSYR----QLLPWDKELILLTEQISQWRAEYTEDIAKDIEETCQLFLPEFTLKVSFQRG--WDKETDYA 234
Cdd:TIGR00611 159 LKQRNAALKQAQRQYgdrtTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGelWDKETDYA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  235 QLLERQFERDKVLSYTSLGAHKADLRIRANGTPVEDMLSRGQLKLLMCALRLAQGEYFTRKNGQRCLYLLDDFASELDAN 314
Cdd:TIGR00611 239 EALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDVASELDDQ 318

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 226737819  315 RRQLLAERLKSTQAQVFVSAITSGQVKDMLDVNS---RLFSVEHGKI 358
Cdd:TIGR00611 319 RRRLLAELLQSLGVQVFVTAISLDHLKEMWDPNRvtiALVSVDRGTI 365
recF PRK00064
recombination protein F; Reviewed
 1-359 9.84e-156

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 441.52  E-value: 9.84e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQANRVIQHDENAFILHGRLSGldeE 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEK---G 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  81 SRGYSIGLSKDREGNSTVRIDGSDGHKIAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRFFAAWSDLKRV 160
Cdd:PRK00064  78 GRELPLGLEIDKKGGRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 161 LKQRNAALRQASsYRQLLPWDKELILLTEQISQWRAEYTEDIAKDIEETCQLFLPEF-TLKVSFQRGWDK-----ETDYA 234
Cdd:PRK00064 158 LKQRNALLKQAD-YAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFeLASLSYQSSVEDdaekiEEDLL 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 235 QLLERQFERDKVLSYTSLGAHKADLRIRANGTPVEDMLSRGQLKLLMCALRLAQGEYFTRKNGQRCLYLLDDFASELDAN 314
Cdd:PRK00064 237 EALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDVASELDDG 316

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*
gi 226737819 315 RRQLLAERLKSTQAQVFVSAITSGQVKDMLDvNSRLFSVEHGKIE 359
Cdd:PRK00064 317 RRAALLERLKGLGAQVFITTTDLEDLADLLE-NAKIFHVEQGKIT 360
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-345 7.17e-130

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 375.65  E-value: 7.17e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   2 ILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQANRVIQHDENAFILHGRLSGLDEES 81
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  82 RgysIGLSKDREGNSTVRIDGSDGHKIAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRFFAAWSDLKRVL 161
Cdd:COG1195   81 R---LGLGLSRGGKKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERAL 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 162 KQRNAALRQA--SSYRQLLPWDKELILLTEQISQWRAEYTEDIAKDIEETC-QLFLPEFTLKVSFQRGWDKET-----DY 233
Cdd:COG1195  158 KQRNALLKQGreADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYaALSGGKEELELRYRSGWLYESaeleeAL 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 234 AQLLERQFERDKVLSYTSLGAHKADLRIRANGTPVEDMLSRGQLKLLMCALRLAQGEYFTRKNGQRCLYLLDDFASELDA 313
Cdd:COG1195  238 LEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVFAELDE 317

                        330       340       350
                 ....*....|....*....|....*....|..
gi 226737819 314 NRRQLLAERLKSTQAQVFVSAITSGQVKDMLD 345
Cdd:COG1195  318 ERREALLELLADLGGQVFITTTDPEDFPALLE 349
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 3-249 1.37e-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: 149.74  E-value: 1.37e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819     3 LSRLLIRHFRNI-EQADLPLADGFNFLVGPNGSGKTSILEAI-YTLG--HGRAFRSAQANRVIQHDENAFILHGRLSGL- 77
Cdd:pfam02463    2 LKRIEIEGFKSYaKTVILPFSPGFTAIVGPNGSGKSNILDAIlFVLGerSAKSLRSERLSDLIHSKSGAFVNSAEVEITf 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819    78 DEESRG-------YSIGLSKDREGNSTVRIDGSDGHKiAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRF 150
Cdd:pfam02463   82 DNEDHElpidkeeVSIRRRVYRGGDSEYYINGKNVTK-KEVAELLESQGISPEAYNFLVQGGKIEIIAMMKPERRLEIEE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   151 FAAWSDLKRVLKQRNAALRQASSYRQLLPWDKELILLTEQISQWRAeytEDIAKDIEETCQLFLPEFTLKVSFQRGWDKE 230
Cdd:pfam02463  161 EAAGSRLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQA---KKALEYYQLKEKLELEEEYLLYLDYLKLNEE 237

                          250
                   ....*....|....*....
gi 226737819   231 TDYAQLLERQFERDKVLSY 249
Cdd:pfam02463  238 RIDLLQELLRDEQEEIESS 256
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-359 1.37e-33

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: 125.49  E-value: 1.37e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   3 LSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQANRVIQHDENAFILHGRLsgldeESR 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVL-----ERQ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  83 GY--SIGLSKDREGNSTVRIDGSDGHKIAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRFFAAWSDLKRV 160
Cdd:cd03242   76 GGelALELTIRSGGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKA 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 161 LKQRNAALRqassyrqllpwdkelillteqisqwraeytediakdieetcqlflpeftlkvsfqrgwdketdyaqllerq 240
Cdd:cd03242  156 LRQRNALLK----------------------------------------------------------------------- 164

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 241 ferdkvlsytslGAHKADLRIRANGTPVEDMLSRGQLKLLMCALRLAQGEYFTRKNGQRCLYLLDDFASELDANRRQLLA 320
Cdd:cd03242  165 ------------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLAELDLGRQAALL 232

                        330       340       350
                 ....*....|....*....|....*....|....*....
gi 226737819 321 ERLKSTQaQVFVSAITSGQVKDMLDVNSRLFSVEHGKIE 359
Cdd:cd03242  233 DAIEGRV-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 ...
 1-358 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: 508.05  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819    1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQANRVIQHDENAFILHGRLSGLDEE 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   81 SRGYSIGLSKDREGNSTVRIDGSDghKIAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRFFAAWSDLKRV 160
Cdd:TIGR00611  81 VTIPLEGLLKKKGKKAKVNIDGQD--KLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  161 LKQRNAALRQASSYR----QLLPWDKELILLTEQISQWRAEYTEDIAKDIEETCQLFLPEFTLKVSFQRG--WDKETDYA 234
Cdd:TIGR00611 159 LKQRNAALKQAQRQYgdrtTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGelWDKETDYA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  235 QLLERQFERDKVLSYTSLGAHKADLRIRANGTPVEDMLSRGQLKLLMCALRLAQGEYFTRKNGQRCLYLLDDFASELDAN 314
Cdd:TIGR00611 239 EALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDVASELDDQ 318

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 226737819  315 RRQLLAERLKSTQAQVFVSAITSGQVKDMLDVNS---RLFSVEHGKI 358
Cdd:TIGR00611 319 RRRLLAELLQSLGVQVFVTAISLDHLKEMWDPNRvtiALVSVDRGTI 365
recF PRK00064
recombination protein F; Reviewed
 1-359 9.84e-156

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 441.52  E-value: 9.84e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQANRVIQHDENAFILHGRLSGldeE 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEK---G 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  81 SRGYSIGLSKDREGNSTVRIDGSDGHKIAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRFFAAWSDLKRV 160
Cdd:PRK00064  78 GRELPLGLEIDKKGGRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 161 LKQRNAALRQASsYRQLLPWDKELILLTEQISQWRAEYTEDIAKDIEETCQLFLPEF-TLKVSFQRGWDK-----ETDYA 234
Cdd:PRK00064 158 LKQRNALLKQAD-YAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFeLASLSYQSSVEDdaekiEEDLL 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 235 QLLERQFERDKVLSYTSLGAHKADLRIRANGTPVEDMLSRGQLKLLMCALRLAQGEYFTRKNGQRCLYLLDDFASELDAN 314
Cdd:PRK00064 237 EALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDVASELDDG 316

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*
gi 226737819 315 RRQLLAERLKSTQAQVFVSAITSGQVKDMLDvNSRLFSVEHGKIE 359
Cdd:PRK00064 317 RRAALLERLKGLGAQVFITTTDLEDLADLLE-NAKIFHVEQGKIT 360
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-345 7.17e-130

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 375.65  E-value: 7.17e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   2 ILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQANRVIQHDENAFILHGRLSGLDEES 81
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  82 RgysIGLSKDREGNSTVRIDGSDGHKIAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRFFAAWSDLKRVL 161
Cdd:COG1195   81 R---LGLGLSRGGKKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERAL 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 162 KQRNAALRQA--SSYRQLLPWDKELILLTEQISQWRAEYTEDIAKDIEETC-QLFLPEFTLKVSFQRGWDKET-----DY 233
Cdd:COG1195  158 KQRNALLKQGreADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYaALSGGKEELELRYRSGWLYESaeleeAL 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 234 AQLLERQFERDKVLSYTSLGAHKADLRIRANGTPVEDMLSRGQLKLLMCALRLAQGEYFTRKNGQRCLYLLDDFASELDA 313
Cdd:COG1195  238 LEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVFAELDE 317

                        330       340       350
                 ....*....|....*....|....*....|..
gi 226737819 314 NRRQLLAERLKSTQAQVFVSAITSGQVKDMLD 345
Cdd:COG1195  318 ERREALLELLADLGGQVFITTTDPEDFPALLE 349
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 3-249 1.37e-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: 149.74  E-value: 1.37e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819     3 LSRLLIRHFRNI-EQADLPLADGFNFLVGPNGSGKTSILEAI-YTLG--HGRAFRSAQANRVIQHDENAFILHGRLSGL- 77
Cdd:pfam02463    2 LKRIEIEGFKSYaKTVILPFSPGFTAIVGPNGSGKSNILDAIlFVLGerSAKSLRSERLSDLIHSKSGAFVNSAEVEITf 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819    78 DEESRG-------YSIGLSKDREGNSTVRIDGSDGHKiAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRF 150
Cdd:pfam02463   82 DNEDHElpidkeeVSIRRRVYRGGDSEYYINGKNVTK-KEVAELLESQGISPEAYNFLVQGGKIEIIAMMKPERRLEIEE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   151 FAAWSDLKRVLKQRNAALRQASSYRQLLPWDKELILLTEQISQWRAeytEDIAKDIEETCQLFLPEFTLKVSFQRGWDKE 230
Cdd:pfam02463  161 EAAGSRLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQA---KKALEYYQLKEKLELEEEYLLYLDYLKLNEE 237

                          250
                   ....*....|....*....
gi 226737819   231 TDYAQLLERQFERDKVLSY 249
Cdd:pfam02463  238 RIDLLQELLRDEQEEIESS 256
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-359 1.37e-33

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: 125.49  E-value: 1.37e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   3 LSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQANRVIQHDENAFILHGRLsgldeESR 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVL-----ERQ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  83 GY--SIGLSKDREGNSTVRIDGSDGHKIAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRFFAAWSDLKRV 160
Cdd:cd03242   76 GGelALELTIRSGGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKA 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 161 LKQRNAALRqassyrqllpwdkelillteqisqwraeytediakdieetcqlflpeftlkvsfqrgwdketdyaqllerq 240
Cdd:cd03242  156 LRQRNALLK----------------------------------------------------------------------- 164

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 241 ferdkvlsytslGAHKADLRIRANGTPVEDMLSRGQLKLLMCALRLAQGEYFTRKNGQRCLYLLDDFASELDANRRQLLA 320
Cdd:cd03242  165 ------------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLAELDLGRQAALL 232

                        330       340       350
                 ....*....|....*....|....*....|....*....
gi 226737819 321 ERLKSTQaQVFVSAITSGQVKDMLDVNSRLFSVEHGKIE 359
Cdd:cd03242  233 DAIEGRV-QTFVTTTDLADFDALWLRRAQIFRVDAGTLS 270
recF PRK14079
recombination protein F; Provisional
 1-319 1.63e-32

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 124.51  E-value: 1.63e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYtLGHGRAFRSAQANRVIQHDENAFILHGRLsgldEE 80
Cdd:PRK14079   1 MRLLSLRQLNYRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAIY-LALTGELPNGRLADLVRFGEGEAWVHAEV----ET 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  81 SRGYSIGLSKDREGNSTVRIDGSDGhKIAELAKLLPMQLITPEGFTLLNGGPKYRRAFIDWGCFHNEPRFFAAWSDLKRV 160
Cdd:PRK14079  76 GGGLSRLEVGLGPGRRELKLDGVRV-SLRELARLPGAVLIRPEDLELVLGPPEGRRAYLDRLLSRLSARYAALLSAYERA 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819 161 LKQRNAALRqASSYRQLLPWDKELILLTEQISQWRAEYTEDIAKDIEETCQLFLPEFTLKVSFQRGWDKETdYAQLLERQ 240
Cdd:PRK14079 155 VQQRNAALK-SGGGWGLHVWDDELVKLGDEIMALRRRALTRLSELAREAYAELGSRKPLRLELSESTAPEG-YLAALEAR 232

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 226737819 241 FERDKVLSYTSLGAHKADLRIRANGTPVEDMLSRGQLKLLMCALRLAQGEYFTRKNGQRCLYLLDDFASELDANRRQLL 319
Cdd:PRK14079 233 RAEELARGATVVGPHRDDLVLTLEGRPAHRYASRGEARTVALALRLAEHRLLWEHFGEAPVLLVDDFTAELDPRRRGAL 311
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 196-359 1.61e-24

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: 105.44  E-value: 1.61e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   196 AEYTEDIAKDIEETCQLFLPEFTLKVSFQRGWDKETDYAQLLERQFERDKVLSYTSLGAHKADLRIRANGTPVEDMLSRG 275
Cdd:pfam02463 1002 EEKKKLIRAIIEETCQRLKEFLELFVSINKGWNKVFFYLELGGSAELRLEDPDDPFSGGIEISARPPGKGVKNLDLLSGG 1081

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   276 QLKLLMCALRLAqgeyfTRKNGQRCLYLLDDFASELDANRRQLLAERLK--STQAQVFVSAITSGQVKDMlDVNSRLFSV 353
Cdd:pfam02463 1082 EKTLVALALIFA-----IQKYKPAPFYLLDEIDAALDDQNVSRVANLLKelSKNAQFIVISLREEMLEKA-DKLVGVTMV 1155


                   ....*.
gi 226737819   354 EHGKIE 359
Cdd:pfam02463 1156 ENGVST 1161
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-64 4.33e-13

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: 69.65  E-value: 4.33e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 226737819   1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYtlghgRAFRSAQANRVIQHD 64
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALR-----LLLGPSSSRKFDEED 59
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-46 2.47e-10

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 60.40  E-value: 2.47e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 226737819   1 MILSRLLIRHFRNIEQADLPL--ADGFNFLVGPNGSGKTSILEAIYTL 46
Cdd:COG3950    1 MRIKSLTIENFRGFEDLEIDFdnPPRLTVLVGENGSGKTTLLEAIALA 48
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-44 3.27e-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: 57.99  E-value: 3.27e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 226737819    1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIY 44
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALD 44
COG4637 COG4637
Predicted ATPase [General function prediction only];
3-48 3.95e-09

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 57.63  E-value: 3.95e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 226737819   3 LSRLLIRHFRNIEQADLPLADgFNFLVGPNGSGKTSILEAIYTLGH 48
Cdd:COG4637    2 ITRIRIKNFKSLRDLELPLGP-LTVLIGANGSGKSNLLDALRFLSD 46
AAA_23 pfam13476
AAA domain;
6-72 4.17e-08

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 52.88  E-value: 4.17e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 226737819    6 LLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAI-YTLGHGRAFRSAQANRVIQHDENAFILHG 72
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAIkLALYGKTSRLKRKSGGGFVKGDIRIGLEG 68
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
2-56 8.82e-07

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 48.85  E-value: 8.82e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 226737819   2 ILSRLLIRHFRNIEQAD-LPLADGFNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQ 56
Cdd:COG0419    1 KLLRLRLENFRSYRDTEtIDFDDGLNLIVGPNGAGKSTILEAIRYALYGKARSRSK 56
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
1-43 3.68e-06

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 48.91  E-value: 3.68e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 226737819   1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAI 43
Cdd:PRK03918   1 MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAI 43
COG4938 COG4938
Predicted ATPase [General function prediction only];
3-46 9.05e-06

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 46.89  E-value: 9.05e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 226737819   3 LSRLLIRHFRNIEQADLPLADgFNFLVGPNGSGKTSILEAIYTL 46
Cdd:COG4938    1 IKSISIKNFGPFKEAELELKP-LTLLIGPNGSGKSTLIQALLLL 43
ABC_RecN cd03241
ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC ...
 3-103 1.05e-05

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


Pssm-ID: 213208 [Multi-domain]  Cd Length: 276  Bit Score: 46.43  E-value: 1.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   3 LSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAIYTLGHGRA----FRSAQANRVIQ-------HDENAFILH 71
Cdd:cd03241    1 LLELSIKNFALIEELELDFEEGLTVLTGETGAGKSILLDALSLLLGGRAsadlIRSGAEKAVVEgvfdisdEEEAKALLL 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 226737819  72 GRLSGLDEESRgysIGLSKDREGNSTVRIDGS 103
Cdd:cd03241   81 ELGIEDDDDLI---IRREISRKGRSRYFINGQ 109
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-333 2.26e-05

AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system.


Pssm-ID: 433102 [Multi-domain]  Cd Length: 303  Bit Score: 45.84  E-value: 2.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819   25 FNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQANRVIQHDENAFILHGRLSGLDEESRGYSIGLSKDREGNSTVRIDGSD 104
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVIGLTDERSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVRYRYGLDLER 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  105 GHkIAELAKLLPMQLITPEGFTLL------NGGPKYRRAFIDWgcFHNEPRFFAAWSDLKRVLKQrnAALRQASSYRQLL 178
Cdd:pfam13304  81 ED-VEEKLSSKPTLLEKRLLLREDseerepKFPPEAEELRLGL--DVEERIELSLSELSDLISGL--LLLSIISPLSFLL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819  179 PWDKELILLTEQISQWRAEYTEDIakDIEETCQLFLPEFtlkvsfqrgwdKETDYAQLLERQFERDKVLSYTSLGAHKAD 258
Cdd:pfam13304 156 LLDEGLLLEDWAVLDLAADLALFP--DLKELLQRLVRGL-----------KLADLNLSDLGEGIEKSLLVDDRLRERGLI 222

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 226737819  259 LRIRANGTPVE-DMLSRGQLKLLmcALRLAQgeYFTRKNGQrcLYLLDDFASELDANRRQLLAERLKST---QAQVFVS 333
Cdd:pfam13304 223 LLENGGGGELPaFELSDGTKRLL--ALLAAL--LSALPKGG--LLLIDEPESGLHPKLLRRLLELLKELsrnGAQLILT 295
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 3-43 3.06e-05

ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.


Pssm-ID: 213207 [Multi-domain]  Cd Length: 204  Bit Score: 44.52  E-value: 3.06e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 226737819   3 LSRLLIRHFRNI-EQADLPLADGFNFLVGPNGSGKTSILEAI 43
Cdd:cd03240    1 IDKLSIRNIRSFhERSEIEFFSPLTLIVGQNGAGKTTIIEAL 42
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 3-43 5.99e-05

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: 43.61  E-value: 5.99e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 226737819   3 LSRLLIRHFRN-IEQADLPLADGFNFLVGPNGSGKTSILEAI 43
Cdd:cd03278    1 LKKLELKGFKSfADKTTIPFPPGLTAIVGPNGSGKSNIIDAI 42
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
1-42 9.49e-05

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 44.26  E-value: 9.49e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 226737819   1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEA 42
Cdd:PRK02224   1 MRFDRVRLENFKCYADADLRLEDGVTVIHGVNGSGKSSLLEA 42
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 5-43 9.64e-05

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


Pssm-ID: 213194 [Multi-domain]  Cd Length: 162  Bit Score: 42.35  E-value: 9.64e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 226737819   5 RLLIRHFR-NIEQADLPLADG-FNFLVGPNGSGKTSILEAI 43
Cdd:cd03227    1 KIVLGRFPsYFVPNDVTFGEGsLTIITGPNGSGKSTILDAI 41
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
1-43 1.18e-04

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 43.99  E-value: 1.18e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 226737819   1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAI 43
Cdd:COG4717    1 MKIKELEIYGFGKFRDRTIEFSPGLNVIYGPNEAGKSTLLAFI 43
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
1-46 2.68e-04

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 42.34  E-value: 2.68e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 226737819   1 MILSrLLIRHFRNI-EQADLPLADG------FNFLVGPNGSGKTSILEAIYTL 46
Cdd:COG1106    1 MLIS-FSIENFRSFkDELTLSMVASglrllrVNLIYGANASGKSNLLEALYFL 52
PRK01156 PRK01156
chromosome segregation protein; Provisional
 1-43 2.86e-04

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 42.97  E-value: 2.86e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 226737819   1 MILSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAI 43
Cdd:PRK01156   1 MIIKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAI 43
ABC_SMC_head cd03239
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ...
 19-43 7.26e-04

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


Pssm-ID: 213206 [Multi-domain]  Cd Length: 178  Bit Score: 39.98  E-value: 7.26e-04
                         10        20
                 ....*....|....*....|....*
gi 226737819  19 LPLADGFNFLVGPNGSGKTSILEAI 43
Cdd:cd03239   18 VGGSNSFNAIVGPNGSGKSNIVDAI 42
AAA_27 pfam13514
AAA domain; This domain is found in a number of double-strand DNA break proteins. This domain ...
 1-104 1.68e-03

AAA domain; This domain is found in a number of double-strand DNA break proteins. This domain contains a P-loop motif.


Pssm-ID: 433272 [Multi-domain]  Cd Length: 207  Bit Score: 39.07  E-value: 1.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226737819    1 MILSRL-LIR--HFRNiEQADLPLAD-GFNFLVGPNGSGKTSILEAIYTLGHGRAFRSAQANRviqHDENAFilhgRLSG 76
Cdd:pfam13514   1 MRIRRLdLERygPFTD-RSLDFPAGGpDLHLIYGPNEAGKSTALRAISDLLFGIPLRTPYNFL---HDYSDL----RIGA 72

                          90       100
                  ....*....|....*....|....*...
gi 226737819   77 LDEESRGYSIGLSKdREGNSTVRIDGSD 104
Cdd:pfam13514  73 TLENADGETLEFRR-RKGRKNTLLDADG 99
ABC_SMC6_euk cd03276
ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of ...
 26-49 2.92e-03

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


Pssm-ID: 213243 [Multi-domain]  Cd Length: 198  Bit Score: 38.35  E-value: 2.92e-03
                         10        20
                 ....*....|....*....|....
gi 226737819  26 NFLVGPNGSGKTSILEAIyTLGHG 49
Cdd:cd03276   24 NFIVGNNGSGKSAILTAL-TIGLG 46
RecN COG0497
DNA repair ATPase RecN [Replication, recombination and repair];
3-51 4.77e-03

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


Pssm-ID: 440263 [Multi-domain]  Cd Length: 555  Bit Score: 38.90  E-value: 4.77e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 226737819   3 LSRLLIRHFRNIEQADLPLADGFNFLVGPNGSGKTSILEAI-YTLGhGRA 51
Cdd:COG0497    2 LTELSIRNFALIDELELEFGPGLTVLTGETGAGKSILLDALgLLLG-GRA 50
ABC_SMC5_euk cd03277
ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of ...
 24-43 6.60e-03

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: 37.58  E-value: 6.60e-03
                         10        20
                 ....*....|....*....|
gi 226737819  24 GFNFLVGPNGSGKTSILEAI 43
Cdd:cd03277   24 SLNMIIGPNGSGKSSIVCAI 43
AAA_29 pfam13555
P-loop containing region of AAA domain;
23-55 8.34e-03

P-loop containing region of AAA domain;


Pssm-ID: 433304 [Multi-domain]  Cd Length: 61  Bit Score: 34.50  E-value: 8.34e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 226737819   23 DGFNFLVGPNGSGKTSILEAIYTL---GHGRAFRSA 55
Cdd:pfam13555  22 RGNTLLTGPSGSGKSTLLDAIQTLlvpAKRARFNKA 57
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH