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Conserved domains on  [gi|489719533|ref|WP_003623649|]
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DNA replication/repair protein RecF [Lactobacillus delbrueckii]

Protein Classification

DNA replication/repair protein RecF( domain architecture ID 11477886)

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:0005524|GO:0003697|GO:0006281|GO:0006260

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
recF PRK00064
recombination protein F; Reviewed
 1-369 4.64e-149

recombination protein F; Reviewed


:

Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 425.34  E-value: 4.64e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   1 MYLSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDREMIAFGQDFASLAGRVHKRQLD 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  81 LDLRIVISKKGKS-AWVNRVEQARLSKYVGHLNAILFSPEDMELVKGAPSLRRRFMDLEFGQINPEYLYFASQYRQLLQQ 159
Cdd:PRK00064  81 LPLGLEIDKKGGRkVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 160 RNNYLKQlarrqaSDQVLLGVLTEQVATAASELIWRRYRYLADLNRYAAEAYRAISGQREELRVLYRPSAKeitaaDQPA 239
Cdd:PRK00064 161 RNALLKQ------ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSVE-----DDAE 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 240 QIKQKLLDRFAEIADDELRRATTQLGPHRDDLEFQLDGKNAHLFASQGQQRTIALSLKLAEIQLIKQLTGEEPILLLDDV 319
Cdd:PRK00064 230 KIEEDLLEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDV 309

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489719533 320 MSELDQNRQAALLNFIHG-QTQTFITTTDLDSISQEIvKQPRIFYIHSGQI 369
Cdd:PRK00064 310 ASELDDGRRAALLERLKGlGAQVFITTTDLEDLADLL-ENAKIFHVEQGKI 359
 
Name Accession Description Interval E-value
recF PRK00064
recombination protein F; Reviewed
 1-369 4.64e-149

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 425.34  E-value: 4.64e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   1 MYLSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDREMIAFGQDFASLAGRVHKRQLD 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  81 LDLRIVISKKGKS-AWVNRVEQARLSKYVGHLNAILFSPEDMELVKGAPSLRRRFMDLEFGQINPEYLYFASQYRQLLQQ 159
Cdd:PRK00064  81 LPLGLEIDKKGGRkVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 160 RNNYLKQlarrqaSDQVLLGVLTEQVATAASELIWRRYRYLADLNRYAAEAYRAISGQREELRVLYRPSAKeitaaDQPA 239
Cdd:PRK00064 161 RNALLKQ------ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSVE-----DDAE 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 240 QIKQKLLDRFAEIADDELRRATTQLGPHRDDLEFQLDGKNAHLFASQGQQRTIALSLKLAEIQLIKQLTGEEPILLLDDV 319
Cdd:PRK00064 230 KIEEDLLEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDV 309

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489719533 320 MSELDQNRQAALLNFIHG-QTQTFITTTDLDSISQEIvKQPRIFYIHSGQI 369
Cdd:PRK00064 310 ASELDDGRRAALLERLKGlGAQVFITTTDLEDLADLL-ENAKIFHVEQGKI 359
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-355 1.15e-142

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 408.77  E-value: 1.15e-142
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   2 YLSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDREMIAFGQDFASLAGRVHKRQLDL 81
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  82 DLRIVISKKG-KSAWVNRVEQARLSKYVGHLNAILFSPEDMELVKGAPSLRRRFMDLEFGQINPEYLYFASQYRQLLQQR 160
Cdd:COG1195   81 RLGLGLSRGGkKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 161 NNYLKQlarRQASDQVLLGVLTEQVATAASELIWRRYRYLADLNRYAAEAYRAISGQREELRVLYRPSAkeitaADQPAQ 240
Cdd:COG1195  161 NALLKQ---GREADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALSGGKEELELRYRSGW-----LYESAE 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 241 IKQKLLDRFAEIADDELRRATTQLGPHRDDLEFQLDGKNAHLFASQGQQRTIALSLKLAEIQLIKQLTGEEPILLLDDVM 320
Cdd:COG1195  233 LEEALLEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVF 312

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 489719533 321 SELDQNRQAALLNFIHG-QTQTFITTTDLDSISQEI 355
Cdd:COG1195  313 AELDEERREALLELLADlGGQVFITTTDPEDFPALL 348
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-365 9.78e-116

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: 340.87  E-value: 9.78e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533    1 MYLSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDREMIAFGQDFASLAGRVHK--RQ 78
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKgdRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   79 LDLDLRIVISKKGKSAWVNRVEQARLSKYVGHLNAILFSPEDMELVKGAPSLRRRFMDLEFGQINPEYLYFASQYRQLLQ 158
Cdd:TIGR00611  81 VTIPLEGLLKKKGKKAKVNIDGQDKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  159 QRNNYLKQLARRQaSDQVLLGVLTEQVATAASELIWRRYRYLADLNRYAAEAYRAISGQREELRVLYRPSAKEITaadqp 238
Cdd:TIGR00611 161 QRNAALKQAQRQY-GDRTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGELWDKE----- 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  239 AQIKQKLLDRFaeiaDDELRRATTQLGPHRDDLEFQLDGKNAHLFASQGQQRTIALSLKLAEIQLIKQLTGEEPILLLDD 318
Cdd:TIGR00611 235 TDYAEALARNF----ERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDD 310

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 489719533  319 VMSELDQNRQAALLNFI-HGQTQTFITTTDLDSISQ-EIVKQPRIFYIH 365
Cdd:TIGR00611 311 VASELDDQRRRLLAELLqSLGVQVFVTAISLDHLKEmWDPNRVTIALVS 359
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-369 3.01e-95

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: 285.35  E-value: 3.01e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   3 LSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDREMIAFGQDFASLAGRVHKRQLDLD 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  83 LRIVI-SKKGKSAWVNRVEQARLSKYVGHLNAILFSPEDMELVKGAPSLRRRFMDLEFGQINPEYLYFASQYRQLLQQRN 161
Cdd:cd03242   81 LELTIrSGGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 162 NYLKqlarrqasdqvllgvlteqvataaseliwrryryladlnryaaeayraisgqreelrvlyrpsakeitaadqpaqi 241
Cdd:cd03242  161 ALLK---------------------------------------------------------------------------- 164

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 242 kqklldrfaeiaddelrrattqlGPHRDDLEFQLDGKNAHLFASQGQQRTIALSLKLAEIQLIKQLTGEEPILLLDDVMS 321
Cdd:cd03242  165 -----------------------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLA 221

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 489719533 322 ELDQNRQAALLNFIHGQTQTFITTTDLDSISQEIVKQPRIFYIHSGQI 369
Cdd:cd03242  222 ELDLGRQAALLDAIEGRVQTFVTTTDLADFDALWLRRAQIFRVDAGTL 269
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-345 4.04e-07

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: 51.24  E-value: 4.04e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   25 VNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDREmIAFGQDFASLAGRVHKRQLDLDLRIVISKKGKSawvNRVEQARL 104
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVIGLTDE-RSRNGGIGGIPSLLNGIDPKEPIEFEISEFLED---GVRYRYGL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  105 SKYVGHLNAILFSPEDmelVKGAPSLRRRFMDLEFGQINPEYlyfasqYRQLLQQRNNYLKQLARRQASDQVLLGVLTEQ 184
Cdd:pfam13304  77 DLEREDVEEKLSSKPT---LLEKRLLLREDSEEREPKFPPEA------EELRLGLDVEERIELSLSELSDLISGLLLLSI 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  185 VATAASELIWRRYRYLADLNRYAAEAYRAISGQREELRVLYRPSAKEITAADQpaqiKQKLLDRFAEIADDELRRATTQL 264
Cdd:pfam13304 148 ISPLSFLLLLDEGLLLEDWAVLDLAADLALFPDLKELLQRLVRGLKLADLNLS----DLGEGIEKSLLVDDRLRERGLIL 223

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  265 GPHRDDLEFQLDGknahlfASQGQQRTIALSLklaeiqLIKQLTGEEPILLLDDVMSELDQNRQAALLNFI----HGQTQ 340
Cdd:pfam13304 224 LENGGGGELPAFE------LSDGTKRLLALLA------ALLSALPKGGLLLIDEPESGLHPKLLRRLLELLkelsRNGAQ 291


                  ....*
gi 489719533  341 TFITT 345
Cdd:pfam13304 292 LILTT 296
 
Name Accession Description Interval E-value
recF PRK00064
recombination protein F; Reviewed
 1-369 4.64e-149

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 425.34  E-value: 4.64e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   1 MYLSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDREMIAFGQDFASLAGRVHKRQLD 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  81 LDLRIVISKKGKS-AWVNRVEQARLSKYVGHLNAILFSPEDMELVKGAPSLRRRFMDLEFGQINPEYLYFASQYRQLLQQ 159
Cdd:PRK00064  81 LPLGLEIDKKGGRkVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 160 RNNYLKQlarrqaSDQVLLGVLTEQVATAASELIWRRYRYLADLNRYAAEAYRAISGQREELRVLYRPSAKeitaaDQPA 239
Cdd:PRK00064 161 RNALLKQ------ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSVE-----DDAE 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 240 QIKQKLLDRFAEIADDELRRATTQLGPHRDDLEFQLDGKNAHLFASQGQQRTIALSLKLAEIQLIKQLTGEEPILLLDDV 319
Cdd:PRK00064 230 KIEEDLLEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDV 309

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489719533 320 MSELDQNRQAALLNFIHG-QTQTFITTTDLDSISQEIvKQPRIFYIHSGQI 369
Cdd:PRK00064 310 ASELDDGRRAALLERLKGlGAQVFITTTDLEDLADLL-ENAKIFHVEQGKI 359
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-355 1.15e-142

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 408.77  E-value: 1.15e-142
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   2 YLSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDREMIAFGQDFASLAGRVHKRQLDL 81
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  82 DLRIVISKKG-KSAWVNRVEQARLSKYVGHLNAILFSPEDMELVKGAPSLRRRFMDLEFGQINPEYLYFASQYRQLLQQR 160
Cdd:COG1195   81 RLGLGLSRGGkKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 161 NNYLKQlarRQASDQVLLGVLTEQVATAASELIWRRYRYLADLNRYAAEAYRAISGQREELRVLYRPSAkeitaADQPAQ 240
Cdd:COG1195  161 NALLKQ---GREADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALSGGKEELELRYRSGW-----LYESAE 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 241 IKQKLLDRFAEIADDELRRATTQLGPHRDDLEFQLDGKNAHLFASQGQQRTIALSLKLAEIQLIKQLTGEEPILLLDDVM 320
Cdd:COG1195  233 LEEALLEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVF 312

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 489719533 321 SELDQNRQAALLNFIHG-QTQTFITTTDLDSISQEI 355
Cdd:COG1195  313 AELDEERREALLELLADlGGQVFITTTDPEDFPALL 348
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-365 9.78e-116

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: 340.87  E-value: 9.78e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533    1 MYLSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDREMIAFGQDFASLAGRVHK--RQ 78
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKgdRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   79 LDLDLRIVISKKGKSAWVNRVEQARLSKYVGHLNAILFSPEDMELVKGAPSLRRRFMDLEFGQINPEYLYFASQYRQLLQ 158
Cdd:TIGR00611  81 VTIPLEGLLKKKGKKAKVNIDGQDKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  159 QRNNYLKQLARRQaSDQVLLGVLTEQVATAASELIWRRYRYLADLNRYAAEAYRAISGQREELRVLYRPSAKEITaadqp 238
Cdd:TIGR00611 161 QRNAALKQAQRQY-GDRTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGELWDKE----- 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  239 AQIKQKLLDRFaeiaDDELRRATTQLGPHRDDLEFQLDGKNAHLFASQGQQRTIALSLKLAEIQLIKQLTGEEPILLLDD 318
Cdd:TIGR00611 235 TDYAEALARNF----ERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDD 310

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 489719533  319 VMSELDQNRQAALLNFI-HGQTQTFITTTDLDSISQ-EIVKQPRIFYIH 365
Cdd:TIGR00611 311 VASELDDQRRRLLAELLqSLGVQVFVTAISLDHLKEmWDPNRVTIALVS 359
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-369 3.01e-95

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: 285.35  E-value: 3.01e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   3 LSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDREMIAFGQDFASLAGRVHKRQLDLD 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  83 LRIVI-SKKGKSAWVNRVEQARLSKYVGHLNAILFSPEDMELVKGAPSLRRRFMDLEFGQINPEYLYFASQYRQLLQQRN 161
Cdd:cd03242   81 LELTIrSGGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 162 NYLKqlarrqasdqvllgvlteqvataaseliwrryryladlnryaaeayraisgqreelrvlyrpsakeitaadqpaqi 241
Cdd:cd03242  161 ALLK---------------------------------------------------------------------------- 164

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 242 kqklldrfaeiaddelrrattqlGPHRDDLEFQLDGKNAHLFASQGQQRTIALSLKLAEIQLIKQLTGEEPILLLDDVMS 321
Cdd:cd03242  165 -----------------------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLA 221

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 489719533 322 ELDQNRQAALLNFIHGQTQTFITTTDLDSISQEIVKQPRIFYIHSGQI 369
Cdd:cd03242  222 ELDLGRQAALLDAIEGRVQTFVTTTDLADFDALWLRRAQIFRVDAGTL 269
recF PRK14079
recombination protein F; Provisional
 1-348 1.04e-63

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 207.33  E-value: 1.04e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   1 MYLSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYfLAISRSHRTSNDREMIAFGQDFASLAGRVHKRQLD 80
Cdd:PRK14079   1 MRLLSLRQLNYRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAIY-LALTGELPNGRLADLVRFGEGEAWVHAEVETGGGL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  81 LDLRIVISKKGKSAWVNRVeQARLSKYVGHLNAILFSPEDMELVKGAPSLRRRFMDLEFGQINPEYLYFASQYRQLLQQR 160
Cdd:PRK14079  80 SRLEVGLGPGRRELKLDGV-RVSLRELARLPGAVLIRPEDLELVLGPPEGRRAYLDRLLSRLSARYAALLSAYERAVQQR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 161 NNYLKQLARRQasdqvlLGVLTEQVATAASELIWRRYRYLADLNRYAAEAYRAIsGQREELRVlyrpsakEITAADQPAQ 240
Cdd:PRK14079 159 NAALKSGGGWG------LHVWDDELVKLGDEIMALRRRALTRLSELAREAYAEL-GSRKPLRL-------ELSESTAPEG 224

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533 241 IKQKLLDRFAEiaddELRRATTQLGPHRDDLEFQLDGKNAHLFASQGQQRTIALSLKLAEIQLIKQLTGEEPILLLDDVM 320
Cdd:PRK14079 225 YLAALEARRAE----ELARGATVVGPHRDDLVLTLEGRPAHRYASRGEARTVALALRLAEHRLLWEHFGEAPVLLVDDFT 300

                        330       340
                 ....*....|....*....|....*...
gi 489719533 321 SELDQNRQAALLNFIHGQTQTFITTTDL 348
Cdd:PRK14079 301 AELDPRRRGALLALAASLPQAIVAGTEA 328
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-46 9.54e-10

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: 59.63  E-value: 9.54e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 489719533   1 MYLSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYFL 46
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRLL 46
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-345 4.04e-07

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: 51.24  E-value: 4.04e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   25 VNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDREmIAFGQDFASLAGRVHKRQLDLDLRIVISKKGKSawvNRVEQARL 104
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVIGLTDE-RSRNGGIGGIPSLLNGIDPKEPIEFEISEFLED---GVRYRYGL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  105 SKYVGHLNAILFSPEDmelVKGAPSLRRRFMDLEFGQINPEYlyfasqYRQLLQQRNNYLKQLARRQASDQVLLGVLTEQ 184
Cdd:pfam13304  77 DLEREDVEEKLSSKPT---LLEKRLLLREDSEEREPKFPPEA------EELRLGLDVEERIELSLSELSDLISGLLLLSI 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  185 VATAASELIWRRYRYLADLNRYAAEAYRAISGQREELRVLYRPSAKEITAADQpaqiKQKLLDRFAEIADDELRRATTQL 264
Cdd:pfam13304 148 ISPLSFLLLLDEGLLLEDWAVLDLAADLALFPDLKELLQRLVRGLKLADLNLS----DLGEGIEKSLLVDDRLRERGLIL 223

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  265 GPHRDDLEFQLDGknahlfASQGQQRTIALSLklaeiqLIKQLTGEEPILLLDDVMSELDQNRQAALLNFI----HGQTQ 340
Cdd:pfam13304 224 LENGGGGELPAFE------LSDGTKRLLALLA------ALLSALPKGGLLLIDEPESGLHPKLLRRLLELLkelsRNGAQ 291


                  ....*
gi 489719533  341 TFITT 345
Cdd:pfam13304 292 LILTT 296
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-44 7.23e-07

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 50.00  E-value: 7.23e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 489719533   1 MYLSRFKQSGFRNLAPLNLEFD--PHVNVFLGENAQGKTNLLEAIY 44
Cdd:COG3950    1 MRIKSLTIENFRGFEDLEIDFDnpPRLTVLVGENGSGKTTLLEAIA 46
COG4637 COG4637
Predicted ATPase [General function prediction only];
3-47 1.21e-06

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 49.93  E-value: 1.21e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489719533   3 LSRFKQSGFRNLAPLNLEFDPhVNVFLGENAQGKTNLLEAIYFLA 47
Cdd:COG4637    2 ITRIRIKNFKSLRDLELPLGP-LTVLIGANGSGKSNLLDALRFLS 45
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-345 7.85e-05

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: 44.51  E-value: 7.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533    1 MYLSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIY-FLAISRSHRTSNDREMIAFGQDFASLAGRVHKRQL 79
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDiFLNNKEKFFEDDFLVLYLKDVIKIDKEDLNIFENI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   80 DLDLRIVISKKgksAWVNRVEQARLSKYVGHLNAILFSPEDMELVKGAPSLRRRFMDLEFGQ-----INPEYLYFASQYr 154
Cdd:pfam13175  81 SFSIDIEIDVE---FLLILFGYLEIKKKYLCLASKGKAKEYEKTLHPKGANKADLLLELKISdlkkyLKQFKIYIYNNY- 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  155 qLLQQRNNYLKQLARRQASDQVLLGVLTEQVATAA----SELIWRRYR----YLADLNRYAAEAYRAISGQR-------- 218
Cdd:pfam13175 157 -YLDEKKNVFDKKSKYELPSLKEEFLNSEKEEIKVdkedLKKLINELEksinYHENVLENLQIKKLLISADRnasdedse 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  219 -------EELRVLYRPSAKEITAADQPAQIKQKLLDRFAEIADDELRR--------ATTQLGPHRDDLEFQLDGKNAHL- 282
Cdd:pfam13175 236 kinsllgALKQRIFEEALQEELELTEKLKETQNKLKEIDKTLAEELKNilfkkidkLKDFGYPPFLNPEIEIKKDDEDLp 315

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489719533  283 --FASQGQQRTIALSLKLAEIQLIKQLTGEEPILLLDD------------VMSELDQNrqaaLLNfiHGQTQTFITT 345
Cdd:pfam13175 316 lnKNGSGVQRLILLIFFIAEAERKEDEIEEKNVILAIEepeahlhpqaqrVLIKLLKE----LAN--DNKTQVIITT 386
DUF2813 pfam11398
Protein of unknown function (DUF2813); This entry contains YjbD from Escherichia coli, which ...
 1-43 9.63e-05

Protein of unknown function (DUF2813); This entry contains YjbD from Escherichia coli, which is annotated as a nucleotide triphosphate hydrolase.


Pssm-ID: 431868 [Multi-domain]  Cd Length: 372  Bit Score: 43.88  E-value: 9.63e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 489719533    1 MYLSRFKQSGFRNLAPLNLEFDPHvNVFLGENAQGKTNLLEAI 43
Cdd:pfam11398   1 MHLERIEVVGFRGINRLSLHFDQL-TVLIGENAWGKSSLLDAL 42
AAA_23 pfam13476
AAA domain;
10-43 1.30e-04

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 42.48  E-value: 1.30e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 489719533   10 GFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAI 43
Cdd:pfam13476   5 NFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAI 38
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
23-52 5.94e-04

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 41.57  E-value: 5.94e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 489719533  23 PHVNVFLGENAQGKTNLLEAIYFL--AISRSH 52
Cdd:COG1106   29 LRVNLIYGANASGKSNLLEALYFLrnLVLNSS 60
ABC_RecN cd03241
ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC ...
 12-143 1.75e-03

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: 39.88  E-value: 1.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  12 RNLAP---LNLEFDPHVNVFLGENAQGKTNLLEAIYFLAISRSH----RTSNDREMIA--FGQD-----FASLAGRVHKR 77
Cdd:cd03241    7 KNFALieeLELDFEEGLTVLTGETGAGKSILLDALSLLLGGRASadliRSGAEKAVVEgvFDISdeeeaKALLLELGIED 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489719533  78 QLDLDLRIVISKKGKS-AWVN--RVEQARLSKYVGHLNAILFSPEDMELVKgaPSLRRRFMDLEFGQIN 143
Cdd:cd03241   87 DDDLIIRREISRKGRSrYFINgqSVTLKLLRELGSLLVDIHGQHDHQNLLN--PERQLDLLDGGLDDVE 153
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 20-105 5.17e-03

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: 37.97  E-value: 5.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533  20 EFDPHVNVFLGENAQGKTNLLEAIyFLAISRSHRTSN-----DREMIAFGQ-------DFASLAGRVHK--RQLDLDLRI 85
Cdd:cd03240   19 EFFSPLTLIVGQNGAGKTTIIEAL-KYALTGELPPNSkggahDPKLIREGEvraqvklAFENANGKKYTitRSLAILENV 97

                         90       100
                 ....*....|....*....|
gi 489719533  86 VISKKGKSAWVNRVEQARLS 105
Cdd:cd03240   98 IFCHQGESNWPLLDMRGRCS 117
COG4938 COG4938
Predicted ATPase [General function prediction only];
3-52 5.28e-03

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 38.41  E-value: 5.28e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 489719533   3 LSRFKQSGFRNLAPLNLEFDPhVNVFLGENAQGKTNLLEAIYFLAISRSH 52
Cdd:COG4938    1 IKSISIKNFGPFKEAELELKP-LTLLIGPNGSGKSTLIQALLLLLQSNFI 49
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
19-59 6.61e-03

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 37.68  E-value: 6.61e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 489719533  19 LEFDPHVNVFLGENAQGKTNLLEAIYFLAISRSHRTSNDRE 59
Cdd:COG0419   19 IDFDDGLNLIVGPNGAGKSTILEAIRYALYGKARSRSKLRS 59
PRK01156 PRK01156
chromosome segregation protein; Provisional
 1-93 9.54e-03

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 37.96  E-value: 9.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489719533   1 MYLSRFKQSGFRNLAPLNLEFDPHVNVFLGENAQGKTNLLEAIYFlAISRSHRTSNDREMIAFGQDFASLAGRVHKRQLD 80
Cdd:PRK01156   1 MIIKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAIRF-ALFTDKRTEKIEDMIKKGKNNLEVELEFRIGGHV 79

                         90
                 ....*....|...
gi 489719533  81 LDLRIVISKKGKS 93
Cdd:PRK01156  80 YQIRRSIERRGKG 92
COG3910 COG3910
Predicted ATPase [General function prediction only];
11-43 9.76e-03

Predicted ATPase [General function prediction only];


Pssm-ID: 443116 [Multi-domain]  Cd Length: 239  Bit Score: 37.44  E-value: 9.76e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 489719533  11 FRNLAPLnlEFDPHVNVFLGENAQGKTNLLEAI 43
Cdd:COG3910   27 VRNLEGL--EFHPPVTFFVGENGSGKSTLLEAI 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.
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