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Conserved domains on  [gi|568906282|ref|XP_006496004|]
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PMS1 protein homolog 1 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
 1-318 4.72e-113

DNA mismatch repair protein MutL; All proteins in this family for which the functions are known are involved in the process of generalized mismatch 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: 273155 [Multi-domain]  Cd Length: 312  Bit Score: 349.25  E-value: 4.72e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282    1 MKQLPAATVRLLSSSQTITSVVSVVKELIENSLDAGATSIEVKLENYGFDKIEIRDNGEGIKAVDVPVMAVKYYTSKISS 80
Cdd:TIGR00585   3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282   81 HEDLGNLTTYGFRGEALGSICNVAEVVVTTRTSADD-FSTQYVLDGsGHILSQKPSHLGQGTTVTALKLFKNLPVRKQFy 159
Cdd:TIGR00585  83 FEDLERIETLGFRGEALASISSVSRLTITTKTSAADgLAYQALLEG-GMIESIKPAPRPVGTTVEVRDLFYNLPVRRKF- 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  160 stAKKCKDELKNVQDLLISYGVLKPDVRITFVHN-KAVIWQKS-RVPDHRMA-LMSVLGTAVMGNMESVeQHCEQSQIYL 236
Cdd:TIGR00585 161 --LKSPKKEFRKILDVLQRYALIHPDISFSLTHDgKKVLQLSTkPNQSTKENrIRSVFGTAVLRKLIPL-DEWEDLDLQL 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  237 SGFFPKHDADHNSTSLStperSFIFINSRPVHQKDILKLIRRYYNLKCLKEStrlYPIFFLKIDVPSAEVDINLTPDKSQ 316
Cdd:TIGR00585 238 EGFISQPNVTRSRRSGW----QFLFINGRPVELKLLLKAIREVYHEYLPKGQ---YPVFVLNLEIDPELVDVNVHPDKKE 310


                  ..
gi 568906282  317 VL 318
Cdd:TIGR00585 311 VR 312
HMG-box_SF super family cl00082
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 558-629 5.11e-24

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


The actual alignment was detected with superfamily member cd21985:

Pssm-ID: 469606 [Multi-domain]  Cd Length: 73  Bit Score: 96.07  E-value: 5.11e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568906282 558 VKKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYNNQMKKAIEQE 629
Cdd:cd21985    2 IRKPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAAKDLERYNSQKKRAAEQP 73
NHP6B super family cl26372
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
559-708 1.10e-05

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


The actual alignment was detected with superfamily member COG5648:

Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 47.55  E-value: 1.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 559 KKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYnnQMKKAIEQETqvsLKDGR 638
Cdd:COG5648   72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERY--QREKEEYNKK---LPNKA 146

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 639 KKRATSSWGWTQKHKVKDSSNQPKLDELFQSQNEKKKSENIKITeipfsMENLKANLKKQKEVDLEEKDE 708
Cdd:COG5648  147 PIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKK-----KKYIDKYKKLKEEYDSFYPEA 211
 
Name Accession Description Interval E-value
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
 1-318 4.72e-113

DNA mismatch repair protein MutL; All proteins in this family for which the functions are known are involved in the process of generalized mismatch 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: 273155 [Multi-domain]  Cd Length: 312  Bit Score: 349.25  E-value: 4.72e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282    1 MKQLPAATVRLLSSSQTITSVVSVVKELIENSLDAGATSIEVKLENYGFDKIEIRDNGEGIKAVDVPVMAVKYYTSKISS 80
Cdd:TIGR00585   3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282   81 HEDLGNLTTYGFRGEALGSICNVAEVVVTTRTSADD-FSTQYVLDGsGHILSQKPSHLGQGTTVTALKLFKNLPVRKQFy 159
Cdd:TIGR00585  83 FEDLERIETLGFRGEALASISSVSRLTITTKTSAADgLAYQALLEG-GMIESIKPAPRPVGTTVEVRDLFYNLPVRRKF- 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  160 stAKKCKDELKNVQDLLISYGVLKPDVRITFVHN-KAVIWQKS-RVPDHRMA-LMSVLGTAVMGNMESVeQHCEQSQIYL 236
Cdd:TIGR00585 161 --LKSPKKEFRKILDVLQRYALIHPDISFSLTHDgKKVLQLSTkPNQSTKENrIRSVFGTAVLRKLIPL-DEWEDLDLQL 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  237 SGFFPKHDADHNSTSLStperSFIFINSRPVHQKDILKLIRRYYNLKCLKEStrlYPIFFLKIDVPSAEVDINLTPDKSQ 316
Cdd:TIGR00585 238 EGFISQPNVTRSRRSGW----QFLFINGRPVELKLLLKAIREVYHEYLPKGQ---YPVFVLNLEIDPELVDVNVHPDKKE 310


                  ..
gi 568906282  317 VL 318
Cdd:TIGR00585 311 VR 312
HATPase_MutL-MLH-PMS-like cd16926
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ...
 8-193 1.35e-76

Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, human MutL homologs (MLH/ PMS), and related domains; This family includes the histidine kinase-like ATPase (HATPase) domains of Escherichia coli MutL, human MLH1 (mutL homolog 1), human PMS1 (PMS1 homolog 1, mismatch repair system component), human MLH3 (mutL homolog 3), and human PMS2 (PMS1 homolog 2, mismatch repair system component). MutL homologs (MLH/PMS) participate in MMR (DNA mismatch repair), and in addition have role(s) in DNA damage signaling and suppression of homologous recombination (recombination between partially homologous parental DNAs). The primary role of MutL in MMR is to mediate protein-protein interactions during mismatch recognition and strand removal; a ternary complex is formed between MutS, MutL, and the mismatched DNA, which activates the MutH endonuclease.


Pssm-ID: 340403 [Multi-domain]  Cd Length: 188  Bit Score: 247.74  E-value: 1.35e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282   8 TVRLLSSSQTITSVVSVVKELIENSLDAGATSIEVKLENYGFDKIEIRDNGEGIKAVDVPVMAVKYYTSKISSHEDLGNL 87
Cdd:cd16926    1 VVNKIAAGEVIERPASVVKELVENSIDAGATRIDVEIEEGGLKLIRVTDNGSGISREDLELAFERHATSKISSFEDLFSI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  88 TTYGFRGEALGSICNVAEVVVTTRTSADDFSTQYVLDGSGHILSQKPSHLGQGTTVTALKLFKNLPVRKQFYSTAKKckd 167
Cdd:cd16926   81 TTLGFRGEALASIASVSRLTITTRTADDDVGTRLVVDGGGIIEEVKPAAAPVGTTVTVRDLFYNTPARRKFLKSPKT--- 157

                        170       180
                 ....*....|....*....|....*.
gi 568906282 168 ELKNVQDLLISYGVLKPDVRITFVHN 193
Cdd:cd16926  158 ELSKILDLVQRLALAHPDVSFSLTHD 183
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
21-317 8.56e-68

DNA mismatch repair ATPase MutL [Replication, recombination and repair];


Pssm-ID: 440092 [Multi-domain]  Cd Length: 515  Bit Score: 235.32  E-value: 8.56e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  21 VV----SVVKELIENSLDAGATSIEVKLENYGFDKIEIRDNGEGIKAVDVPvMAVKYY-TSKISSHEDLGNLTTYGFRGE 95
Cdd:COG0323   20 VVerpaSVVKELVENAIDAGATRIEVEIEEGGKSLIRVTDNGCGMSPEDLP-LAFERHaTSKIRSAEDLFRIRTLGFRGE 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  96 ALGSICNVAEVVVTTRTSADDFSTQYVLDGsGHILSQKPSHLGQGTTVTALKLFKNLPVRKQFYSTAKKckdELKNVQDL 175
Cdd:COG0323   99 ALASIASVSRLTLTTRTAGAELGTRIEVEG-GKVVEVEPAAAPKGTTVEVRDLFFNTPARRKFLKSDAT---ELAHITDV 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 176 LISYGVLKPDVRITFVHNKAVIWQKSRVPDHRMALMSVLGTAVMGNMESVEQhcEQSQIYLSGFfpkhdadhnstsLSTP 255
Cdd:COG0323  175 VRRLALAHPDIAFTLIHNGREVFQLPGAGDLLQRIAAIYGREFAENLLPVEA--EREGLRLSGY------------IGKP 240

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568906282 256 E--RS-----FIFINSRPVHQKDILKLIRRYYnlkclkeSTRL----YPIFFLKIDVPSAEVDINLTPDKSQV 317
Cdd:COG0323  241 EfsRSnrdyqYFFVNGRPVRDKLLSHAVREAY-------RDLLpkgrYPVAVLFLELDPELVDVNVHPTKTEV 306
mutL PRK00095
DNA mismatch repair endonuclease MutL;
23-325 5.41e-61

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 218.93  E-value: 5.41e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  23 SVVKELIENSLDAGATSIEVKLENYGFDKIEIRDNGEGIKAVDVPVMAVKYYTSKISSHEDLGNLTTYGFRGEALGSICN 102
Cdd:PRK00095  25 SVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNGCGISKEDLALALARHATSKIASLDDLEAIRTLGFRGEALPSIAS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 103 VAEVVVTTRTSADDFSTQYVLDGsGHILSQKPSHLGQGTTVTALKLFKNLPVRKQFYSTAKKckdELKNVQDLL----IS 178
Cdd:PRK00095 105 VSRLTLTSRTADAAEGWQIVYEG-GEIVEVKPAAHPVGTTIEVRDLFFNTPARRKFLKSEKT---ELGHIDDVVnrlaLA 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 179 YgvlkPDVRITFVHNKAVIWQKSRVPDHRMALMSVLGTAVMGNMESVEqhCEQSQIYLSGFfpkhdadhnstsLSTPE-- 256
Cdd:PRK00095 181 H----PDVAFTLTHNGKLVLQTRGAGQLLQRLAAILGREFAENALPID--AEHGDLRLSGY------------VGLPTls 242

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568906282 257 RS-----FIFINSRPVHQKDILKLIRRYYnlkclkeSTRL----YPIFFLKIDVPSAEVDINLTPDKSQVLLQNKESV 325
Cdd:PRK00095 243 RAnrdyqYLFVNGRYVRDKLLNHAIRQAY-------HDLLprgrYPAFVLFLELDPHQVDVNVHPAKHEVRFRDERLV 313
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 558-629 5.11e-24

high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; PMS1, also called DNA mismatch repair protein PMS1, is probably involved in the repair of mismatches in DNA.


Pssm-ID: 438801 [Multi-domain]  Cd Length: 73  Bit Score: 96.07  E-value: 5.11e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568906282 558 VKKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYNNQMKKAIEQE 629
Cdd:cd21985    2 IRKPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAAKDLERYNSQKKRAAEQP 73
DNA_mis_repair pfam01119
DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain ...
 211-331 4.53e-23

DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain of the mutL/hexB/PMS1 family. This domain has a ribosomal S5 domain 2-like fold.


Pssm-ID: 426060 [Multi-domain]  Cd Length: 117  Bit Score: 94.87  E-value: 4.53e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  211 MSVLGTAVMGNMESVEqhCEQSQIYLSGFFPKHDadhnsTSLSTPERSFIFINSRPVHQKDILKLIRRYYNLKclkESTR 290
Cdd:pfam01119   1 AAIYGKEFAENLLPIE--KEDDGLRLSGYISKPT-----LSRSNRDYQYLFVNGRPVRDKLLSHAIREAYRDL---LPKG 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 568906282  291 LYPIFFLKIDVPSAEVDINLTPDKSQVLLQNKESVLIALEN 331
Cdd:pfam01119  71 RYPVAVLFLEIDPELVDVNVHPTKREVRFRDEREVYDFIKE 111
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
559-708 1.10e-05

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 47.55  E-value: 1.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 559 KKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYnnQMKKAIEQETqvsLKDGR 638
Cdd:COG5648   72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERY--QREKEEYNKK---LPNKA 146

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 639 KKRATSSWGWTQKHKVKDSSNQPKLDELFQSQNEKKKSENIKITeipfsMENLKANLKKQKEVDLEEKDE 708
Cdd:COG5648  147 PIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKK-----KKYIDKYKKLKEEYDSFYPEA 211
HMG smart00398
high mobility group;
557-624 1.54e-05

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 43.46  E-value: 1.54e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568906282   557 AVKKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYNNQMKK 624
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPE 68
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 24-144 2.18e-04

Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 41.48  E-value: 2.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282    24 VVKELIENSLDAGATS--IEVKLENYGFD-KIEIRDNGEGIKAVDVPVMAVKYYTSKISSHEdlgnlttygFRGEALG-S 99
Cdd:smart00387   9 VLSNLLDNAIKYTPEGgrITVTLERDGDHvEITVEDNGPGIPPEDLEKIFEPFFRTDKRSRK---------IGGTGLGlS 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 568906282   100 ICNvaevvvttrtsaddfstQYVLDGSGHIlsQKPSHLGQGTTVT 144
Cdd:smart00387  80 IVK-----------------KLVELHGGEI--SVESEPGGGTTFT 105
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 559-623 8.81e-03

HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail.


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 35.84  E-value: 8.81e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568906282  559 KKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYNNQMK 623
Cdd:pfam09011   5 KRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMG 69
 
Name Accession Description Interval E-value
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
 1-318 4.72e-113

DNA mismatch repair protein MutL; All proteins in this family for which the functions are known are involved in the process of generalized mismatch 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: 273155 [Multi-domain]  Cd Length: 312  Bit Score: 349.25  E-value: 4.72e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282    1 MKQLPAATVRLLSSSQTITSVVSVVKELIENSLDAGATSIEVKLENYGFDKIEIRDNGEGIKAVDVPVMAVKYYTSKISS 80
Cdd:TIGR00585   3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282   81 HEDLGNLTTYGFRGEALGSICNVAEVVVTTRTSADD-FSTQYVLDGsGHILSQKPSHLGQGTTVTALKLFKNLPVRKQFy 159
Cdd:TIGR00585  83 FEDLERIETLGFRGEALASISSVSRLTITTKTSAADgLAYQALLEG-GMIESIKPAPRPVGTTVEVRDLFYNLPVRRKF- 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  160 stAKKCKDELKNVQDLLISYGVLKPDVRITFVHN-KAVIWQKS-RVPDHRMA-LMSVLGTAVMGNMESVeQHCEQSQIYL 236
Cdd:TIGR00585 161 --LKSPKKEFRKILDVLQRYALIHPDISFSLTHDgKKVLQLSTkPNQSTKENrIRSVFGTAVLRKLIPL-DEWEDLDLQL 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  237 SGFFPKHDADHNSTSLStperSFIFINSRPVHQKDILKLIRRYYNLKCLKEStrlYPIFFLKIDVPSAEVDINLTPDKSQ 316
Cdd:TIGR00585 238 EGFISQPNVTRSRRSGW----QFLFINGRPVELKLLLKAIREVYHEYLPKGQ---YPVFVLNLEIDPELVDVNVHPDKKE 310


                  ..
gi 568906282  317 VL 318
Cdd:TIGR00585 311 VR 312
HATPase_MutL-MLH-PMS-like cd16926
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ...
 8-193 1.35e-76

Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, human MutL homologs (MLH/ PMS), and related domains; This family includes the histidine kinase-like ATPase (HATPase) domains of Escherichia coli MutL, human MLH1 (mutL homolog 1), human PMS1 (PMS1 homolog 1, mismatch repair system component), human MLH3 (mutL homolog 3), and human PMS2 (PMS1 homolog 2, mismatch repair system component). MutL homologs (MLH/PMS) participate in MMR (DNA mismatch repair), and in addition have role(s) in DNA damage signaling and suppression of homologous recombination (recombination between partially homologous parental DNAs). The primary role of MutL in MMR is to mediate protein-protein interactions during mismatch recognition and strand removal; a ternary complex is formed between MutS, MutL, and the mismatched DNA, which activates the MutH endonuclease.


Pssm-ID: 340403 [Multi-domain]  Cd Length: 188  Bit Score: 247.74  E-value: 1.35e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282   8 TVRLLSSSQTITSVVSVVKELIENSLDAGATSIEVKLENYGFDKIEIRDNGEGIKAVDVPVMAVKYYTSKISSHEDLGNL 87
Cdd:cd16926    1 VVNKIAAGEVIERPASVVKELVENSIDAGATRIDVEIEEGGLKLIRVTDNGSGISREDLELAFERHATSKISSFEDLFSI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  88 TTYGFRGEALGSICNVAEVVVTTRTSADDFSTQYVLDGSGHILSQKPSHLGQGTTVTALKLFKNLPVRKQFYSTAKKckd 167
Cdd:cd16926   81 TTLGFRGEALASIASVSRLTITTRTADDDVGTRLVVDGGGIIEEVKPAAAPVGTTVTVRDLFYNTPARRKFLKSPKT--- 157

                        170       180
                 ....*....|....*....|....*.
gi 568906282 168 ELKNVQDLLISYGVLKPDVRITFVHN 193
Cdd:cd16926  158 ELSKILDLVQRLALAHPDVSFSLTHD 183
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
21-317 8.56e-68

DNA mismatch repair ATPase MutL [Replication, recombination and repair];


Pssm-ID: 440092 [Multi-domain]  Cd Length: 515  Bit Score: 235.32  E-value: 8.56e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  21 VV----SVVKELIENSLDAGATSIEVKLENYGFDKIEIRDNGEGIKAVDVPvMAVKYY-TSKISSHEDLGNLTTYGFRGE 95
Cdd:COG0323   20 VVerpaSVVKELVENAIDAGATRIEVEIEEGGKSLIRVTDNGCGMSPEDLP-LAFERHaTSKIRSAEDLFRIRTLGFRGE 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  96 ALGSICNVAEVVVTTRTSADDFSTQYVLDGsGHILSQKPSHLGQGTTVTALKLFKNLPVRKQFYSTAKKckdELKNVQDL 175
Cdd:COG0323   99 ALASIASVSRLTLTTRTAGAELGTRIEVEG-GKVVEVEPAAAPKGTTVEVRDLFFNTPARRKFLKSDAT---ELAHITDV 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 176 LISYGVLKPDVRITFVHNKAVIWQKSRVPDHRMALMSVLGTAVMGNMESVEQhcEQSQIYLSGFfpkhdadhnstsLSTP 255
Cdd:COG0323  175 VRRLALAHPDIAFTLIHNGREVFQLPGAGDLLQRIAAIYGREFAENLLPVEA--EREGLRLSGY------------IGKP 240

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568906282 256 E--RS-----FIFINSRPVHQKDILKLIRRYYnlkclkeSTRL----YPIFFLKIDVPSAEVDINLTPDKSQV 317
Cdd:COG0323  241 EfsRSnrdyqYFFVNGRPVRDKLLSHAVREAY-------RDLLpkgrYPVAVLFLELDPELVDVNVHPTKTEV 306
mutL PRK00095
DNA mismatch repair endonuclease MutL;
23-325 5.41e-61

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 218.93  E-value: 5.41e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  23 SVVKELIENSLDAGATSIEVKLENYGFDKIEIRDNGEGIKAVDVPVMAVKYYTSKISSHEDLGNLTTYGFRGEALGSICN 102
Cdd:PRK00095  25 SVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNGCGISKEDLALALARHATSKIASLDDLEAIRTLGFRGEALPSIAS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 103 VAEVVVTTRTSADDFSTQYVLDGsGHILSQKPSHLGQGTTVTALKLFKNLPVRKQFYSTAKKckdELKNVQDLL----IS 178
Cdd:PRK00095 105 VSRLTLTSRTADAAEGWQIVYEG-GEIVEVKPAAHPVGTTIEVRDLFFNTPARRKFLKSEKT---ELGHIDDVVnrlaLA 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 179 YgvlkPDVRITFVHNKAVIWQKSRVPDHRMALMSVLGTAVMGNMESVEqhCEQSQIYLSGFfpkhdadhnstsLSTPE-- 256
Cdd:PRK00095 181 H----PDVAFTLTHNGKLVLQTRGAGQLLQRLAAILGREFAENALPID--AEHGDLRLSGY------------VGLPTls 242

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568906282 257 RS-----FIFINSRPVHQKDILKLIRRYYnlkclkeSTRL----YPIFFLKIDVPSAEVDINLTPDKSQVLLQNKESV 325
Cdd:PRK00095 243 RAnrdyqYLFVNGRYVRDKLLNHAIRQAY-------HDLLprgrYPAFVLFLELDPHQVDVNVHPAKHEVRFRDERLV 313
MutL_Trans_hPMS_1_like cd03485
MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 205-338 4.25e-48

MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM1 (hPSM1) and yeast MLH2. hPSM1 and yMLH2 are members of the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. PMS1 forms a heterodimer with MLH1. The MLH1-PMS1 complex functions in meiosis. Loss of yMLH2 results in a small but significant decrease in spore viability and a significant increase in gene conversion frequencies. A role for hMLH1-hPMS1 in DNA mismatch repair has not been established. Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families, however there is no convincing evidence to support hPMS1 having a role in HNPCC predisposition.


Pssm-ID: 239567 [Multi-domain]  Cd Length: 132  Bit Score: 167.06  E-value: 4.25e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 205 DHRMALMSVLGTAVMGNMESVEQHCEQSQIYLSGFFPKHDADHNSTslsTPERSFIFINSRPVHQ-KDILKLIRRYYNLK 283
Cdd:cd03485    1 DHKEALARVLGTAVAANMVPVQSTDEDPQISLEGFLPKPGSDVSKT---KSDGKFISVNSRPVSLgKDIGKLLRQYYSSA 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 568906282 284 CLKESTRLYPIFFLKIDVPSAEVDINLTPDKSQVLLQNKESVLIALENLMMTCYG 338
Cdd:cd03485   78 YRKSSLRRYPVFFLNILCPPGLVDVNIEPDKDDVLLQNKEAVLQAVENLLESLYG 132
MutL_Trans cd00782
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 206-333 1.91e-27

MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome. Mutation in hMLH1 accounts for a large fraction of HNPCC families. There is no convincing evidence to support hPMS1 having a role in HNPCC predisposition. It has been suggested that hMLH3 may be a low risk gene for colorectal cancer; however there is little evidence to support it having a role in classical HNPCC. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH.


Pssm-ID: 238405 [Multi-domain]  Cd Length: 122  Bit Score: 107.63  E-value: 1.91e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 206 HRMALMSVLGTAVMGNMESVEqhCEQSQIYLSGFFPKHDAdhnstSLSTPERSFIFINSRPVHQKDILKLIRRYYNLKCL 285
Cdd:cd00782    1 LKDRIAQVYGKEVAKNLIEVE--LESGDFRISGYISKPDF-----GRSSKDRQFLFVNGRPVRDKLLSKAINEAYRSYLP 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 568906282 286 KestRLYPIFFLKIDVPSAEVDINLTPDKSQVLLQNKESVLIALENLM 333
Cdd:cd00782   74 K---GRYPVFVLNLELPPELVDVNVHPTKREVRFSDEEEVLELIREAL 118
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 558-629 5.11e-24

high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; PMS1, also called DNA mismatch repair protein PMS1, is probably involved in the repair of mismatches in DNA.


Pssm-ID: 438801 [Multi-domain]  Cd Length: 73  Bit Score: 96.07  E-value: 5.11e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568906282 558 VKKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYNNQMKKAIEQE 629
Cdd:cd21985    2 IRKPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAAKDLERYNSQKKRAAEQP 73
DNA_mis_repair pfam01119
DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain ...
 211-331 4.53e-23

DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain of the mutL/hexB/PMS1 family. This domain has a ribosomal S5 domain 2-like fold.


Pssm-ID: 426060 [Multi-domain]  Cd Length: 117  Bit Score: 94.87  E-value: 4.53e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282  211 MSVLGTAVMGNMESVEqhCEQSQIYLSGFFPKHDadhnsTSLSTPERSFIFINSRPVHQKDILKLIRRYYNLKclkESTR 290
Cdd:pfam01119   1 AAIYGKEFAENLLPIE--KEDDGLRLSGYISKPT-----LSRSNRDYQYLFVNGRPVRDKLLSHAIREAYRDL---LPKG 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 568906282  291 LYPIFFLKIDVPSAEVDINLTPDKSQVLLQNKESVLIALEN 331
Cdd:pfam01119  71 RYPVAVLFLEIDPELVDVNVHPTKREVRFRDEREVYDFIKE 111
MutL_Trans_hPMS_2_like cd03484
MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 210-331 1.34e-18

MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM2 (hPSM2). hPSM2 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to yeast PMS1. The yeast MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a role in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Cells lacking hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome.


Pssm-ID: 239566 [Multi-domain]  Cd Length: 142  Bit Score: 83.09  E-value: 1.34e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 210 LMSVLGTAVMGNMESVEQH---------------CEQSQIYLSGFFPKhdADHNSTSlSTPERSFIFINSRPVHQKDILK 274
Cdd:cd03484    6 IINVFGGKVIKGLIPINLEldvnptkeeldsdedLADSEVKITGYISK--PSHGCGR-SSSDRQFFYINGRPVDLKKVAK 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 568906282 275 LIRRYYNlkclKESTRLYPIFFLKIDVPSAEVDINLTPDKSQVLLQNKESVLIALEN 331
Cdd:cd03484   83 LINEVYK----SFNSRQYPFFILNISLPTSLYDVNVTPDKRTVLLHDEDRLIDTLKT 135
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 206-318 2.38e-15

MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families.


Pssm-ID: 238202 [Multi-domain]  Cd Length: 107  Bit Score: 72.68  E-value: 2.38e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 206 HRMALMSVLGTAVMGNMESVEqhCEQSQIYLSGFFPKHDADHnstslSTPERSFIFINSRPVHQ-KDILKLIRRYYNLKC 284
Cdd:cd00329    1 LKDRLAEILGDKVADKLIYVE--GESDGFRVEGAISYPDSGR-----SSKDRQFSFVNGRPVREgGTHVKAVREAYTRAL 73

                         90       100       110
                 ....*....|....*....|....*....|....
gi 568906282 285 LKESTRLYPIFFLKIDVPSAEVDINLTPDKSQVL 318
Cdd:cd00329   74 NGDDVRRYPVAVLSLKIPPSLVDVNVHPTKEEVR 107
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
 24-102 2.08e-07

Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.


Pssm-ID: 460579 [Multi-domain]  Cd Length: 109  Bit Score: 50.06  E-value: 2.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282   24 VVKELIENSLD--AGATSIEVKLENYGFDKIEIRDNGEGIKAVDVPVMAVKYYTSKISSHEdlgnlttygfrGEALG-SI 100
Cdd:pfam02518   9 VLSNLLDNALKhaAKAGEITVTLSEGGELTLTVEDNGIGIPPEDLPRIFEPFSTADKRGGG-----------GTGLGlSI 77


                  ..
gi 568906282  101 CN 102
Cdd:pfam02518  78 VR 79
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
559-708 1.10e-05

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 47.55  E-value: 1.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 559 KKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYnnQMKKAIEQETqvsLKDGR 638
Cdd:COG5648   72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERY--QREKEEYNKK---LPNKA 146

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 639 KKRATSSWGWTQKHKVKDSSNQPKLDELFQSQNEKKKSENIKITeipfsMENLKANLKKQKEVDLEEKDE 708
Cdd:COG5648  147 PIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKK-----KKYIDKYKKLKEEYDSFYPEA 211
MutL_Trans_MLH3 cd03486
MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 259-333 1.46e-05

MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH3 (MutL homologue 3). MLH3 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with MLH3. The MLH1-MLH3 complex plays a role in meiosis. A role for hMLH1-hMLH3 in DNA mismatch repair (MMR) has not been established. It has been suggested that hMLH3 may be a low risk gene for colorectal cancer; however there is little evidence to support it having a role in classical HNPCC.


Pssm-ID: 239568 [Multi-domain]  Cd Length: 141  Bit Score: 45.77  E-value: 1.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 259 FIFINSRPVHQKDILKLIRRYY----------------NLKCLKESTRLYPIFFLKIDVPSAEVDINLTPDKSQVLLQNK 322
Cdd:cd03486   46 FIYVNGRLYLKTRFHKLINKLFrktsavaknksspqskSSRRGKRSQESYPVFVLNITCPASEYDLSQEPSKTIIEFKDW 125

                         90
                 ....*....|.
gi 568906282 323 ESVLIALENLM 333
Cdd:cd03486  126 KTLLPLILEVV 136
HMG smart00398
high mobility group;
557-624 1.54e-05

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 43.46  E-value: 1.54e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568906282   557 AVKKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYNNQMKK 624
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPE 68
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 559-627 7.64e-05

second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2), intrastrand cross-link recognition protein (Ixr1) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Both ABF2 and Ixr1 contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438828 [Multi-domain]  Cd Length: 64  Bit Score: 41.50  E-value: 7.64e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568906282 559 KKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSeeekhkyeekaKKDLERYNNQMKKAIE 627
Cdd:cd22012    3 KRPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLD-----------ESEKEPYQEEYEKALE 60
HATPase_c_3 pfam13589
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents, additionally, ...
 23-113 1.35e-04

Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents, additionally, the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.


Pssm-ID: 433332 [Multi-domain]  Cd Length: 135  Bit Score: 42.70  E-value: 1.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282   23 SVVKELIENSLDAGATSIEVKLENY--GFDKIEIRDNGEGIKAVDVpVMAVKYYTSKISSHEDLGNLTTYGFrGEALGSI 100
Cdd:pfam13589   3 GALAELIDNSIDADATNIKIEVNKNrgGGTEIVIEDDGHGMSPEEL-INALRLATSAKEAKRGSTDLGRYGI-GLKLASL 80

                          90
                  ....*....|...
gi 568906282  101 CNVAEVVVTTRTS 113
Cdd:pfam13589  81 SLGAKLTVTSKKE 93
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 557-624 1.78e-04

high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal proteins NHP6A, NHP6B and similar proteins; This subfamily includes Saccharomyces cerevisiae high-mobility-group proteins NHP6A and its closely related paralog NHP6B. NHP6A and NHP6B seem to be functionally redundant. They are DNA-binding proteins that induce severe bending of DNA and are required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. They augment the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex. They may also play essential roles in transcriptional initiation fidelity of some but not all tRNA genes.


Pssm-ID: 438792 [Multi-domain]  Cd Length: 81  Bit Score: 40.81  E-value: 1.78e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568906282 557 AVKKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYNNQMKK 624
Cdd:cd01390   13 APKRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAAKDKKRYEEEKAA 80
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 24-144 2.18e-04

Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 41.48  E-value: 2.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282    24 VVKELIENSLDAGATS--IEVKLENYGFD-KIEIRDNGEGIKAVDVPVMAVKYYTSKISSHEdlgnlttygFRGEALG-S 99
Cdd:smart00387   9 VLSNLLDNAIKYTPEGgrITVTLERDGDHvEITVEDNGPGIPPEDLEKIFEPFFRTDKRSRK---------IGGTGLGlS 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 568906282   100 ICNvaevvvttrtsaddfstQYVLDGSGHIlsQKPSHLGQGTTVT 144
Cdd:smart00387  80 IVK-----------------KLVELHGGEI--SVESEPGGGTTFT 105
HATPase_DpiB-CitA-like cd16915
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 21-85 2.94e-04

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli K-12 DpiB, DcuS, and Bacillus subtilis CitS, DctS, and YufL; This family includes histidine kinase-like ATPase domains of Escherichia coli K-12 DpiB and DcuS, and Bacillus subtilis CitS, DctS and MalK histidine kinases (HKs) all of which are two component transduction systems (TCSs). E. coli K-12 DpiB (also known as CitA) is the histidine kinase (HK) of DpiA-DpiB, a two-component signal transduction system (TCS) required for the expression of citrate-specific fermentation genes and genes involved in plasmid inheritance. E. coli K-12 DcuS (also known as YjdH) is the HK of DcuS-DcuR, a TCS that in the presence of the extracellular C4-dicarboxlates, activates the expression of the genes of anaerobic fumarate respiration and of aerobic C4-dicarboxylate uptake. CitS is the HK of Bacillus subtilis CitS-CitT, a TCS which regulates expression of CitM, the Mg-citrate transporter. Bacillus subtilis DctS forms a tripartite sensor unit (DctS/DctA/DctB) for sensing C4 dicarboxylates. Bacillus subtilis MalK (also known as YfuL) is the HK of MalK-MalR (YufL-YufM) a TCS which regulates the expression of the malate transporters MaeN (YufR) and YflS, and is essential for utilization of malate in minimal medium. Proteins having this DpiB-CitA-like HATPase domain generally have sensor domains such as Cache and PAS, and a histidine kinase A (HisKA)-like SpoOB-type, alpha-helical domain.


Pssm-ID: 340392 [Multi-domain]  Cd Length: 104  Bit Score: 41.12  E-value: 2.94e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568906282  21 VVSVVKELIENSLDAGATS------IEVKLENYGFD-KIEIRDNGEGIKAVDVPVMAVKYYTSKISSHEDLG 85
Cdd:cd16915    1 LITIVGNLIDNALDALAATgapnkqVEVFLRDEGDDlVIEVRDTGPGIAPELRDKVFERGVSTKGQGERGIG 72
HATPase_TopVIB-like cd16933
Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family ...
 18-77 2.98e-04

Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family includes the histidine kinase-like ATPase (HATPase) domain of the B subunit of topoisomerase VI (Topo VIB). Topo VI is a heterotetrameric complex composed of two TopVIA and two TopVIB subunits and is categorized as a type II B DNA topoisomerase. It is found in archaea and also in plants. Type II enzymes cleave both strands of a DNA duplex and pass a second duplex through the resulting break in an ATP-dependent mechanism. DNA cleavage by Topo VI generates two-nucleotide 5'-protruding ends.


Pssm-ID: 340410 [Multi-domain]  Cd Length: 203  Bit Score: 43.11  E-value: 2.98e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568906282  18 ITSVVSVVKELIENSLDAGATS-----IEVKLENYGFD--KIEIRDNGEGIKAVDVPVMAVK-YYTSK 77
Cdd:cd16933   17 IRSLYTTVRELVENSLDATEEAgilpdIKVEIEEIGKDhyKVIVEDNGPGIPEEQIPKVFGKvLYGSK 84
HMG-box_ABF2-like_rpt1 cd22010
first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 559-600 6.00e-04

first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. ABF2 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438826 [Multi-domain]  Cd Length: 68  Bit Score: 39.06  E-value: 6.00e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 568906282 559 KKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLS 600
Cdd:cd22010    2 KRPLSAYFLYFQEHRSDFVKENPDAKMTEISKIGGDKWKNLS 43
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 560-623 2.55e-03

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.


Pssm-ID: 438810 [Multi-domain]  Cd Length: 67  Bit Score: 37.28  E-value: 2.55e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568906282 560 KPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYNNQMK 623
Cdd:cd21994    1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMK 64
HMG-box_AtHMGB6-like_rpt1 cd22006
first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 559-624 2.78e-03

first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438822 [Multi-domain]  Cd Length: 68  Bit Score: 37.05  E-value: 2.78e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568906282 559 KKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYNNQMKK 624
Cdd:cd22006    1 KKPKTAYFLWCKDQREEVKKENPNADFSEVSKILGAKWKNLSEEEKKPYEEKYKEEKEKYLKVVGE 66
PRK04184 PRK04184
DNA topoisomerase VI subunit B; Validated
 20-67 3.17e-03

DNA topoisomerase VI subunit B; Validated


Pssm-ID: 235246 [Multi-domain]  Cd Length: 535  Bit Score: 41.03  E-value: 3.17e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 568906282  20 SVVSVVKELIENSLDAGATS-------IEVKLENYGFD--KIEIRDNGEGIKAVDVP 67
Cdd:PRK04184  36 ALYTTVKELVDNSLDACEEAgilpdikIEIKRVDEGKDhyRVTVEDNGPGIPPEEIP 92
MutL_Trans_MutL cd03482
MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 213-317 3.63e-03

MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of the enzymes. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Prokaryotic MutS and MutL are homodimers.


Pssm-ID: 239564 [Multi-domain]  Cd Length: 123  Bit Score: 38.33  E-value: 3.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906282 213 VLGTAVMGnmESVEQHCEQSQIYLSGFFPKHDAdhnstSLSTPERSFIFINSRPVHQKDILKLIRRYYnlkclkeSTRLY 292
Cdd:cd03482    8 ILGEDFAE--QALAIDEEAGGLRLSGWIALPTF-----ARSQADIQYFYVNGRMVRDKLISHAVRQAY-------SDVLH 73

                         90       100
                 ....*....|....*....|....*....
gi 568906282 293 ----PIFFLKIDVPSAEVDINLTPDKSQV 317
Cdd:cd03482   74 ggrhPAYVLYLELDPAQVDVNVHPAKHEV 102
HATPase_GyrB-like cd16928
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ...
 25-61 6.39e-03

Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes histidine kinase-like ATPase domain of the B subunit of DNA gyrase. Bacterial DNA gyrase is a type II topoisomerase (type II as it transiently cleaves both strands of DNA) which catalyzes the introduction of negative supercoils into DNA, possibly by a mechanism in which one segment of the double-stranded DNA substrate is passed through a transient break in a second segment. It consists of GyrA and GyrB subunits in an A2B2 stoichiometry; GyrA subunits catalyze strand-breakage and reunion reactions, and GyrB subunits hydrolyze ATP. DNA gyrase is found in bacteria, plants and archaea, but as it is absent in humans it is a possible drug target for the treatment of bacterial and parasite infections.


Pssm-ID: 340405 [Multi-domain]  Cd Length: 180  Bit Score: 38.67  E-value: 6.39e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 568906282  25 VKELIENSLD---AG-ATSIEVKLENYGFdkIEIRDNGEGI 61
Cdd:cd16928    5 VWEIVDNSIDealAGyATEIEVTLHEDNS--ITVEDNGRGI 43
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 559-623 8.81e-03

HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail.


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 35.84  E-value: 8.81e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568906282  559 KKPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKHKYEEKAKKDLERYNNQMK 623
Cdd:pfam09011   5 KRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMG 69
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 560-628 9.37e-03

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 35.19  E-value: 9.37e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568906282 560 KPMSASALFIQDHRTQFLTENPKTGLEDATEQIKARWETLSEEEKhkyeekakkdlERYNNQMKKAIEQ 628
Cdd:cd00084    1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEK-----------QPYEEKAKEDKER 58
 
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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