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Conserved domains on  [gi|20334706|gb|AAM16278|]
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MutL-like protein 3, partial [Mus musculus]

Protein Classification

HATPase_MutL-MLH-PMS-like and MutL_Trans_MLH3 domain-containing protein( domain architecture ID 13014524)

HATPase_MutL-MLH-PMS-like and MutL_Trans_MLH3 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HATPase_MutL-MLH-PMS-like cd16926
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ...
 12-192 4.40e-64

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: 201.13  E-value: 4.40e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  12 KLRSGLAISSLGQCVEELTLNSIDAEATCVAIRVNMETFQ-VQVIDNGLGMAGDDVEKVGNRYFTSKCHSVRDLENPAFY 90
Cdd:cd16926   4 KIAAGEVIERPASVVKELVENSIDAGATRIDVEIEEGGLKlIRVTDNGSGISREDLELAFERHATSKISSFEDLFSITTL 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  91 GFRGEALASIADMAgAVEISSKKNTTLKTFVKMFQNGKALatHEADLTRPSVGTTVTVYNLFYQFPVRRKSM-DPRLEFE 169
Cdd:cd16926  84 GFRGEALASIASVS-RLTITTRTADDDVGTRLVVDGGGII--EEVKPAAAPVGTTVTVRDLFYNTPARRKFLkSPKTELS 160

                       170       180
                ....*....|....*....|...
gi 20334706 170 KVRQRVEALSLMHPSISFSLRND 192
Cdd:cd16926 161 KILDLVQRLALAHPDVSFSLTHD 183
MutL_Trans_MLH3 cd03486
MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 206-338 4.43e-61

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: 191.76  E-value: 4.43e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706 206 DICSRFCQIYGLGKSQKLREIRFKYKEFEFSGYISSEAHYNKNMQFLFVNRRLVLRTKLHKLIDFLLRKESIICRPKNGS 285
Cdd:cd03486   1 SILSVFKQIYGLVLAQKLKEVSAKFQEYEVSGYISSEGHYSKSFQFIYVNGRLYLKTRFHKLINKLFRKTSAVAKNKSSP 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 20334706 286 ASRQMnssPRHRSASELHGIYVINVQCPFCEYDVCIEPAKTLIELQSWDTVLI 338
Cdd:cd03486  81 QSKSS---RRGKRSQESYPVFVLNITCPASEYDLSQEPSKTIIEFKDWKTLLP 130
 
Name Accession Description Interval E-value
HATPase_MutL-MLH-PMS-like cd16926
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ...
 12-192 4.40e-64

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: 201.13  E-value: 4.40e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  12 KLRSGLAISSLGQCVEELTLNSIDAEATCVAIRVNMETFQ-VQVIDNGLGMAGDDVEKVGNRYFTSKCHSVRDLENPAFY 90
Cdd:cd16926   4 KIAAGEVIERPASVVKELVENSIDAGATRIDVEIEEGGLKlIRVTDNGSGISREDLELAFERHATSKISSFEDLFSITTL 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  91 GFRGEALASIADMAgAVEISSKKNTTLKTFVKMFQNGKALatHEADLTRPSVGTTVTVYNLFYQFPVRRKSM-DPRLEFE 169
Cdd:cd16926  84 GFRGEALASIASVS-RLTITTRTADDDVGTRLVVDGGGII--EEVKPAAAPVGTTVTVRDLFYNTPARRKFLkSPKTELS 160

                       170       180
                ....*....|....*....|...
gi 20334706 170 KVRQRVEALSLMHPSISFSLRND 192
Cdd:cd16926 161 KILDLVQRLALAHPDVSFSLTHD 183
MutL_Trans_MLH3 cd03486
MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 206-338 4.43e-61

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: 191.76  E-value: 4.43e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706 206 DICSRFCQIYGLGKSQKLREIRFKYKEFEFSGYISSEAHYNKNMQFLFVNRRLVLRTKLHKLIDFLLRKESIICRPKNGS 285
Cdd:cd03486   1 SILSVFKQIYGLVLAQKLKEVSAKFQEYEVSGYISSEGHYSKSFQFIYVNGRLYLKTRFHKLINKLFRKTSAVAKNKSSP 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 20334706 286 ASRQMnssPRHRSASELHGIYVINVQCPFCEYDVCIEPAKTLIELQSWDTVLI 338
Cdd:cd03486  81 QSKSS---RRGKRSQESYPVFVLNITCPASEYDLSQEPSKTIIEFKDWKTLLP 130
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
 1-326 4.65e-56

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: 184.77  E-value: 4.65e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706     1 MIRCLSDDVKTKLRSGLAISSLGQCVEELTLNSIDAEATcvAIRVNMETF---QVQVIDNGLGMAGDDVEKVGNRYFTSK 77
Cdd:TIGR00585   2 TIKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGAT--RIDVEIEEGglkLIEVSDNGSGIDKEDLPLACERHATSK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706    78 CHSVRDLENPAFYGFRGEALASIADMAgAVEISSKKNTTLKTFVKMFQNGKALATHEADlTRPsVGTTVTVYNLFYQFPV 157
Cdd:TIGR00585  80 IQSFEDLERIETLGFRGEALASISSVS-RLTITTKTSAADGLAYQALLEGGMIESIKPA-PRP-VGTTVEVRDLFYNLPV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706   158 RRKSM-DPRLEFEKVRQRVEALSLMHPSISFSLRNDvsGSMVLQLPK-----TKDicSRFCQIYGLGKSQKLREIRF-KY 230
Cdd:TIGR00585 157 RRKFLkSPKKEFRKILDVLQRYALIHPDISFSLTHD--GKKVLQLSTkpnqsTKE--NRIRSVFGTAVLRKLIPLDEwED 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706   231 KEFEFSGYISSEAH---YNKNMQFLFVNRRLVLRTKLHKLIDfllrkesiicrpkngSASRQMNssPRHRsaselHGIYV 307
Cdd:TIGR00585 233 LDLQLEGFISQPNVtrsRRSGWQFLFINGRPVELKLLLKAIR---------------EVYHEYL--PKGQ-----YPVFV 290

                         330
                  ....*....|....*....
gi 20334706   308 INVQCPFCEYDVCIEPAKT 326
Cdd:TIGR00585 291 LNLEIDPELVDVNVHPDKK 309
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
26-326 8.35e-50

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


Pssm-ID: 440092 [Multi-domain]  Cd Length: 515  Bit Score: 173.69  E-value: 8.35e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  26 VEELTLNSIDAEATcvAIRVNME----TFqVQVIDNGLGMAGDDVEKVGNRYFTSKCHSVRDLENPAFYGFRGEALASIA 101
Cdd:COG0323  28 VKELVENAIDAGAT--RIEVEIEeggkSL-IRVTDNGCGMSPEDLPLAFERHATSKIRSAEDLFRIRTLGFRGEALASIA 104

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706 102 dmagAV---EISSK-KNTTLKTFVKMfQNGKALATHEADLtrpSVGTTVTVYNLFYQFPVRRKSMD-PRLEFEKVRQRVE 176
Cdd:COG0323 105 ----SVsrlTLTTRtAGAELGTRIEV-EGGKVVEVEPAAA---PKGTTVEVRDLFFNTPARRKFLKsDATELAHITDVVR 176

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706 177 ALSLMHPSISFSLRNDvsGSMVLQLPKTKDICSRFCQIYGLGKSQKLREIRFKYKEFEFSGYISSEAHY--NKNMQFLFV 254
Cdd:COG0323 177 RLALAHPDIAFTLIHN--GREVFQLPGAGDLLQRIAAIYGREFAENLLPVEAEREGLRLSGYIGKPEFSrsNRDYQYFFV 254

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 20334706 255 NRRLVlRtklhkliDFLLRK------ESIIcrpkngsasrqmnssPRHRsaselHGIYVINVQCPFCEYDVCIEPAKT 326
Cdd:COG0323 255 NGRPV-R-------DKLLSHavreayRDLL---------------PKGR-----YPVAVLFLELDPELVDVNVHPTKT 304
mutL PRK00095
DNA mismatch repair endonuclease MutL;
26-326 2.42e-44

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 160.38  E-value: 2.42e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706   26 VEELTLNSIDAEATcvAIRVNME----TfQVQVIDNGLGMAGDDVEKVGNRYFTSKCHSVRDLENPAFYGFRGEALASIA 101
Cdd:PRK00095  27 VKELVENALDAGAT--RIDIEIEegglK-LIRVRDNGCGISKEDLALALARHATSKIASLDDLEAIRTLGFRGEALPSIA 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  102 DMAgAVEISSKKNTTLKTFVKMFQNGKAL----ATHeadltrpSVGTTVTVYNLFYQFPVRRKSM-DPRLEFEKVRQRVE 176
Cdd:PRK00095 104 SVS-RLTLTSRTADAAEGWQIVYEGGEIVevkpAAH-------PVGTTIEVRDLFFNTPARRKFLkSEKTELGHIDDVVN 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  177 ALSLMHPSISFSLRNDvsGSMVLQLPKTKDICSRFCQIYGLGKSQKLREIRFKYKEFEFSGYISS-EAHY-NKNMQFLFV 254
Cdd:PRK00095 176 RLALAHPDVAFTLTHN--GKLVLQTRGAGQLLQRLAAILGREFAENALPIDAEHGDLRLSGYVGLpTLSRaNRDYQYLFV 253

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 20334706  255 NRRLVlRtklhkliDFLLrkesiicrpkNGsASRQ--MNSSPRHRsaselHGIYVINVQCPFCEYDVCIEPAKT 326
Cdd:PRK00095 254 NGRYV-R-------DKLL----------NH-AIRQayHDLLPRGR-----YPAFVLFLELDPHQVDVNVHPAKH 303
DNA_mis_repair pfam01119
DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain ...
 213-326 1.36e-07

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: 49.42  E-value: 1.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706   213 QIYGLGKSQKLREIRFKYKEFEFSGYIS--SEAHYNKNMQFLFVNRRLVLRTKLHKLIDfllrkesiicrpkngSASRqm 290
Cdd:pfam01119   2 AIYGKEFAENLLPIEKEDDGLRLSGYISkpTLSRSNRDYQYLFVNGRPVRDKLLSHAIR---------------EAYR-- 64

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 20334706   291 NSSPRHRsaselHGIYVINVQCPFCEYDVCIEPAKT 326
Cdd:pfam01119  65 DLLPKGR-----YPVAVLFLEIDPELVDVNVHPTKR 95
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
 22-80 1.38e-06

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: 46.21  E-value: 1.38e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 20334706    22 LGQCVEELTLNSIDAEATCVAIRVNME---TFQVQVIDNGLGMAGDDVEKVGNRYFTSKCHS 80
Cdd:pfam02518   6 LRQVLSNLLDNALKHAAKAGEITVTLSeggELTLTVEDNGIGIPPEDLPRIFEPFSTADKRG 67
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 22-77 9.98e-05

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


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 41.10  E-value: 9.98e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706     22 LGQCVEELTLNSIDAEATCVAIRVNMET----FQVQVIDNGLGMAGDDVEKVGNRYFTSK 77
Cdd:smart00387   6 LRQVLSNLLDNAIKYTPEGGRITVTLERdgdhVEITVEDNGPGIPPEDLEKIFEPFFRTD 65
 
Name Accession Description Interval E-value
HATPase_MutL-MLH-PMS-like cd16926
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ...
 12-192 4.40e-64

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: 201.13  E-value: 4.40e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  12 KLRSGLAISSLGQCVEELTLNSIDAEATCVAIRVNMETFQ-VQVIDNGLGMAGDDVEKVGNRYFTSKCHSVRDLENPAFY 90
Cdd:cd16926   4 KIAAGEVIERPASVVKELVENSIDAGATRIDVEIEEGGLKlIRVTDNGSGISREDLELAFERHATSKISSFEDLFSITTL 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  91 GFRGEALASIADMAgAVEISSKKNTTLKTFVKMFQNGKALatHEADLTRPSVGTTVTVYNLFYQFPVRRKSM-DPRLEFE 169
Cdd:cd16926  84 GFRGEALASIASVS-RLTITTRTADDDVGTRLVVDGGGII--EEVKPAAAPVGTTVTVRDLFYNTPARRKFLkSPKTELS 160

                       170       180
                ....*....|....*....|...
gi 20334706 170 KVRQRVEALSLMHPSISFSLRND 192
Cdd:cd16926 161 KILDLVQRLALAHPDVSFSLTHD 183
MutL_Trans_MLH3 cd03486
MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 206-338 4.43e-61

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: 191.76  E-value: 4.43e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706 206 DICSRFCQIYGLGKSQKLREIRFKYKEFEFSGYISSEAHYNKNMQFLFVNRRLVLRTKLHKLIDFLLRKESIICRPKNGS 285
Cdd:cd03486   1 SILSVFKQIYGLVLAQKLKEVSAKFQEYEVSGYISSEGHYSKSFQFIYVNGRLYLKTRFHKLINKLFRKTSAVAKNKSSP 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 20334706 286 ASRQMnssPRHRSASELHGIYVINVQCPFCEYDVCIEPAKTLIELQSWDTVLI 338
Cdd:cd03486  81 QSKSS---RRGKRSQESYPVFVLNITCPASEYDLSQEPSKTIIEFKDWKTLLP 130
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
 1-326 4.65e-56

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: 184.77  E-value: 4.65e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706     1 MIRCLSDDVKTKLRSGLAISSLGQCVEELTLNSIDAEATcvAIRVNMETF---QVQVIDNGLGMAGDDVEKVGNRYFTSK 77
Cdd:TIGR00585   2 TIKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGAT--RIDVEIEEGglkLIEVSDNGSGIDKEDLPLACERHATSK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706    78 CHSVRDLENPAFYGFRGEALASIADMAgAVEISSKKNTTLKTFVKMFQNGKALATHEADlTRPsVGTTVTVYNLFYQFPV 157
Cdd:TIGR00585  80 IQSFEDLERIETLGFRGEALASISSVS-RLTITTKTSAADGLAYQALLEGGMIESIKPA-PRP-VGTTVEVRDLFYNLPV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706   158 RRKSM-DPRLEFEKVRQRVEALSLMHPSISFSLRNDvsGSMVLQLPK-----TKDicSRFCQIYGLGKSQKLREIRF-KY 230
Cdd:TIGR00585 157 RRKFLkSPKKEFRKILDVLQRYALIHPDISFSLTHD--GKKVLQLSTkpnqsTKE--NRIRSVFGTAVLRKLIPLDEwED 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706   231 KEFEFSGYISSEAH---YNKNMQFLFVNRRLVLRTKLHKLIDfllrkesiicrpkngSASRQMNssPRHRsaselHGIYV 307
Cdd:TIGR00585 233 LDLQLEGFISQPNVtrsRRSGWQFLFINGRPVELKLLLKAIR---------------EVYHEYL--PKGQ-----YPVFV 290

                         330
                  ....*....|....*....
gi 20334706   308 INVQCPFCEYDVCIEPAKT 326
Cdd:TIGR00585 291 LNLEIDPELVDVNVHPDKK 309
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
26-326 8.35e-50

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


Pssm-ID: 440092 [Multi-domain]  Cd Length: 515  Bit Score: 173.69  E-value: 8.35e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  26 VEELTLNSIDAEATcvAIRVNME----TFqVQVIDNGLGMAGDDVEKVGNRYFTSKCHSVRDLENPAFYGFRGEALASIA 101
Cdd:COG0323  28 VKELVENAIDAGAT--RIEVEIEeggkSL-IRVTDNGCGMSPEDLPLAFERHATSKIRSAEDLFRIRTLGFRGEALASIA 104

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706 102 dmagAV---EISSK-KNTTLKTFVKMfQNGKALATHEADLtrpSVGTTVTVYNLFYQFPVRRKSMD-PRLEFEKVRQRVE 176
Cdd:COG0323 105 ----SVsrlTLTTRtAGAELGTRIEV-EGGKVVEVEPAAA---PKGTTVEVRDLFFNTPARRKFLKsDATELAHITDVVR 176

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706 177 ALSLMHPSISFSLRNDvsGSMVLQLPKTKDICSRFCQIYGLGKSQKLREIRFKYKEFEFSGYISSEAHY--NKNMQFLFV 254
Cdd:COG0323 177 RLALAHPDIAFTLIHN--GREVFQLPGAGDLLQRIAAIYGREFAENLLPVEAEREGLRLSGYIGKPEFSrsNRDYQYFFV 254

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 20334706 255 NRRLVlRtklhkliDFLLRK------ESIIcrpkngsasrqmnssPRHRsaselHGIYVINVQCPFCEYDVCIEPAKT 326
Cdd:COG0323 255 NGRPV-R-------DKLLSHavreayRDLL---------------PKGR-----YPVAVLFLELDPELVDVNVHPTKT 304
mutL PRK00095
DNA mismatch repair endonuclease MutL;
26-326 2.42e-44

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 160.38  E-value: 2.42e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706   26 VEELTLNSIDAEATcvAIRVNME----TfQVQVIDNGLGMAGDDVEKVGNRYFTSKCHSVRDLENPAFYGFRGEALASIA 101
Cdd:PRK00095  27 VKELVENALDAGAT--RIDIEIEegglK-LIRVRDNGCGISKEDLALALARHATSKIASLDDLEAIRTLGFRGEALPSIA 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  102 DMAgAVEISSKKNTTLKTFVKMFQNGKAL----ATHeadltrpSVGTTVTVYNLFYQFPVRRKSM-DPRLEFEKVRQRVE 176
Cdd:PRK00095 104 SVS-RLTLTSRTADAAEGWQIVYEGGEIVevkpAAH-------PVGTTIEVRDLFFNTPARRKFLkSEKTELGHIDDVVN 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  177 ALSLMHPSISFSLRNDvsGSMVLQLPKTKDICSRFCQIYGLGKSQKLREIRFKYKEFEFSGYISS-EAHY-NKNMQFLFV 254
Cdd:PRK00095 176 RLALAHPDVAFTLTHN--GKLVLQTRGAGQLLQRLAAILGREFAENALPIDAEHGDLRLSGYVGLpTLSRaNRDYQYLFV 253

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 20334706  255 NRRLVlRtklhkliDFLLrkesiicrpkNGsASRQ--MNSSPRHRsaselHGIYVINVQCPFCEYDVCIEPAKT 326
Cdd:PRK00095 254 NGRYV-R-------DKLL----------NH-AIRQayHDLLPRGR-----YPAFVLFLELDPHQVDVNVHPAKH 303
MutL_Trans cd00782
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 207-337 4.33e-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: 103.00  E-value: 4.33e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706 207 ICSRFCQIYGLGKSQKLREIRFKYKEFEFSGYISSEAHY--NKNMQFLFVNRRLVLRTKLHKLIDFLLRkesiicrpkng 284
Cdd:cd00782   1 LKDRIAQVYGKEVAKNLIEVELESGDFRISGYISKPDFGrsSKDRQFLFVNGRPVRDKLLSKAINEAYR----------- 69

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 20334706 285 sasrqmNSSPRHRsaselHGIYVINVQCPFCEYDVCIEPAKTLIELQSWDTVL 337
Cdd:cd00782  70 ------SYLPKGR-----YPVFVLNLELPPELVDVNVHPTKREVRFSDEEEVL 111
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 207-328 8.93e-16

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: 72.29  E-value: 8.93e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706 207 ICSRFCQIYGLGKSQKLREIRFKYKEFEFSGYISS--EAHYNKNMQFLFVNRRLVLRTKLH-KLIDFLLRkesiicrpkn 283
Cdd:cd00329   1 LKDRLAEILGDKVADKLIYVEGESDGFRVEGAISYpdSGRSSKDRQFSFVNGRPVREGGTHvKAVREAYT---------- 70

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 20334706 284 gsasRQMNSSPRHRsaselHGIYVINVQCPFCEYDVCIEPAKTLI 328
Cdd:cd00329  71 ----RALNGDDVRR-----YPVAVLSLKIPPSLVDVNVHPTKEEV 106
DNA_mis_repair pfam01119
DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain ...
 213-326 1.36e-07

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: 49.42  E-value: 1.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706   213 QIYGLGKSQKLREIRFKYKEFEFSGYIS--SEAHYNKNMQFLFVNRRLVLRTKLHKLIDfllrkesiicrpkngSASRqm 290
Cdd:pfam01119   2 AIYGKEFAENLLPIEKEDDGLRLSGYISkpTLSRSNRDYQYLFVNGRPVRDKLLSHAIR---------------EAYR-- 64

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 20334706   291 NSSPRHRsaselHGIYVINVQCPFCEYDVCIEPAKT 326
Cdd:pfam01119  65 DLLPKGR-----YPVAVLFLEIDPELVDVNVHPTKR 95
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
 22-80 1.38e-06

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: 46.21  E-value: 1.38e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 20334706    22 LGQCVEELTLNSIDAEATCVAIRVNME---TFQVQVIDNGLGMAGDDVEKVGNRYFTSKCHS 80
Cdd:pfam02518   6 LRQVLSNLLDNALKHAAKAGEITVTLSeggELTLTVEDNGIGIPPEDLPRIFEPFSTADKRG 67
MutL_Trans_hPMS_1_like cd03485
MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 250-337 3.29e-05

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: 43.03  E-value: 3.29e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706 250 QFLFVNRRLVLRTK-LHKLIDFLLRKESiicrpkngsasrqmnssprHRSASELHGIYVINVQCPFCEYDVCIEPAKTLI 328
Cdd:cd03485  51 KFISVNSRPVSLGKdIGKLLRQYYSSAY-------------------RKSSLRRYPVFFLNILCPPGLVDVNIEPDKDDV 111


                ....*....
gi 20334706 329 ELQSWDTVL 337
Cdd:cd03485 112 LLQNKEAVL 120
MutL_Trans_hPMS_2_like cd03484
MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 225-337 9.15e-05

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: 41.87  E-value: 9.15e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706 225 EIRFKYKEFEFSGYISSEAHY----NKNMQFLFVNRRLVLRTKLHKLIDFLLRKESiicrpkngsaSRQmnsSPrhrsas 300
Cdd:cd03484  37 DEDLADSEVKITGYISKPSHGcgrsSSDRQFFYINGRPVDLKKVAKLINEVYKSFN----------SRQ---YP------ 97

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 20334706 301 elhgIYVINVQCPFCEYDVCIEPAKTLIELQSWDTVL 337
Cdd:cd03484  98 ----FFILNISLPTSLYDVNVTPDKRTVLLHDEDRLI 130
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 22-77 9.98e-05

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


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 41.10  E-value: 9.98e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706     22 LGQCVEELTLNSIDAEATCVAIRVNMET----FQVQVIDNGLGMAGDDVEKVGNRYFTSK 77
Cdd:smart00387   6 LRQVLSNLLDNAIKYTPEGGRITVTLERdgdhVEITVEDNGPGIPPEDLEKIFEPFFRTD 65
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 22-77 2.34e-03

Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms];


Pssm-ID: 444024 [Multi-domain]  Cd Length: 422  Bit Score: 39.56  E-value: 2.34e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  22 LGQCVEELTLNSIDA-EAT---CVAIRVNMETFQVQVIDNGLGMAGDDVEKVGNRYFTSK 77
Cdd:COG5000 318 LEQVLINLLKNAIEAiEEGgeiEVSTRREDGRVRIEVSDNGPGIPEEVLERIFEPFFTTK 377
BaeS COG0642
Signal transduction histidine kinase [Signal transduction mechanisms];
22-77 3.78e-03

Signal transduction histidine kinase [Signal transduction mechanisms];


Pssm-ID: 440407 [Multi-domain]  Cd Length: 328  Bit Score: 38.74  E-value: 3.78e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706  22 LGQCVEELTLNSIDA--EATCVAIRVNME--TFQVQVIDNGLGMAGDDVEKVGNRYFTSK 77
Cdd:COG0642 224 LRQVLLNLLSNAIKYtpEGGTVTVSVRREgdRVRISVEDTGPGIPPEDLERIFEPFFRTD 283
MutL_Trans_MLH1 cd03483
MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 213-269 4.22e-03

MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). 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 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 hMLH1 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 hMLH1 accounts for a large fraction of HNPCC families.


Pssm-ID: 239565 [Multi-domain]  Cd Length: 127  Bit Score: 36.83  E-value: 4.22e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 20334706 213 QIYGLGKSQKLREIRFKYKE----FEFSGYISSeAHYN--KNMQFLFVNRRLVLRTKLHKLID 269
Cdd:cd03483   8 SVYGAAVANELIEVEISDDDddlgFKVKGLISN-ANYSkkKIIFILFINNRLVECSALRRAIE 69
HATPase_c_3 pfam13589
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents, additionally, ...
 26-117 9.94e-03

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: 35.77  E-value: 9.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20334706    26 VEELTLNSIDAEATCVAIRVN---METFQVQVIDNGLGMAGDDVEKVGN-------RYFTSKCHSVrdlenpafYGFrGE 95
Cdd:pfam13589   5 LAELIDNSIDADATNIKIEVNknrGGGTEIVIEDDGHGMSPEELINALRlatsakeAKRGSTDLGR--------YGI-GL 75

                          90       100
                  ....*....|....*....|...
gi 20334706    96 ALASIadMAGA-VEISSKKNTTL 117
Cdd:pfam13589  76 KLASL--SLGAkLTVTSKKEGKS 96
 
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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