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Conserved domains on  [gi|42565155|ref|NP_189075|]
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MUTL protein homolog 1 [Arabidopsis thaliana]

Protein Classification

GIY-YIG nuclease family protein( domain architecture ID 10259808)

GIY-YIG nuclease family protein similar to Escherichia virus T4 endonuclease segA that may be involved in the movement of the endonuclease-encoding DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ABC_MutS_homologs cd03243
ATP-binding cassette domain of MutS homologs; The MutS protein initiates DNA mismatch repair ...
 748-934 8.75e-74

ATP-binding cassette domain of MutS homologs; The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.


:

Pssm-ID: 213210 [Multi-domain]  Cd Length: 202  Bit Score: 242.93  E-value: 8.75e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  748 VSSGTAVHNTVDMQS--LFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQ 825
Cdd:cd03243   14 TKGETFVPNDINLGSgrLLLITGPNMGGKSTYLRSIGLAVLLAQIGCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFM 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  826 VEMSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESLDTSGCLGIVSTHLHGIFSLPLTAKNITYKAMGAENV 905
Cdd:cd03243   94 AELLELKEILSLATPRSLVLIDELGRGTSTAEGLAIAYAVLEHLLEKGCRTLFATHFHELADLPEQVPGVKNLHMEELIT 173

                        170       180
                 ....*....|....*....|....*....
gi 42565155  906 EGQTKPTWKLTDGVCRESLAFETAKREGV 934
Cdd:cd03243  174 TGGLTFTYKLIDGICDPSYALQIAELAGL 202
GIY-YIG_MSH cd10438
Catalytic GIY-YIG domain of eukaryotic DNA mismatch repair protein MutS homologs; This family ...
 1025-1094 1.70e-34

Catalytic GIY-YIG domain of eukaryotic DNA mismatch repair protein MutS homologs; This family represents a putative GIY-YIG nuclease domain C-terminally fused to the DNA-repair ATPase on a small group of eukaryotic DNA mismatch repair protein mutS homologs (MSH). The MSH proteins in this family do not have the zinc finger domain, but have a predicted mitochondrial localization. They might play roles in the recognition and repair of errors made during the replication of DNA. The prototype of this family is the protein encoded by the chloroplast mutator (CHM) locus from Arabidopsis thaliana. It is suggested that this protein could be involved in the maintenance of mitochondrial genome stability.


:

Pssm-ID: 198385  Cd Length: 72  Bit Score: 126.43  E-value: 1.70e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 42565155 1025 SCVYVMRRPDKRLYIGQTDDLEGRIRAHRAKEG--LQGSSFLYLMVQGKSMACQLETLLINQLHEQGYSLAN 1094
Cdd:cd10438    1 SCVYILRRGDGEYYVGETDNLSGRLEQHRASLGetLVISGFLYLLVGGKSEARSLESALIQQLQGQGANLAS 72
MutS_I super family cl03286
MutS domain I; This domain is found in proteins of the MutS family (DNA mismatch repair ...
 126-226 3.65e-12

MutS domain I; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with globular domain I, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in.


The actual alignment was detected with superfamily member pfam01624:

Pssm-ID: 426350 [Multi-domain]  Cd Length: 113  Bit Score: 64.14  E-value: 3.65e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    126 WEMlqfKSRFPREVLLCRVGEFYEAIGIDACILVEYAGLN--PFGGLRSDSIPKAGCPIMNLRQTLDDLTRNGYSVCIVE 203
Cdd:pfam01624    8 LEL---KSKYPDAVLFFRVGDFYELFGEDAEIAARELGITltVRKGGSGKRIPMAGVPEHAFERYARRLVNKGYKVAICE 84

                           90       100
                   ....*....|....*....|...
gi 42565155    204 EVQGPTPARSRKGRFISGHAHPG 226
Cdd:pfam01624   85 QTETPAEAKGVVKREVVRVVTPG 107
 
Name Accession Description Interval E-value
ABC_MutS_homologs cd03243
ATP-binding cassette domain of MutS homologs; The MutS protein initiates DNA mismatch repair ...
 748-934 8.75e-74

ATP-binding cassette domain of MutS homologs; The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.


Pssm-ID: 213210 [Multi-domain]  Cd Length: 202  Bit Score: 242.93  E-value: 8.75e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  748 VSSGTAVHNTVDMQS--LFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQ 825
Cdd:cd03243   14 TKGETFVPNDINLGSgrLLLITGPNMGGKSTYLRSIGLAVLLAQIGCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFM 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  826 VEMSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESLDTSGCLGIVSTHLHGIFSLPLTAKNITYKAMGAENV 905
Cdd:cd03243   94 AELLELKEILSLATPRSLVLIDELGRGTSTAEGLAIAYAVLEHLLEKGCRTLFATHFHELADLPEQVPGVKNLHMEELIT 173

                        170       180
                 ....*....|....*....|....*....
gi 42565155  906 EGQTKPTWKLTDGVCRESLAFETAKREGV 934
Cdd:cd03243  174 TGGLTFTYKLIDGICDPSYALQIAELAGL 202
MUTSac smart00534
ATPase domain of DNA mismatch repair MUTS family;
763-946 1.11e-54

ATPase domain of DNA mismatch repair MUTS family;


Pssm-ID: 197777 [Multi-domain]  Cd Length: 185  Bit Score: 188.15  E-value: 1.11e-54
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155     763 LFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQVEMSEIRSIVSQATSRS 842
Cdd:smart00534    1 VVIITGPNMGGKSTYLRQVALIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNATKNS 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155     843 LVLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIVSTHLHGIFSLPLTAKNITYKAMGAENVEGQTKPTWKLTDGVCR 921
Cdd:smart00534   81 LVLLDELGRGTSTYDGLAIAAAILEYLlEKIGARTLFATHYHELTKLADNHPGVRNLHMSALEETENITFLYKLKPGVAG 160

                           170       180
                    ....*....|....*....|....*
gi 42565155     922 ESLAFETAKREGVPESVIQRAEALY 946
Cdd:smart00534  161 KSYGIEVAKLAGLPKEVIERAKRIL 185
MutS_V pfam00488
MutS domain V; This domain is found in proteins of the MutS family (DNA mismatch repair ...
 764-946 9.89e-43

MutS domain V; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain V of Thermus aquaticus MutS as characterized in, which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters.


Pssm-ID: 425714 [Multi-domain]  Cd Length: 188  Bit Score: 154.27  E-value: 9.89e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    764 FLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQVEMSEIRSIVSQATSRSL 843
Cdd:pfam00488    1 LIITGPNMGGKSTYLRQVALIVLMAQIGSFVPAESAEIGIVDRIFTRIGASDDLAKGRSTFMVEMLETANILHNATDKSL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    844 VLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIVSTHLHGIFSLPLTAKNITYKAMGAENVEGQTKPTWKLTDGVCRE 922
Cdd:pfam00488   81 VILDELGRGTSTYDGLAIAWAVAEHLaEKIKARTLFATHYHELTKLAEKLPAVKNLHMAAVEDDDDIVFLYKVQPGAADK 160

                          170       180
                   ....*....|....*....|....
gi 42565155    923 SLAFETAKREGVPESVIQRAEALY 946
Cdd:pfam00488  161 SYGIHVAELAGLPESVVERAREIL 184
GIY-YIG_MSH cd10438
Catalytic GIY-YIG domain of eukaryotic DNA mismatch repair protein MutS homologs; This family ...
 1025-1094 1.70e-34

Catalytic GIY-YIG domain of eukaryotic DNA mismatch repair protein MutS homologs; This family represents a putative GIY-YIG nuclease domain C-terminally fused to the DNA-repair ATPase on a small group of eukaryotic DNA mismatch repair protein mutS homologs (MSH). The MSH proteins in this family do not have the zinc finger domain, but have a predicted mitochondrial localization. They might play roles in the recognition and repair of errors made during the replication of DNA. The prototype of this family is the protein encoded by the chloroplast mutator (CHM) locus from Arabidopsis thaliana. It is suggested that this protein could be involved in the maintenance of mitochondrial genome stability.


Pssm-ID: 198385  Cd Length: 72  Bit Score: 126.43  E-value: 1.70e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 42565155 1025 SCVYVMRRPDKRLYIGQTDDLEGRIRAHRAKEG--LQGSSFLYLMVQGKSMACQLETLLINQLHEQGYSLAN 1094
Cdd:cd10438    1 SCVYILRRGDGEYYVGETDNLSGRLEQHRASLGetLVISGFLYLLVGGKSEARSLESALIQQLQGQGANLAS 72
mutS1 TIGR01070
DNA mismatch repair protein MutS; [DNA metabolism, DNA replication, recombination, and repair]
 643-945 3.42e-34

DNA mismatch repair protein MutS; [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273427 [Multi-domain]  Cd Length: 840  Bit Score: 141.83  E-value: 3.42e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    643 GEEWFTTPKVEIALVRYHEASENAKARVLELLRELSVKLQTKINVLVFASMLLVISKALFSHACEGRRRKWVFPTlvgFS 722
Cdd:TIGR01070  482 NAERYITPELKEKEDKVLEAEGKILALEKELFEELRELLKKYLEALQEAARALAELDVLANLAEVAETLHYTRPR---FG 558

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    723 LDEGAKPLDGASrmkltglsPYWFDVSSGTAVHNTVDM---QSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESA 799
Cdd:TIGR01070  559 DDPQLRIREGRH--------PVVEQVLRTPFVPNDLEMahnRRMLLITGPNMGGKSTYMRQTALIALLAQIGSFVPAESA 630

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    800 CIPHFDSIMLHMKSYDSPVDGKSSFQVEMSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIV 878
Cdd:TIGR01070  631 ELPLFDRIFTRIGASDDLASGRSTFMVEMTEAANILHNATENSLVLFDEIGRGTSTYDGLALAWAIAEYLhEHIRAKTLF 710

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 42565155    879 STHLHGIFSLPLTAKNITYKAMGAENVEGQTKPTWKLTDGVCRESLAFETAKREGVPESVIQRAEAL 945
Cdd:TIGR01070  711 ATHYFELTALEESLPGLKNVHVAALEHNGTIVFLHQVLPGPASKSYGLAVAALAGLPKEVIARARQI 777
PRK05399 PRK05399
DNA mismatch repair protein MutS; Provisional
 754-964 3.43e-27

DNA mismatch repair protein MutS; Provisional


Pssm-ID: 235444 [Multi-domain]  Cd Length: 854  Bit Score: 119.43  E-value: 3.43e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155   754 VHNTVDM---QSLFLLTGPNGGGKSSLLRSIcaaALLGI---SGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQVE 827
Cdd:PRK05399  597 VPNDCDLdeeRRLLLITGPNMAGKSTYMRQV---ALIVLlaqIGSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVE 673

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155   828 MSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIVSTHLHgifslPLTA--------KNITyk 898
Cdd:PRK05399  674 MTETANILNNATERSLVLLDEIGRGTSTYDGLSIAWAVAEYLhDKIGAKTLFATHYH-----ELTEleeklpgvKNVH-- 746

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42565155   899 aMGAENVEGQTKPTWKLTDGVCRESLAFETAKREGVPESVIQRAEAL--YLSVYAKDASAEVVKPDQI 964
Cdd:PRK05399  747 -VAVKEHGGDIVFLHKVVPGAADKSYGIHVAKLAGLPASVIKRAREIlaQLESASEKAKAASAEEDQL 813
MutS COG0249
DNA mismatch repair ATPase MutS [Replication, recombination and repair];
756-945 9.19e-26

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


Pssm-ID: 440019 [Multi-domain]  Cd Length: 861  Bit Score: 114.77  E-value: 9.19e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  756 NTVDM---QSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIM--------LHMksydspvdGKSSF 824
Cdd:COG0249  605 NDCDLdpdRRILLITGPNMAGKSTYMRQVALIVLLAQIGSFVPAESARIGIVDRIFtrvgasddLAR--------GQSTF 676

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  825 QVEMSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIVSTHLHgifslPLTA--------KNI 895
Cdd:COG0249  677 MVEMTETANILNNATERSLVLLDEIGRGTSTYDGLSIAWAVAEYLhDKIRARTLFATHYH-----ELTElaeklpgvKNY 751

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 42565155  896 TykaMGAENVEGQTKPTWKLTDGVCRESLAFETAKREGVPESVIQRAEAL 945
Cdd:COG0249  752 H---VAVKEWGGDIVFLHKVVPGPADRSYGIHVAKLAGLPASVIERAREI 798
MutS_I pfam01624
MutS domain I; This domain is found in proteins of the MutS family (DNA mismatch repair ...
 126-226 3.65e-12

MutS domain I; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with globular domain I, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in.


Pssm-ID: 426350 [Multi-domain]  Cd Length: 113  Bit Score: 64.14  E-value: 3.65e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    126 WEMlqfKSRFPREVLLCRVGEFYEAIGIDACILVEYAGLN--PFGGLRSDSIPKAGCPIMNLRQTLDDLTRNGYSVCIVE 203
Cdd:pfam01624    8 LEL---KSKYPDAVLFFRVGDFYELFGEDAEIAARELGITltVRKGGSGKRIPMAGVPEHAFERYARRLVNKGYKVAICE 84

                           90       100
                   ....*....|....*....|...
gi 42565155    204 EVQGPTPARSRKGRFISGHAHPG 226
Cdd:pfam01624   85 QTETPAEAKGVVKREVVRVVTPG 107
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
1026-1057 1.08e-06

Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 47.43  E-value: 1.08e-06
                         10        20        30
                 ....*....|....*....|....*....|...
gi 42565155 1026 CVYVMR-RPDKRLYIGQTDDLEGRIRAHRAKEG 1057
Cdd:COG2827    4 YVYILRcADNGTLYTGVTNDLERRLAEHNSGKG 36
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 1026-1090 2.66e-04

GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.


Pssm-ID: 426314 [Multi-domain]  Cd Length: 78  Bit Score: 40.40  E-value: 2.66e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 42565155   1026 CVYVMRRPD-KRLYIGQTDDLEGRIRAHRAKEGLQGSSFLY------LMVQG---KSMACQLETLLINQLHEQGY 1090
Cdd:pfam01541    3 GIYIIRNKDnKLLYVGSTKNLERRLNQHNAGKGAKYTRGKGvepfklIYLEEfptKSEALELEKYLIKLYRPNKY 77
PRK00329 PRK00329
GIY-YIG nuclease superfamily protein; Validated
 1026-1057 7.65e-03

GIY-YIG nuclease superfamily protein; Validated


Pssm-ID: 178979  Cd Length: 86  Bit Score: 36.82  E-value: 7.65e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 42565155  1026 CVYVMRRPDKRLYIGQTDDLEGRIRAHRAKEG 1057
Cdd:PRK00329    8 FLYLLRCADGSLYTGITTDVERRFAQHQSGKG 39
 
Name Accession Description Interval E-value
ABC_MutS_homologs cd03243
ATP-binding cassette domain of MutS homologs; The MutS protein initiates DNA mismatch repair ...
 748-934 8.75e-74

ATP-binding cassette domain of MutS homologs; The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.


Pssm-ID: 213210 [Multi-domain]  Cd Length: 202  Bit Score: 242.93  E-value: 8.75e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  748 VSSGTAVHNTVDMQS--LFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQ 825
Cdd:cd03243   14 TKGETFVPNDINLGSgrLLLITGPNMGGKSTYLRSIGLAVLLAQIGCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFM 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  826 VEMSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESLDTSGCLGIVSTHLHGIFSLPLTAKNITYKAMGAENV 905
Cdd:cd03243   94 AELLELKEILSLATPRSLVLIDELGRGTSTAEGLAIAYAVLEHLLEKGCRTLFATHFHELADLPEQVPGVKNLHMEELIT 173

                        170       180
                 ....*....|....*....|....*....
gi 42565155  906 EGQTKPTWKLTDGVCRESLAFETAKREGV 934
Cdd:cd03243  174 TGGLTFTYKLIDGICDPSYALQIAELAGL 202
MUTSac smart00534
ATPase domain of DNA mismatch repair MUTS family;
763-946 1.11e-54

ATPase domain of DNA mismatch repair MUTS family;


Pssm-ID: 197777 [Multi-domain]  Cd Length: 185  Bit Score: 188.15  E-value: 1.11e-54
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155     763 LFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQVEMSEIRSIVSQATSRS 842
Cdd:smart00534    1 VVIITGPNMGGKSTYLRQVALIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNATKNS 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155     843 LVLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIVSTHLHGIFSLPLTAKNITYKAMGAENVEGQTKPTWKLTDGVCR 921
Cdd:smart00534   81 LVLLDELGRGTSTYDGLAIAAAILEYLlEKIGARTLFATHYHELTKLADNHPGVRNLHMSALEETENITFLYKLKPGVAG 160

                           170       180
                    ....*....|....*....|....*
gi 42565155     922 ESLAFETAKREGVPESVIQRAEALY 946
Cdd:smart00534  161 KSYGIEVAKLAGLPKEVIERAKRIL 185
ABC_MSH6_euk cd03286
ATP-binding cassette domain of eukaryotic MutS6 homolog; The MutS protein initiates DNA ...
 740-942 4.45e-44

ATP-binding cassette domain of eukaryotic MutS6 homolog; The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.


Pssm-ID: 213253 [Multi-domain]  Cd Length: 218  Bit Score: 159.13  E-value: 4.45e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  740 GLSPYWFDVSSGTAVHNTVDM----QSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYD 815
Cdd:cd03286    5 LRHPCLNASTASSFVPNDVDLgatsPRILVLTGPNMGGKSTLLRTVCLAVIMAQMGMDVPAKSMRLSLVDRIFTRIGARD 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  816 SPVDGKSSFQVEMSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIVSTHLHGIFSLPLTAKN 894
Cdd:cd03286   85 DIMKGESTFMVELSETANILRHATPDSLVILDELGRGTSTHDGYAIAHAVLEYLvKKVKCLTLFSTHYHSLCDEFHEHGG 164

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 42565155  895 ITYKAMGAEnVEGQTKPT-------WKLTDGVCRESLAFETAKREGVPESVIQRA 942
Cdd:cd03286  165 VRLGHMACA-VKNESDPTirditflYKLVAGICPKSYGLYVALMAGIPDGVVERA 218
MutS_V pfam00488
MutS domain V; This domain is found in proteins of the MutS family (DNA mismatch repair ...
 764-946 9.89e-43

MutS domain V; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain V of Thermus aquaticus MutS as characterized in, which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters.


Pssm-ID: 425714 [Multi-domain]  Cd Length: 188  Bit Score: 154.27  E-value: 9.89e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    764 FLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQVEMSEIRSIVSQATSRSL 843
Cdd:pfam00488    1 LIITGPNMGGKSTYLRQVALIVLMAQIGSFVPAESAEIGIVDRIFTRIGASDDLAKGRSTFMVEMLETANILHNATDKSL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    844 VLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIVSTHLHGIFSLPLTAKNITYKAMGAENVEGQTKPTWKLTDGVCRE 922
Cdd:pfam00488   81 VILDELGRGTSTYDGLAIAWAVAEHLaEKIKARTLFATHYHELTKLAEKLPAVKNLHMAAVEDDDDIVFLYKVQPGAADK 160

                          170       180
                   ....*....|....*....|....
gi 42565155    923 SLAFETAKREGVPESVIQRAEALY 946
Cdd:pfam00488  161 SYGIHVAELAGLPESVVERAREIL 184
ABC_MutS1 cd03284
ATP-binding cassette domain of MutS1 homolog; The MutS protein initiates DNA mismatch repair ...
 748-942 7.42e-39

ATP-binding cassette domain of MutS1 homolog; The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.


Pssm-ID: 213251 [Multi-domain]  Cd Length: 216  Bit Score: 144.33  E-value: 7.42e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  748 VSSGTAVHNTVDM---QSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSF 824
Cdd:cd03284   14 LDNEPFVPNDTELdpeRQILLITGPNMAGKSTYLRQVALIALLAQIGSFVPASKAEIGVVDRIFTRIGASDDLAGGRSTF 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  825 QVEMSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIVSTHLHGIFSLPLTAKNITYKAMGAE 903
Cdd:cd03284   94 MVEMVETANILNNATERSLVLLDEIGRGTSTYDGLSIAWAIVEYLhEKIGAKTLFATHYHELTELEGKLPRVKNFHVAVK 173

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 42565155  904 NVEGQTKPTWKLTDGVCRESLAFETAKREGVPESVIQRA 942
Cdd:cd03284  174 EKGGGVVFLHKIVEGAADKSYGIEVARLAGLPEEVIERA 212
GIY-YIG_MSH cd10438
Catalytic GIY-YIG domain of eukaryotic DNA mismatch repair protein MutS homologs; This family ...
 1025-1094 1.70e-34

Catalytic GIY-YIG domain of eukaryotic DNA mismatch repair protein MutS homologs; This family represents a putative GIY-YIG nuclease domain C-terminally fused to the DNA-repair ATPase on a small group of eukaryotic DNA mismatch repair protein mutS homologs (MSH). The MSH proteins in this family do not have the zinc finger domain, but have a predicted mitochondrial localization. They might play roles in the recognition and repair of errors made during the replication of DNA. The prototype of this family is the protein encoded by the chloroplast mutator (CHM) locus from Arabidopsis thaliana. It is suggested that this protein could be involved in the maintenance of mitochondrial genome stability.


Pssm-ID: 198385  Cd Length: 72  Bit Score: 126.43  E-value: 1.70e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 42565155 1025 SCVYVMRRPDKRLYIGQTDDLEGRIRAHRAKEG--LQGSSFLYLMVQGKSMACQLETLLINQLHEQGYSLAN 1094
Cdd:cd10438    1 SCVYILRRGDGEYYVGETDNLSGRLEQHRASLGetLVISGFLYLLVGGKSEARSLESALIQQLQGQGANLAS 72
mutS1 TIGR01070
DNA mismatch repair protein MutS; [DNA metabolism, DNA replication, recombination, and repair]
 643-945 3.42e-34

DNA mismatch repair protein MutS; [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273427 [Multi-domain]  Cd Length: 840  Bit Score: 141.83  E-value: 3.42e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    643 GEEWFTTPKVEIALVRYHEASENAKARVLELLRELSVKLQTKINVLVFASMLLVISKALFSHACEGRRRKWVFPTlvgFS 722
Cdd:TIGR01070  482 NAERYITPELKEKEDKVLEAEGKILALEKELFEELRELLKKYLEALQEAARALAELDVLANLAEVAETLHYTRPR---FG 558

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    723 LDEGAKPLDGASrmkltglsPYWFDVSSGTAVHNTVDM---QSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESA 799
Cdd:TIGR01070  559 DDPQLRIREGRH--------PVVEQVLRTPFVPNDLEMahnRRMLLITGPNMGGKSTYMRQTALIALLAQIGSFVPAESA 630

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    800 CIPHFDSIMLHMKSYDSPVDGKSSFQVEMSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIV 878
Cdd:TIGR01070  631 ELPLFDRIFTRIGASDDLASGRSTFMVEMTEAANILHNATENSLVLFDEIGRGTSTYDGLALAWAIAEYLhEHIRAKTLF 710

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 42565155    879 STHLHGIFSLPLTAKNITYKAMGAENVEGQTKPTWKLTDGVCRESLAFETAKREGVPESVIQRAEAL 945
Cdd:TIGR01070  711 ATHYFELTALEESLPGLKNVHVAALEHNGTIVFLHQVLPGPASKSYGLAVAALAGLPKEVIARARQI 777
ABC_MSH3_euk cd03287
ATP-binding cassette domain of eukaryotic MutS3 homolog; The MutS protein initiates DNA ...
 765-942 6.97e-31

ATP-binding cassette domain of eukaryotic MutS3 homolog; The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.


Pssm-ID: 213254 [Multi-domain]  Cd Length: 222  Bit Score: 121.44  E-value: 6.97e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  765 LLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQVEMSEIRSIVSQATSRSLV 844
Cdd:cd03287   35 IITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNCTSRSLV 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  845 LIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIVSTHLHGI------FSLPLTAKNITY---KAMGAENVEGQTKPTWK 914
Cdd:cd03287  115 ILDELGRGTSTHDGIAIAYATLHYLlEEKKCLVLFVTHYPSLgeilrrFEGSIRNYHMSYlesQKDFETSDSQSITFLYK 194

                        170       180
                 ....*....|....*....|....*...
gi 42565155  915 LTDGVCRESLAFETAKREGVPESVIQRA 942
Cdd:cd03287  195 LVRGLASRSFGLNVARLAGLPKSIISRA 222
ABC_MutS2 cd03280
ATP-binding cassette domain of MutS2; MutS2 homologs in bacteria and eukaryotes. The MutS ...
 761-934 1.43e-30

ATP-binding cassette domain of MutS2; MutS2 homologs in bacteria and eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.


Pssm-ID: 213247 [Multi-domain]  Cd Length: 200  Bit Score: 119.66  E-value: 1.43e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  761 QSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESAC-IPHFDSIMLHMKSYDSPVDGKSSFQVEMSEIRSIVSQAT 839
Cdd:cd03280   28 KRVLVITGPNAGGKTVTLKTLGLLTLMAQSGLPIPAAEGSsLPVFENIFADIGDEQSIEQSLSTFSSHMKNIARILQHAD 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  840 SRSLVLIDEICRGTETAKGTCIAGSVVESLDTSGCLGIVSTHLHGIfslpltaKNITYKAMGAEN--VE--GQT-KPTWK 914
Cdd:cd03280  108 PDSLVLLDELGSGTDPVEGAALAIAILEELLERGALVIATTHYGEL-------KAYAYKREGVENasMEfdPETlKPTYR 180

                        170       180
                 ....*....|....*....|
gi 42565155  915 LTDGVCRESLAFETAKREGV 934
Cdd:cd03280  181 LLIGVPGRSNALEIARRLGL 200
ABC_MSH2_euk cd03285
ATP-binding cassette domain of eukaryotic MutS2 homolog; The MutS protein initiates DNA ...
 756-942 1.04e-29

ATP-binding cassette domain of eukaryotic MutS2 homolog; The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.


Pssm-ID: 213252 [Multi-domain]  Cd Length: 222  Bit Score: 117.86  E-value: 1.04e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  756 NTVDM----QSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQVEMSEI 831
Cdd:cd03285   21 NDVTLtrgkSRFLIITGPNMGGKSTYIRQIGVIVLMAQIGCFVPCDSADIPIVDCILARVGASDSQLKGVSTFMAEMLET 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  832 RSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESLDTS-GCLGIVSTHLHGIFSLPLTAKNITYKAMGA--ENVEGQ 908
Cdd:cd03285  101 AAILKSATENSLIIIDELGRGTSTYDGFGLAWAIAEYIATQiKCFCLFATHFHELTALADEVPNVKNLHVTAltDDASRT 180

                        170       180       190
                 ....*....|....*....|....*....|....
gi 42565155  909 TKPTWKLTDGVCRESLAFETAKREGVPESVIQRA 942
Cdd:cd03285  181 LTMLYKVEKGACDQSFGIHVAELANFPKEVIEMA 214
ABC_MSH5_euk cd03281
ATP-binding cassette domain of eukaryotic MutS5 homolog; The MutS protein initiates DNA ...
 759-934 1.80e-28

ATP-binding cassette domain of eukaryotic MutS5 homolog; The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.


Pssm-ID: 213248 [Multi-domain]  Cd Length: 213  Bit Score: 114.32  E-value: 1.80e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  759 DMQSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQVEMSEIRSIVSQA 838
Cdd:cd03281   27 GGPSIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPADSATIGLVDKIFTRMSSRESVSSGQSAFMIDLYQVSKALRLA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  839 TSRSLVLIDEICRGTETAKGTCIAGSVVESLDTSG--C-LGIVSTHLHGIF--SLPLTAKNITYKAM------GAENVEG 907
Cdd:cd03281  107 TRRSLVLIDEFGKGTDTEDGAGLLIATIEHLLKRGpeCpRVIVSTHFHELFnrSLLPERLKIKFLTMevllnpTSTSPNE 186

                        170       180
                 ....*....|....*....|....*..
gi 42565155  908 QTKPTWKLTDGVCRESLAFETAKREGV 934
Cdd:cd03281  187 DITYLYRLVPGLADTSFAIHCAKLAGI 213
PRK05399 PRK05399
DNA mismatch repair protein MutS; Provisional
 754-964 3.43e-27

DNA mismatch repair protein MutS; Provisional


Pssm-ID: 235444 [Multi-domain]  Cd Length: 854  Bit Score: 119.43  E-value: 3.43e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155   754 VHNTVDM---QSLFLLTGPNGGGKSSLLRSIcaaALLGI---SGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQVE 827
Cdd:PRK05399  597 VPNDCDLdeeRRLLLITGPNMAGKSTYMRQV---ALIVLlaqIGSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVE 673

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155   828 MSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIVSTHLHgifslPLTA--------KNITyk 898
Cdd:PRK05399  674 MTETANILNNATERSLVLLDEIGRGTSTYDGLSIAWAVAEYLhDKIGAKTLFATHYH-----ELTEleeklpgvKNVH-- 746

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42565155   899 aMGAENVEGQTKPTWKLTDGVCRESLAFETAKREGVPESVIQRAEAL--YLSVYAKDASAEVVKPDQI 964
Cdd:PRK05399  747 -VAVKEHGGDIVFLHKVVPGAADKSYGIHVAKLAGLPASVIKRAREIlaQLESASEKAKAASAEEDQL 813
ABC_MutS-like cd03283
ATP-binding cassette domain of MutS-like homolog; The MutS protein initiates DNA mismatch ...
 753-933 1.45e-26

ATP-binding cassette domain of MutS-like homolog; The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.


Pssm-ID: 213250 [Multi-domain]  Cd Length: 199  Bit Score: 108.16  E-value: 1.45e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  753 AVHNTVDM--QSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPhFDSIMLHMKSYDSPVDGKSSFQVEMSE 830
Cdd:cd03283   15 RVANDIDMekKNGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELP-PVKIFTSIRVSDDLRDGISYFYAELRR 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  831 IRSIVSQA--TSRSLVLIDEICRGTETAKGTCIAGSVVESLDTSGCLGIVSTHLHGIFSLPLTAKNITYKAMGAENVEGQ 908
Cdd:cd03283   94 LKEIVEKAkkGEPVLFLLDEIFKGTNSRERQAASAAVLKFLKNKNTIGIISTHDLELADLLDLDSAVRNYHFREDIDDNK 173

                        170       180
                 ....*....|....*....|....*
gi 42565155  909 TKPTWKLTDGVCRESLAFETAKREG 933
Cdd:cd03283  174 LIFDYKLKPGVSPTRNALRLMKKIG 198
MutS COG0249
DNA mismatch repair ATPase MutS [Replication, recombination and repair];
756-945 9.19e-26

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


Pssm-ID: 440019 [Multi-domain]  Cd Length: 861  Bit Score: 114.77  E-value: 9.19e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  756 NTVDM---QSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIM--------LHMksydspvdGKSSF 824
Cdd:COG0249  605 NDCDLdpdRRILLITGPNMAGKSTYMRQVALIVLLAQIGSFVPAESARIGIVDRIFtrvgasddLAR--------GQSTF 676

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  825 QVEMSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESL-DTSGCLGIVSTHLHgifslPLTA--------KNI 895
Cdd:COG0249  677 MVEMTETANILNNATERSLVLLDEIGRGTSTYDGLSIAWAVAEYLhDKIRARTLFATHYH-----ELTElaeklpgvKNY 751

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 42565155  896 TykaMGAENVEGQTKPTWKLTDGVCRESLAFETAKREGVPESVIQRAEAL 945
Cdd:COG0249  752 H---VAVKEWGGDIVFLHKVVPGPADRSYGIHVAKLAGLPASVIERAREI 798
MutS2 COG1193
dsDNA-specific endonuclease/ATPase MutS2 [Replication, recombination and repair];
765-945 1.10e-25

dsDNA-specific endonuclease/ATPase MutS2 [Replication, recombination and repair];


Pssm-ID: 440806 [Multi-domain]  Cd Length: 784  Bit Score: 114.47  E-value: 1.10e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  765 LLTGPNGGGKSSLLRSICAAALLGISGLMVPAESAC-IPHFDSIMlhmksydspVD-GK--------SSFQVEMSEIRSI 834
Cdd:COG1193  329 VITGPNTGGKTVTLKTVGLLTLMAQSGLPIPAAEGSeLPVFDNIF---------ADiGDeqsieqslSTFSSHMTNIVEI 399

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  835 VSQATSRSLVLIDEICRGTETAKGTCIAGSVVESLDTSGCLGIVSTHLHGIfslpltaKNITYKAMGAEN--VE--GQT- 909
Cdd:COG1193  400 LEKADENSLVLLDELGAGTDPQEGAALAIAILEELLERGARVVATTHYSEL-------KAYAYNTEGVENasVEfdVETl 472

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 42565155  910 KPTWKLTDGVCRESLAFETAKREGVPESVIQRAEAL 945
Cdd:COG1193  473 SPTYRLLIGVPGRSNAFEIARRLGLPEEIIERAREL 508
mutS2 TIGR01069
MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch ...
 658-991 1.31e-25

MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]


Pssm-ID: 130141 [Multi-domain]  Cd Length: 771  Bit Score: 114.15  E-value: 1.31e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    658 RYHEASENAKARVLELLRELSVKLQTKINVL-----VFASMLLVISKALFSHACEGRRRKWVFPTLVgfSLDEGAKPLdg 732
Cdd:TIGR01069  230 KLAQLKNEEECEIEKILRTLSEKVQEYLLELkflfkEFDFLDSLQARARYAKAVKGEFPMPSFTGKI--ILENARHPL-- 305

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    733 asrMKLTGLSPywFDVSSGTAvhntvdmQSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPA-ESACIPHFDSIMLHM 811
Cdd:TIGR01069  306 ---LKEPKVVP--FTLNLKFE-------KRVLAITGPNTGGKTVTLKTLGLLALMFQSGIPIPAnEHSEIPYFEEIFADI 373

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    812 KSYDSPVDGKSSFQVEMSEIRSIVSQATSRSLVLIDEICRGTETAKGTCIAGSVVESLDTSGCLGIVSTHlHGIFSLpLT 891
Cdd:TIGR01069  374 GDEQSIEQNLSTFSGHMKNISAILSKTTENSLVLFDELGAGTDPDEGSALAISILEYLLKQNAQVLITTH-YKELKA-LM 451

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    892 AKNITYKAMGAENVEGQTKPTWKLTDGVCRESLAFETAKREGVPESVIQRAEALYlsvyakdaSAEVVKPDQIITSSNnd 971
Cdd:TIGR01069  452 YNNEGVENASVLFDEETLSPTYKLLKGIPGESYAFEIAQRYGIPHFIIEQAKTFY--------GEFKEEINVLIEKLS-- 521

                          330       340
                   ....*....|....*....|
gi 42565155    972 qqiqkpvSSERSLEKDLAKA 991
Cdd:TIGR01069  522 -------ALEKELEQKNEHL 534
PRK00409 PRK00409
recombination and DNA strand exchange inhibitor protein; Reviewed
 767-991 7.00e-25

recombination and DNA strand exchange inhibitor protein; Reviewed


Pssm-ID: 234750 [Multi-domain]  Cd Length: 782  Bit Score: 111.84  E-value: 7.00e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155   767 TGPNGGGKSSLLRSICAAALLGISGLMVPA-ESACIPHFDSIMLHMksyDSPVDGK---SSFQVEMSEIRSIVSQATSRS 842
Cdd:PRK00409  333 TGPNTGGKTVTLKTLGLAALMAKSGLPIPAnEPSEIPVFKEIFADI---GDEQSIEqslSTFSGHMTNIVRILEKADKNS 409

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155   843 LVLIDEICRGTETAKGTCIAGSVVESLDTSGCLGIVSTHlHGifSLpltaknityKAMGAEN--VEG-------QT-KPT 912
Cdd:PRK00409  410 LVLFDELGAGTDPDEGAALAISILEYLRKRGAKIIATTH-YK--EL---------KALMYNRegVENasvefdeETlRPT 477

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 42565155   913 WKLTDGVCRESLAFETAKREGVPESVIQRAEALYlsvyakdaSAEVVKPDQIITSSnndqqiqkpVSSERSLEKDLAKA 991
Cdd:PRK00409  478 YRLLIGIPGKSNAFEIAKRLGLPENIIEEAKKLI--------GEDKEKLNELIASL---------EELERELEQKAEEA 539
ABC_MSH4_euk cd03282
ATP-binding cassette domain of eukaryotic MutS4 homolog; The MutS protein initiates DNA ...
 757-881 5.67e-22

ATP-binding cassette domain of eukaryotic MutS4 homolog; The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.


Pssm-ID: 213249 [Multi-domain]  Cd Length: 204  Bit Score: 95.15  E-value: 5.67e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  757 TVDMQSLFLLTGPNGGGKSSLLRSICAAALLGISGLMVPAESACIPHFDSIMLHMKSYDSPVDGKSSFQVEMSEIRSIVS 836
Cdd:cd03282   25 TRGSSRFHIITGPNMSGKSTYLKQIALLAIMAQIGCFVPAEYATLPIFNRLLSRLSNDDSMERNLSTFASEMSETAYILD 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 42565155  837 QATSRSLVLIDEICRGTETAKGTCIAGSVVESLDTSGCLGIVSTH 881
Cdd:cd03282  105 YADGDSLVLIDELGRGTSSADGFAISLAILECLIKKESTVFFATH 149
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 761-897 3.07e-15

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


Pssm-ID: 213194 [Multi-domain]  Cd Length: 162  Bit Score: 74.32  E-value: 3.07e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  761 QSLFLLTGPNGGGKSSLLRSICAAALL----------GISGLMVPAESACIPHFdsimlhmksydspVDGKSSFQVEMSE 830
Cdd:cd03227   21 GSLTIITGPNGSGKSTILDAIGLALGGaqsatrrrsgVKAGCIVAAVSAELIFT-------------RLQLSGGEKELSA 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 42565155  831 IRSIVSQAT--SRSLVLIDEICRGTETAKGTCIAGSVVESLDtSGCLGIVSTHLHGIFSLPLTAKNITY 897
Cdd:cd03227   88 LALILALASlkPRPLYILDEIDRGLDPRDGQALAEAILEHLV-KGAQVIVITHLPELAELADKLIHIKK 155
MutS_I pfam01624
MutS domain I; This domain is found in proteins of the MutS family (DNA mismatch repair ...
 126-226 3.65e-12

MutS domain I; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with globular domain I, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in.


Pssm-ID: 426350 [Multi-domain]  Cd Length: 113  Bit Score: 64.14  E-value: 3.65e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155    126 WEMlqfKSRFPREVLLCRVGEFYEAIGIDACILVEYAGLN--PFGGLRSDSIPKAGCPIMNLRQTLDDLTRNGYSVCIVE 203
Cdd:pfam01624    8 LEL---KSKYPDAVLFFRVGDFYELFGEDAEIAARELGITltVRKGGSGKRIPMAGVPEHAFERYARRLVNKGYKVAICE 84

                           90       100
                   ....*....|....*....|...
gi 42565155    204 EVQGPTPARSRKGRFISGHAHPG 226
Cdd:pfam01624   85 QTETPAEAKGVVKREVVRVVTPG 107
GIY-YIG_SF cd00719
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ...
 1027-1085 8.91e-08

GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions.


Pssm-ID: 198380 [Multi-domain]  Cd Length: 69  Bit Score: 50.06  E-value: 8.91e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42565155 1027 VYVMRRPDKRL-YIGQTDDLEGRIRAHRAK------EGLQGSSFLYLMV--QGKSMACQLETLLINQL 1085
Cdd:cd00719    2 VYVLYDEDNGLiYVGQTKNLRNRIKEHLRKqrsdwtKGLKPFEILYLEVapEAESELLDLEAALIKKL 69
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
1026-1057 1.08e-06

Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 47.43  E-value: 1.08e-06
                         10        20        30
                 ....*....|....*....|....*....|...
gi 42565155 1026 CVYVMR-RPDKRLYIGQTDDLEGRIRAHRAKEG 1057
Cdd:COG2827    4 YVYILRcADNGTLYTGVTNDLERRLAEHNSGKG 36
CcmA COG4133
ABC-type transport system involved in cytochrome c biogenesis, ATPase component ...
 738-797 4.95e-05

ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443308 [Multi-domain]  Cd Length: 206  Bit Score: 45.55  E-value: 4.95e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  738 LTGLSpywFDVSSGTAVHntvdmqslflLTGPNGGGKSSLLRSICaaallgisGLMVPAE 797
Cdd:COG4133   18 FSGLS---FTLAAGEALA----------LTGPNGSGKTTLLRILA--------GLLPPSA 56
ABC_ATPase cd00267
ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large ...
 763-881 2.04e-04

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


Pssm-ID: 213179 [Multi-domain]  Cd Length: 157  Bit Score: 43.00  E-value: 2.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  763 LFLLTGPNGGGKSSLLRSICaaallgisGLMVPAESACIphfdsimlhmksydspVDGKSSFQVEMSEIR---SIVSQ-- 837
Cdd:cd00267   27 IVALVGPNGSGKSTLLRAIA--------GLLKPTSGEIL----------------IDGKDIAKLPLEELRrriGYVPQls 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 42565155  838 -------------ATSRSLVLIDEICRGTETAKGTCIAGSVVESLDtSGCLGIVSTH 881
Cdd:cd00267   83 ggqrqrvalaralLLNPDLLLLDEPTSGLDPASRERLLELLRELAE-EGRTVIIVTH 138
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 1026-1090 2.66e-04

GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.


Pssm-ID: 426314 [Multi-domain]  Cd Length: 78  Bit Score: 40.40  E-value: 2.66e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 42565155   1026 CVYVMRRPD-KRLYIGQTDDLEGRIRAHRAKEGLQGSSFLY------LMVQG---KSMACQLETLLINQLHEQGY 1090
Cdd:pfam01541    3 GIYIIRNKDnKLLYVGSTKNLERRLNQHNAGKGAKYTRGKGvepfklIYLEEfptKSEALELEKYLIKLYRPNKY 77
GIY-YIG_SLX1_like cd10449
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 1027-1057 5.29e-04

Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its homologs; Structure-specific endonuclease subunit SLX1 is a highly conserved protein from yeast to human, with an N-terminal GIY-YIG endonuclease domain and a C-terminal PHD-type zinc finger postulated to mediate protein-protein or protein-DNA interaction. SLX1 forms active heterodimeric complexes with its SLX4 partner, which has additional roles in the DNA damage response that are distinct from the function of the heterodimeric SLX1-SLX4 nuclease. In yeast, the SLX1-SLX4 complex functions as a 5' flap endonuclease that maintains ribosomal DNA copy number, where SLX1 and SLX4 are shown to be catalytic and regulatory subunits, respectively. This endonuclease introduces single-strand cuts in duplex DNA on the 3' side of junctions with single-strand DNA. In addition to 5' flap endonuclease activity, human SLX1-SLX4 complex has been identified as a Holliday junction resolvase that promotes symmetrical cleavage of static and migrating Holliday junctions. SLX1 also associates with MUS81, EME1, C20orf94, PLK1, and ERCC1. Some eukaryotic SLX1 homologs lack the zinc finger domain, but possess intrinsically unstructured extensions of unknown function. These unstructured segments might be involved in interactions with other proteins.


Pssm-ID: 198396  Cd Length: 67  Bit Score: 39.50  E-value: 5.29e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 42565155 1027 VYVMRRP-DKRLYIGQTDDLEGRIRAHRAKEG 1057
Cdd:cd10449    2 VYILYSEkLDRYYIGYTSDLERRLEQHNSGKS 33
PRK13539 PRK13539
cytochrome c biogenesis protein CcmA; Provisional
 738-797 6.13e-04

cytochrome c biogenesis protein CcmA; Provisional


Pssm-ID: 237421 [Multi-domain]  Cd Length: 207  Bit Score: 42.55  E-value: 6.13e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155   738 LTGLSpywFDVSSGTAVhntvdmqslfLLTGPNGGGKSSLLRSicaaallgISGLMVPAE 797
Cdd:PRK13539   18 FSGLS---FTLAAGEAL----------VLTGPNGSGKTTLLRL--------IAGLLPPAA 56
GIY-YIG_unchar_3 cd10448
GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; The family includes ...
 1025-1063 9.14e-04

GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; The family includes a group of uncharacterized bacterial proteins with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC.


Pssm-ID: 198395  Cd Length: 87  Bit Score: 39.40  E-value: 9.14e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 42565155 1025 SCVYVM-RRPDKRLYIGQTDDLEGRIRAHraKEGLqGSSF 1063
Cdd:cd10448    1 YYVYILaNKRNGTLYIGVTSDLIRRIYEH--KEGL-GSGF 37
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
763-784 1.18e-03

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 41.53  E-value: 1.18e-03
                         10        20
                 ....*....|....*....|..
gi 42565155  763 LFLLTGPNGGGKSSLLRSICAA 784
Cdd:COG0419   25 LNLIVGPNGAGKSTILEAIRYA 46
GIY-YIG_UPF0213 cd10456
The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific ...
 1026-1057 1.29e-03

The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; This family contains a group of uncharacterized proteins found mainly in bacteria and several in dsDNA viruses. Although their function roles have not been recognized, these proteins show significant sequence similarities with the N-terminal GIY-YIG endonuclease domain of structure-specific endonuclease subunit SLX1, which binds another structure-specific endonuclease subunit SLX4 to form an active heterodimeric SLX1-SLX4 complex. This complex functions as a 5' flap endonuclease in yeast, and has also been identified as a Holliday junction resolvase in human.


Pssm-ID: 198403  Cd Length: 68  Bit Score: 38.16  E-value: 1.29e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 42565155 1026 CVYVMRRPDKRLYIGQTDDLEGRIRAHRAKEG 1057
Cdd:cd10456    2 YVYILRCADGSLYTGITTDLERRLAEHNSGKG 33
PRK13538 PRK13538
cytochrome c biogenesis heme-transporting ATPase CcmA;
735-797 1.55e-03

cytochrome c biogenesis heme-transporting ATPase CcmA;


Pssm-ID: 184125 [Multi-domain]  Cd Length: 204  Bit Score: 40.94  E-value: 1.55e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42565155   735 RMKLTGLSpywFDVSSGTAVHntvdmqslflLTGPNGGGKSSLLRSICaaallgisGLMVPAE 797
Cdd:PRK13538   14 RILFSGLS---FTLNAGELVQ----------IEGPNGAGKTSLLRILA--------GLARPDA 55
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 764-849 2.16e-03

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 39.82  E-value: 2.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42565155  764 FLLTGPNGGGKSSLLRSIcaAALLGISGLMVpaesaciphfdsIMLHMKSYDSPVDGKSSFQVEMSEIRSIVSQATSRSL 843
Cdd:cd00009   22 LLLYGPPGTGKTTLARAI--ANELFRPGAPF------------LYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGV 87


                 ....*.
gi 42565155  844 VLIDEI 849
Cdd:cd00009   88 LFIDEI 93
AAA_23 pfam13476
AAA domain;
763-784 3.18e-03

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 40.17  E-value: 3.18e-03
                           10        20
                   ....*....|....*....|..
gi 42565155    763 LFLLTGPNGGGKSSLLRSICAA 784
Cdd:pfam13476   20 LTLITGPNGSGKTTILDAIKLA 41
PRK00329 PRK00329
GIY-YIG nuclease superfamily protein; Validated
 1026-1057 7.65e-03

GIY-YIG nuclease superfamily protein; Validated


Pssm-ID: 178979  Cd Length: 86  Bit Score: 36.82  E-value: 7.65e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 42565155  1026 CVYVMRRPDKRLYIGQTDDLEGRIRAHRAKEG 1057
Cdd:PRK00329    8 FLYLLRCADGSLYTGITTDVERRFAQHQSGKG 39
ABC_sbcCD cd03279
ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are ...
 728-784 9.54e-03

ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.


Pssm-ID: 213246 [Multi-domain]  Cd Length: 213  Bit Score: 38.79  E-value: 9.54e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 42565155  728 KPLdgasRMKLTGLSPYW----FDVSSgtavhntVDMQSLFLLTGPNGGGKSSLLRSICAA 784
Cdd:cd03279    2 KPL----KLELKNFGPFReeqvIDFTG-------LDNNGLFLICGPTGAGKSTILDAITYA 51
 
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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