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Conserved domains on  [gi|2074743980|gb|KAG8389478|]
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hypothetical protein BUALT_Bualt02G0233600 [Buddleja alternifolia]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
 15-327 6.90e-100

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: 317.66  E-value: 6.90e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   15 IRPINKGVVHRICAGQVILDLSSAVKELVENSLDAGASSVEIALKDYGQDSFQVIDNGSGISPLNFRVLALKHHTSKLLD 94
Cdd:TIGR00585    3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   95 FPDLQSLTTFGFRGEALSSLCALGDLTVETRTM-NEVVATHLTYDrSGLLTAERKIARQVGTTVTVKKLFSNLPVRcKEF 173
Cdd:TIGR00585   83 FEDLERIETLGFRGEALASISSVSRLTITTKTSaADGLAYQALLE-GGMIESIKPAPRPVGTTVEVRDLFYNLPVR-RKF 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  174 HRNIRKEYGKLISLLNAYALIAKGVRLVCTNStGKNVRSvvLKTQGSGCLKDNII-TVFGMSTFTCLEPVRLSISDGCVV 252
Cdd:TIGR00585  161 LKSPKKEFRKILDVLQRYALIHPDISFSLTHD-GKKVLQ--LSTKPNQSTKENRIrSVFGTAVLRKLIPLDEWEDLDLQL 237

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2074743980  253 EGFVSKSGYGSGRNIGDrQFFFVNGRPVDMPKVGKLVNELYRGANSK-QYPIAIMNFSIPTQAYDVNVTPDKRKIF 327
Cdd:TIGR00585  238 EGFISQPNVTRSRRSGW-QFLFINGRPVELKLLLKAIREVYHEYLPKgQYPVFVLNLEIDPELVDVNVHPDKKEVR 312
LSm4 cd01723
Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 925-1000 1.02e-54

Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


:

Pssm-ID: 212470 [Multi-domain]  Cd Length: 76  Bit Score: 183.93  E-value: 1.02e-54
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2074743980  925 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVID 1000
Cdd:cd01723      1 LPLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRGNTIKYLRLPDEVID 76
MutL_C smart00853
MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair ...
 749-905 9.05e-39

MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation.


:

Pssm-ID: 214857 [Multi-domain]  Cd Length: 140  Bit Score: 140.95  E-value: 9.05e-39
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   749 VIGQFNLGFIIGKLDQDLFIVDQHAADEKYNYERL-SQSTILNQQPLLRPLKMELSPEEEIVISMHMDTFRKNGFLLEED 827
Cdd:smart00853    1 ALGQVAGTYILAEREDGLYLLDQHAAHERILYEQLlKQAGGLESQPLLIPVRLELSPQEAALLEEHLELLRQLGFELEIF 80

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2074743980   828 ihapSGHRFKLKAVPFSKNVTFGIADVKELISILsdshgdcsmigtyrSDTADSVCPPKVRAMLASRACRSSVMIGDP 905
Cdd:smart00853   81 ----GPQSLILRSVPALLRQQNLQKLIPELLDLL--------------SDEEENARPSRLEALLASLACRSAIRAGDA 140
 
Name Accession Description Interval E-value
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
 15-327 6.90e-100

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: 317.66  E-value: 6.90e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   15 IRPINKGVVHRICAGQVILDLSSAVKELVENSLDAGASSVEIALKDYGQDSFQVIDNGSGISPLNFRVLALKHHTSKLLD 94
Cdd:TIGR00585    3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   95 FPDLQSLTTFGFRGEALSSLCALGDLTVETRTM-NEVVATHLTYDrSGLLTAERKIARQVGTTVTVKKLFSNLPVRcKEF 173
Cdd:TIGR00585   83 FEDLERIETLGFRGEALASISSVSRLTITTKTSaADGLAYQALLE-GGMIESIKPAPRPVGTTVEVRDLFYNLPVR-RKF 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  174 HRNIRKEYGKLISLLNAYALIAKGVRLVCTNStGKNVRSvvLKTQGSGCLKDNII-TVFGMSTFTCLEPVRLSISDGCVV 252
Cdd:TIGR00585  161 LKSPKKEFRKILDVLQRYALIHPDISFSLTHD-GKKVLQ--LSTKPNQSTKENRIrSVFGTAVLRKLIPLDEWEDLDLQL 237

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2074743980  253 EGFVSKSGYGSGRNIGDrQFFFVNGRPVDMPKVGKLVNELYRGANSK-QYPIAIMNFSIPTQAYDVNVTPDKRKIF 327
Cdd:TIGR00585  238 EGFISQPNVTRSRRSGW-QFLFINGRPVELKLLLKAIREVYHEYLPKgQYPVFVLNLEIDPELVDVNVHPDKKEVR 312
HATPase_MutL-MLH-PMS-like cd16926
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ...
 22-210 7.58e-79

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: 255.82  E-value: 7.58e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   22 VVHRICAGQVILDLSSAVKELVENSLDAGASSVEIALKDYGQDSFQVIDNGSGISPLNFRVLALKHHTSKLLDFPDLQSL 101
Cdd:cd16926      1 VVNKIAAGEVIERPASVVKELVENSIDAGATRIDVEIEEGGLKLIRVTDNGSGISREDLELAFERHATSKISSFEDLFSI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  102 TTFGFRGEALSSLCALGDLTVETRTMNEVVATHLTYDRSGLLTAERKIARQVGTTVTVKKLFSNLPVRCKEFhRNIRKEY 181
Cdd:cd16926     81 TTLGFRGEALASIASVSRLTITTRTADDDVGTRLVVDGGGIIEEVKPAAAPVGTTVTVRDLFYNTPARRKFL-KSPKTEL 159

                          170       180
                   ....*....|....*....|....*....
gi 2074743980  182 GKLISLLNAYALIAKGVRLVCTNsTGKNV 210
Cdd:cd16926    160 SKILDLVQRLALAHPDVSFSLTH-DGKLV 187
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
12-344 1.35e-73

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


Pssm-ID: 440092 [Multi-domain]  Cd Length: 515  Bit Score: 253.04  E-value: 1.35e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   12 SRIIRPINKGVVHRICAGQVILDLSSAVKELVENSLDAGASSVEIALKDYGQDSFQVIDNGSGISP--LnfrVLALKHH- 88
Cdd:COG0323      1 MPKIRLLPDELANQIAAGEVVERPASVVKELVENAIDAGATRIEVEIEEGGKSLIRVTDNGCGMSPedL---PLAFERHa 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   89 TSKLLDFPDLQSLTTFGFRGEALSSLCALGDLTVETRTMNEVVATHLTYDrSGLLTAERKIARQVGTTVTVKKLFSNLPV 168
Cdd:COG0323     78 TSKIRSAEDLFRIRTLGFRGEALASIASVSRLTLTTRTAGAELGTRIEVE-GGKVVEVEPAAAPKGTTVEVRDLFFNTPA 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  169 RCKeFHRNIRKEYGKLISLLNAYALIAKGVRLVCTNStGKnvrsVVLKTQGSGCLKDNIITVFGMSTFTCLEPVRLSiSD 248
Cdd:COG0323    157 RRK-FLKSDATELAHITDVVRRLALAHPDIAFTLIHN-GR----EVFQLPGAGDLLQRIAAIYGREFAENLLPVEAE-RE 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  249 GCVVEGFVSKSGYgsGRNIGDRQFFFVNGRPVDMPKVGKLVNELYRGANSK-QYPIAIMNFSIPTQAYDVNVTPDKRKIF 327
Cdd:COG0323    230 GLRLSGYIGKPEF--SRSNRDYQYFFVNGRPVRDKLLSHAVREAYRDLLPKgRYPVAVLFLELDPELVDVNVHPTKTEVR 307

                          330
                   ....*....|....*..
gi 2074743980  328 FSDENAILQSLREALEK 344
Cdd:COG0323    308 FRDEREVYDLVRSAVRE 324
mutL PRK00095
DNA mismatch repair endonuclease MutL;
13-388 1.55e-60

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 218.93  E-value: 1.55e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   13 RIIRPINKGVVHRICAGQVILDLSSAVKELVENSLDAGASSVEIALKDYGQDSFQVIDNGSGISP--LnfrVLALK-HHT 89
Cdd:PRK00095     1 MPIQLLPPQLANQIAAGEVVERPASVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNGCGISKedL---ALALArHAT 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   90 SKLLDFPDLQSLTTFGFRGEALSSLCALGDLTVETRTMNEVVATHLTYDrSGLLTAERKIARQVGTTVTVKKLFSNLPVR 169
Cdd:PRK00095    78 SKIASLDDLEAIRTLGFRGEALPSIASVSRLTLTSRTADAAEGWQIVYE-GGEIVEVKPAAHPVGTTIEVRDLFFNTPAR 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  170 CKeFHRNIRKEYGKLISLLNAYALIAKGVRLVCTNsTGKnvrsVVLKTQGSGCLKDNIITVFGMSTFTCLEPVRLSiSDG 249
Cdd:PRK00095   157 RK-FLKSEKTELGHIDDVVNRLALAHPDVAFTLTH-NGK----LVLQTRGAGQLLQRLAAILGREFAENALPIDAE-HGD 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  250 CVVEGFVSKSGYGSGRNigDRQFFFVNGRPVDMpkvgKLVN---------ELYRGanskQYPIAIMNFSIPTQAYDVNVT 320
Cdd:PRK00095   230 LRLSGYVGLPTLSRANR--DYQYLFVNGRYVRD----KLLNhairqayhdLLPRG----RYPAFVLFLELDPHQVDVNVH 299

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2074743980  321 PDKRKIFFSDENA----ILQSLREALEKIYSSNQASYSVNRVEELNEENLASNIGSLRERSQLPSKQLSPDS 388
Cdd:PRK00095   300 PAKHEVRFRDERLvhdlIVQAIQEALAQSGLIPAAAGANQVLEPAEPEPLPLQQTPLYASGSSPPASSPSSA 371
LSm4 cd01723
Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 925-1000 1.02e-54

Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212470 [Multi-domain]  Cd Length: 76  Bit Score: 183.93  E-value: 1.02e-54
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2074743980  925 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVID 1000
Cdd:cd01723      1 LPLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRGNTIKYLRLPDEVID 76
MutL_C smart00853
MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair ...
 749-905 9.05e-39

MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation.


Pssm-ID: 214857 [Multi-domain]  Cd Length: 140  Bit Score: 140.95  E-value: 9.05e-39
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   749 VIGQFNLGFIIGKLDQDLFIVDQHAADEKYNYERL-SQSTILNQQPLLRPLKMELSPEEEIVISMHMDTFRKNGFLLEED 827
Cdd:smart00853    1 ALGQVAGTYILAEREDGLYLLDQHAAHERILYEQLlKQAGGLESQPLLIPVRLELSPQEAALLEEHLELLRQLGFELEIF 80

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2074743980   828 ihapSGHRFKLKAVPFSKNVTFGIADVKELISILsdshgdcsmigtyrSDTADSVCPPKVRAMLASRACRSSVMIGDP 905
Cdd:smart00853   81 ----GPQSLILRSVPALLRQQNLQKLIPELLDLL--------------SDEEENARPSRLEALLASLACRSAIRAGDA 140
MutL_C pfam08676
MutL C terminal dimerization domain; MutL and MutS are key components of the DNA repair ...
 750-906 5.47e-35

MutL C terminal dimerization domain; MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognizes mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerization.


Pssm-ID: 430147  Cd Length: 145  Bit Score: 130.42  E-value: 5.47e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  750 IGQFNLGFIIGKLDQDLFIVDQHAADEKYNYERLSQST---ILNQQPLLRPLKMELSPEEEIVISMHMDTFRKNGFLLEE 826
Cdd:pfam08676    4 LGQVHGTYILAENEDGLYLIDQHAAHERILYEKLKRALaegGLAAQPLLIPLVLELSPEEAALLEEHKEELAQLGFELEE 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  827 dihaPSGHRFKLKAVPfsknVTFGIADVKELISilsdshgdcSMIGTYRSDTADSVcPPKVRAMLASRACRSSVMIGDPL 906
Cdd:pfam08676   84 ----FGPNSVIVRSVP----ALLRQQNLQELIR---------ELLDELAEKGGSSL-EESLEELLATMACHSAVRAGRRL 145
DNA_mis_repair pfam01119
DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain ...
 228-346 4.62e-28

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: 109.51  E-value: 4.62e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  228 ITVFGMSTFTCLEPVRlSISDGCVVEGFVSKSGYGSGRNigDRQFFFVNGRPVDMPKVGKLVNELYRGA-NSKQYPIAIM 306
Cdd:pfam01119    1 AAIYGKEFAENLLPIE-KEDDGLRLSGYISKPTLSRSNR--DYQYLFVNGRPVRDKLLSHAIREAYRDLlPKGRYPVAVL 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2074743980  307 NFSIPTQAYDVNVTPDKRKIFFSDENAILQSLREALEKIY 346
Cdd:pfam01119   78 FLEIDPELVDVNVHPTKREVRFRDEREVYDFIKEALREAL 117
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
749-914 7.00e-23

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


Pssm-ID: 440092 [Multi-domain]  Cd Length: 515  Bit Score: 103.97  E-value: 7.00e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  749 VIGQFNLGFIIGKLDQDLFIVDQHAADEKYNYERLSQ---STILNQQPLLRPLKMELSPEEEIVISMHMDTFRKNGFLLE 825
Cdd:COG0323    330 ALGQLHGTYILAENEDGLVLIDQHAAHERILYERLKKalaEGGVASQPLLIPETLELSPAEAALLEEHLEELARLGFEIE 409

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  826 EDihapSGHRFKLKAVPfsknVTFGIADVKELI-SILSD--SHGDCSMIGTYRsdtadsvcppkvRAMLASRACRSSVMI 902
Cdd:COG0323    410 PF----GPNTVAVRAVP----ALLGEGDAEELLrDLLDElaEEGSSESLEELR------------EELLATMACHGAIKA 469

                          170
                   ....*....|..
gi 2074743980  903 GDPLGRNEMHKL 914
Cdd:COG0323    470 GRRLSLEEMNAL 481
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 928-994 7.79e-21

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 87.17  E-value: 7.79e-21
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074743980   928 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRV 994
Cdd:smart00651    1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67
mutL PRK00095
DNA mismatch repair endonuclease MutL;
698-914 1.21e-19

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 94.51  E-value: 1.21e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  698 TSERMKLERGFAAASLELSQLENEEGKAKALAAATIELERLFKKEDFEQMKVIGQFNLGFIIGKLDQDLFIVDQHAADEK 777
Cdd:PRK00095   382 ESSAEKNPLQPNASQSEAAAAASAEAAAAAPAAAPEPAEAAEEADSFPLGYALGQLHGTYILAENEDGLYLVDQHAAHER 461

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  778 YNYERL---SQSTILNQQPLLRPLKMELSPEEEIVISMHMDTFRKNGFLLEEdihaPSGHRFKLKAVPfsknVTFGIADV 854
Cdd:PRK00095   462 LLYEQLkdkLAEVGLASQPLLIPLVLELSEDEADRLEEHKELLARLGLELEP----FGPNSFAVREVP----ALLGQQEL 533

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2074743980  855 KELI-SILSDSHGDcsmigtyrsdtaDSVCPPKVRAMLASRACRSSVMIGDPLGRNEMHKL 914
Cdd:PRK00095   534 EELIrDLLDELAEE------------GDSDTLKERELLATMACHGAIRAGRRLTLEEMNAL 582
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 928-994 2.00e-15

LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.


Pssm-ID: 426258  Cd Length: 66  Bit Score: 71.77  E-value: 2.00e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074743980  928 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFwRMPECYIRGNTIKYLRV 994
Cdd:pfam01423    1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVR-KLGLVLIRGNNIVLISP 66
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
923-989 7.19e-08

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 50.57  E-value: 7.19e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074743980  923 TMLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVIcTSKDGDRFWRMPECYIRGNTI 989
Cdd:COG1958      2 SERPLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAE-EIDDGEVVRKLGTVVIRGDNV 67
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 35-77 9.02e-03

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


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 37.24  E-value: 9.02e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 2074743980    35 LSSAVKELVENSLDAGASSVEIAL---KDYGQDSFQVIDNGSGISP 77
Cdd:smart00387    6 LRQVLSNLLDNAIKYTPEGGRITVtleRDGDHVEITVEDNGPGIPP 51
 
Name Accession Description Interval E-value
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
 15-327 6.90e-100

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: 317.66  E-value: 6.90e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   15 IRPINKGVVHRICAGQVILDLSSAVKELVENSLDAGASSVEIALKDYGQDSFQVIDNGSGISPLNFRVLALKHHTSKLLD 94
Cdd:TIGR00585    3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   95 FPDLQSLTTFGFRGEALSSLCALGDLTVETRTM-NEVVATHLTYDrSGLLTAERKIARQVGTTVTVKKLFSNLPVRcKEF 173
Cdd:TIGR00585   83 FEDLERIETLGFRGEALASISSVSRLTITTKTSaADGLAYQALLE-GGMIESIKPAPRPVGTTVEVRDLFYNLPVR-RKF 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  174 HRNIRKEYGKLISLLNAYALIAKGVRLVCTNStGKNVRSvvLKTQGSGCLKDNII-TVFGMSTFTCLEPVRLSISDGCVV 252
Cdd:TIGR00585  161 LKSPKKEFRKILDVLQRYALIHPDISFSLTHD-GKKVLQ--LSTKPNQSTKENRIrSVFGTAVLRKLIPLDEWEDLDLQL 237

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2074743980  253 EGFVSKSGYGSGRNIGDrQFFFVNGRPVDMPKVGKLVNELYRGANSK-QYPIAIMNFSIPTQAYDVNVTPDKRKIF 327
Cdd:TIGR00585  238 EGFISQPNVTRSRRSGW-QFLFINGRPVELKLLLKAIREVYHEYLPKgQYPVFVLNLEIDPELVDVNVHPDKKEVR 312
HATPase_MutL-MLH-PMS-like cd16926
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ...
 22-210 7.58e-79

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: 255.82  E-value: 7.58e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   22 VVHRICAGQVILDLSSAVKELVENSLDAGASSVEIALKDYGQDSFQVIDNGSGISPLNFRVLALKHHTSKLLDFPDLQSL 101
Cdd:cd16926      1 VVNKIAAGEVIERPASVVKELVENSIDAGATRIDVEIEEGGLKLIRVTDNGSGISREDLELAFERHATSKISSFEDLFSI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  102 TTFGFRGEALSSLCALGDLTVETRTMNEVVATHLTYDRSGLLTAERKIARQVGTTVTVKKLFSNLPVRCKEFhRNIRKEY 181
Cdd:cd16926     81 TTLGFRGEALASIASVSRLTITTRTADDDVGTRLVVDGGGIIEEVKPAAAPVGTTVTVRDLFYNTPARRKFL-KSPKTEL 159

                          170       180
                   ....*....|....*....|....*....
gi 2074743980  182 GKLISLLNAYALIAKGVRLVCTNsTGKNV 210
Cdd:cd16926    160 SKILDLVQRLALAHPDVSFSLTH-DGKLV 187
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
12-344 1.35e-73

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


Pssm-ID: 440092 [Multi-domain]  Cd Length: 515  Bit Score: 253.04  E-value: 1.35e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   12 SRIIRPINKGVVHRICAGQVILDLSSAVKELVENSLDAGASSVEIALKDYGQDSFQVIDNGSGISP--LnfrVLALKHH- 88
Cdd:COG0323      1 MPKIRLLPDELANQIAAGEVVERPASVVKELVENAIDAGATRIEVEIEEGGKSLIRVTDNGCGMSPedL---PLAFERHa 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   89 TSKLLDFPDLQSLTTFGFRGEALSSLCALGDLTVETRTMNEVVATHLTYDrSGLLTAERKIARQVGTTVTVKKLFSNLPV 168
Cdd:COG0323     78 TSKIRSAEDLFRIRTLGFRGEALASIASVSRLTLTTRTAGAELGTRIEVE-GGKVVEVEPAAAPKGTTVEVRDLFFNTPA 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  169 RCKeFHRNIRKEYGKLISLLNAYALIAKGVRLVCTNStGKnvrsVVLKTQGSGCLKDNIITVFGMSTFTCLEPVRLSiSD 248
Cdd:COG0323    157 RRK-FLKSDATELAHITDVVRRLALAHPDIAFTLIHN-GR----EVFQLPGAGDLLQRIAAIYGREFAENLLPVEAE-RE 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  249 GCVVEGFVSKSGYgsGRNIGDRQFFFVNGRPVDMPKVGKLVNELYRGANSK-QYPIAIMNFSIPTQAYDVNVTPDKRKIF 327
Cdd:COG0323    230 GLRLSGYIGKPEF--SRSNRDYQYFFVNGRPVRDKLLSHAVREAYRDLLPKgRYPVAVLFLELDPELVDVNVHPTKTEVR 307

                          330
                   ....*....|....*..
gi 2074743980  328 FSDENAILQSLREALEK 344
Cdd:COG0323    308 FRDEREVYDLVRSAVRE 324
mutL PRK00095
DNA mismatch repair endonuclease MutL;
13-388 1.55e-60

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 218.93  E-value: 1.55e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   13 RIIRPINKGVVHRICAGQVILDLSSAVKELVENSLDAGASSVEIALKDYGQDSFQVIDNGSGISP--LnfrVLALK-HHT 89
Cdd:PRK00095     1 MPIQLLPPQLANQIAAGEVVERPASVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNGCGISKedL---ALALArHAT 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   90 SKLLDFPDLQSLTTFGFRGEALSSLCALGDLTVETRTMNEVVATHLTYDrSGLLTAERKIARQVGTTVTVKKLFSNLPVR 169
Cdd:PRK00095    78 SKIASLDDLEAIRTLGFRGEALPSIASVSRLTLTSRTADAAEGWQIVYE-GGEIVEVKPAAHPVGTTIEVRDLFFNTPAR 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  170 CKeFHRNIRKEYGKLISLLNAYALIAKGVRLVCTNsTGKnvrsVVLKTQGSGCLKDNIITVFGMSTFTCLEPVRLSiSDG 249
Cdd:PRK00095   157 RK-FLKSEKTELGHIDDVVNRLALAHPDVAFTLTH-NGK----LVLQTRGAGQLLQRLAAILGREFAENALPIDAE-HGD 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  250 CVVEGFVSKSGYGSGRNigDRQFFFVNGRPVDMpkvgKLVN---------ELYRGanskQYPIAIMNFSIPTQAYDVNVT 320
Cdd:PRK00095   230 LRLSGYVGLPTLSRANR--DYQYLFVNGRYVRD----KLLNhairqayhdLLPRG----RYPAFVLFLELDPHQVDVNVH 299

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2074743980  321 PDKRKIFFSDENA----ILQSLREALEKIYSSNQASYSVNRVEELNEENLASNIGSLRERSQLPSKQLSPDS 388
Cdd:PRK00095   300 PAKHEVRFRDERLvhdlIVQAIQEALAQSGLIPAAAGANQVLEPAEPEPLPLQQTPLYASGSSPPASSPSSA 371
LSm4 cd01723
Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 925-1000 1.02e-54

Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212470 [Multi-domain]  Cd Length: 76  Bit Score: 183.93  E-value: 1.02e-54
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2074743980  925 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVID 1000
Cdd:cd01723      1 LPLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRGNTIKYLRLPDEVID 76
MutL_Trans_hPMS_2_like cd03484
MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 223-347 2.12e-51

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: 177.07  E-value: 2.12e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  223 LKDNIITVFGMSTFTCLEPVRLSISD----------------GCVVEGFVSKSGYGSGRNIGDRQFFFVNGRPVDMPKVG 286
Cdd:cd03484      2 IKDNIINVFGGKVIKGLIPINLELDVnptkeeldsdedladsEVKITGYISKPSHGCGRSSSDRQFFYINGRPVDLKKVA 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2074743980  287 KLVNELYRGANSKQYPIAIMNFSIPTQAYDVNVTPDKRKIFFSDENAILQSLREALEKIYS 347
Cdd:cd03484     82 KLINEVYKSFNSRQYPFFILNISLPTSLYDVNVTPDKRTVLLHDEDRLIDTLKTSLSELFE 142
MutL_C smart00853
MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair ...
 749-905 9.05e-39

MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation.


Pssm-ID: 214857 [Multi-domain]  Cd Length: 140  Bit Score: 140.95  E-value: 9.05e-39
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   749 VIGQFNLGFIIGKLDQDLFIVDQHAADEKYNYERL-SQSTILNQQPLLRPLKMELSPEEEIVISMHMDTFRKNGFLLEED 827
Cdd:smart00853    1 ALGQVAGTYILAEREDGLYLLDQHAAHERILYEQLlKQAGGLESQPLLIPVRLELSPQEAALLEEHLELLRQLGFELEIF 80

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2074743980   828 ihapSGHRFKLKAVPFSKNVTFGIADVKELISILsdshgdcsmigtyrSDTADSVCPPKVRAMLASRACRSSVMIGDP 905
Cdd:smart00853   81 ----GPQSLILRSVPALLRQQNLQKLIPELLDLL--------------SDEEENARPSRLEALLASLACRSAIRAGDA 140
MutL_Trans cd00782
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 223-346 5.51e-38

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: 138.06  E-value: 5.51e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  223 LKDNIITVFGMSTFTCLEPVRLSiSDGCVVEGFVSKSGYGSGRNigDRQFFFVNGRPVDMPKVGKLVNELYRGANSK-QY 301
Cdd:cd00782      1 LKDRIAQVYGKEVAKNLIEVELE-SGDFRISGYISKPDFGRSSK--DRQFLFVNGRPVRDKLLSKAINEAYRSYLPKgRY 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2074743980  302 PIAIMNFSIPTQAYDVNVTPDKRKIFFSDENAILQSLREALEKIY 346
Cdd:cd00782     78 PVFVLNLELPPELVDVNVHPTKREVRFSDEEEVLELIREALRSAL 122
MutL_C pfam08676
MutL C terminal dimerization domain; MutL and MutS are key components of the DNA repair ...
 750-906 5.47e-35

MutL C terminal dimerization domain; MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognizes mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerization.


Pssm-ID: 430147  Cd Length: 145  Bit Score: 130.42  E-value: 5.47e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  750 IGQFNLGFIIGKLDQDLFIVDQHAADEKYNYERLSQST---ILNQQPLLRPLKMELSPEEEIVISMHMDTFRKNGFLLEE 826
Cdd:pfam08676    4 LGQVHGTYILAENEDGLYLIDQHAAHERILYEKLKRALaegGLAAQPLLIPLVLELSPEEAALLEEHKEELAQLGFELEE 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  827 dihaPSGHRFKLKAVPfsknVTFGIADVKELISilsdshgdcSMIGTYRSDTADSVcPPKVRAMLASRACRSSVMIGDPL 906
Cdd:pfam08676   84 ----FGPNSVIVRSVP----ALLRQQNLQELIR---------ELLDELAEKGGSSL-EESLEELLATMACHSAVRAGRRL 145
DNA_mis_repair pfam01119
DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain ...
 228-346 4.62e-28

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: 109.51  E-value: 4.62e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  228 ITVFGMSTFTCLEPVRlSISDGCVVEGFVSKSGYGSGRNigDRQFFFVNGRPVDMPKVGKLVNELYRGA-NSKQYPIAIM 306
Cdd:pfam01119    1 AAIYGKEFAENLLPIE-KEDDGLRLSGYISKPTLSRSNR--DYQYLFVNGRPVRDKLLSHAIREAYRDLlPKGRYPVAVL 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2074743980  307 NFSIPTQAYDVNVTPDKRKIFFSDENAILQSLREALEKIY 346
Cdd:pfam01119   78 FLEIDPELVDVNVHPTKREVRFRDEREVYDFIKEALREAL 117
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
749-914 7.00e-23

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


Pssm-ID: 440092 [Multi-domain]  Cd Length: 515  Bit Score: 103.97  E-value: 7.00e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  749 VIGQFNLGFIIGKLDQDLFIVDQHAADEKYNYERLSQ---STILNQQPLLRPLKMELSPEEEIVISMHMDTFRKNGFLLE 825
Cdd:COG0323    330 ALGQLHGTYILAENEDGLVLIDQHAAHERILYERLKKalaEGGVASQPLLIPETLELSPAEAALLEEHLEELARLGFEIE 409

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  826 EDihapSGHRFKLKAVPfsknVTFGIADVKELI-SILSD--SHGDCSMIGTYRsdtadsvcppkvRAMLASRACRSSVMI 902
Cdd:COG0323    410 PF----GPNTVAVRAVP----ALLGEGDAEELLrDLLDElaEEGSSESLEELR------------EELLATMACHGAIKA 469

                          170
                   ....*....|..
gi 2074743980  903 GDPLGRNEMHKL 914
Cdd:COG0323    470 GRRLSLEEMNAL 481
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 223-327 2.58e-21

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: 90.01  E-value: 2.58e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  223 LKDNIITVFGMSTFTCLEPVRLSiSDGCVVEGFVSKSGygSGRNIGDRQFFFVNGRPV-DMPKVGKLVNELYR----GAN 297
Cdd:cd00329      1 LKDRLAEILGDKVADKLIYVEGE-SDGFRVEGAISYPD--SGRSSKDRQFSFVNGRPVrEGGTHVKAVREAYTralnGDD 77

                           90       100       110
                   ....*....|....*....|....*....|
gi 2074743980  298 SKQYPIAIMNFSIPTQAYDVNVTPDKRKIF 327
Cdd:cd00329     78 VRRYPVAVLSLKIPPSLVDVNVHPTKEEVR 107
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 928-994 7.79e-21

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 87.17  E-value: 7.79e-21
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074743980   928 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRV 994
Cdd:smart00651    1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67
mutL PRK00095
DNA mismatch repair endonuclease MutL;
698-914 1.21e-19

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 94.51  E-value: 1.21e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  698 TSERMKLERGFAAASLELSQLENEEGKAKALAAATIELERLFKKEDFEQMKVIGQFNLGFIIGKLDQDLFIVDQHAADEK 777
Cdd:PRK00095   382 ESSAEKNPLQPNASQSEAAAAASAEAAAAAPAAAPEPAEAAEEADSFPLGYALGQLHGTYILAENEDGLYLVDQHAAHER 461

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  778 YNYERL---SQSTILNQQPLLRPLKMELSPEEEIVISMHMDTFRKNGFLLEEdihaPSGHRFKLKAVPfsknVTFGIADV 854
Cdd:PRK00095   462 LLYEQLkdkLAEVGLASQPLLIPLVLELSEDEADRLEEHKELLARLGLELEP----FGPNSFAVREVP----ALLGQQEL 533

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2074743980  855 KELI-SILSDSHGDcsmigtyrsdtaDSVCPPKVRAMLASRACRSSVMIGDPLGRNEMHKL 914
Cdd:PRK00095   534 EELIrDLLDELAEE------------GDSDTLKERELLATMACHGAIRAGRRLTLEEMNAL 582
MutL_Trans_hPMS_1_like cd03485
MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 223-346 2.61e-18

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: 82.32  E-value: 2.61e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  223 LKDNIITVFGMSTFTCLEPV-RLSISDGCVVEGFVSKSGYGSGRNIGDRQFFFVNGRPVDMPK-VGKLVNELYRGANSK- 299
Cdd:cd03485      2 HKEALARVLGTAVAANMVPVqSTDEDPQISLEGFLPKPGSDVSKTKSDGKFISVNSRPVSLGKdIGKLLRQYYSSAYRKs 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 2074743980  300 ---QYPIAIMNFSIPTQAYDVNVTPDKRKIFFSDENAILQSLREALEKIY 346
Cdd:cd03485     82 slrRYPVFFLNILCPPGLVDVNIEPDKDDVLLQNKEAVLQAVENLLESLY 131
Sm_D3 cd01721
Sm protein D3; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 926-996 1.48e-15

Sm protein D3; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits.


Pssm-ID: 212468  Cd Length: 70  Bit Score: 72.17  E-value: 1.48e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2074743980  926 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGdRFWRMPECYIRGNTIKYLRVPD 996
Cdd:cd01721      1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDG-KVSKLEQVYIRGSQIRFIILPD 70
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 928-994 2.00e-15

LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.


Pssm-ID: 426258  Cd Length: 66  Bit Score: 71.77  E-value: 2.00e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074743980  928 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFwRMPECYIRGNTIKYLRV 994
Cdd:pfam01423    1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVR-KLGLVLIRGNNIVLISP 66
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 930-993 6.62e-15

Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.


Pssm-ID: 212462 [Multi-domain]  Cd Length: 63  Bit Score: 69.97  E-value: 6.62e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2074743980  930 LKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGdRFWRMPECYIRGNTIKYLR 993
Cdd:cd00600      1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDG-KVRVLGLVLIRGSNIVSIR 63
HATPase_c_3 pfam13589
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents, additionally, ...
 35-138 3.02e-11

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: 61.96  E-value: 3.02e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980   35 LSSAVKELVENSLDAGASSVEIALKDY--GQDSFQVIDNGSGISPLNFRVlALKHHTSKLLDFPDLQSLTTFGFrGEALS 112
Cdd:pfam13589    1 LEGALAELIDNSIDADATNIKIEVNKNrgGGTEIVIEDDGHGMSPEELIN-ALRLATSAKEAKRGSTDLGRYGI-GLKLA 78

                           90       100
                   ....*....|....*....|....*.
gi 2074743980  113 SLCALGDLTVETRTMNEVVATHLTYD 138
Cdd:pfam13589   79 SLSLGAKLTVTSKKEGKSSTLTLDRD 104
MutL_Trans_MLH3 cd03486
MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 228-342 3.83e-08

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: 53.47  E-value: 3.83e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  228 ITVFGMSTFTCLEPVRLSISDgCVVEGFVSKSGYGSGrnigDRQFFFVNGRPVDMPKVGKLVNELYRG-------ANSKQ 300
Cdd:cd03486      7 KQIYGLVLAQKLKEVSAKFQE-YEVSGYISSEGHYSK----SFQFIYVNGRLYLKTRFHKLINKLFRKtsavaknKSSPQ 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2074743980  301 -------------YPIAIMNFSIPTQAYDVNVTPDKRKIFFSDENAILQSLREAL 342
Cdd:cd03486     82 skssrrgkrsqesYPVFVLNITCPASEYDLSQEPSKTIIEFKDWKTLLPLILEVV 136
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
923-989 7.19e-08

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 50.57  E-value: 7.19e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074743980  923 TMLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVIcTSKDGDRFWRMPECYIRGNTI 989
Cdd:COG1958      2 SERPLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAE-EIDDGEVVRKLGTVVIRGDNV 67
LSm10 cd01733
Like-Sm protein 10; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form ...
 921-995 1.18e-07

Like-Sm protein 10; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-membered ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.


Pssm-ID: 212480  Cd Length: 78  Bit Score: 49.85  E-value: 1.18e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2074743980  921 EQTMLplSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFwRMPECYIRGNTIKYLRVP 995
Cdd:cd01733      7 ENSLV--CLLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH-HFDEFFVQGRNIRYVHIP 78
MutL_Trans_MLH1 cd03483
MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 224-345 1.88e-07

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: 51.08  E-value: 1.88e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  224 KDNIITVFGMSTFTCLEPVRLSISD---GCVVEGFVSKSGYGSGRNIgdrQFFFVNGRPVDMPKVGKLVNELY-----RG 295
Cdd:cd03483      3 KDNIRSVYGAAVANELIEVEISDDDddlGFKVKGLISNANYSKKKII---FILFINNRLVECSALRRAIENVYanylpKG 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 2074743980  296 AnskqYPIAIMNFSIPTQAYDVNVTPDKRKIFFSDENAILQSLREALEKI 345
Cdd:cd03483     80 A----HPFVYLSLEIPPENVDVNVHPTKREVHFLNEEEIIERIQKLVEDK 125
Sm_D1 cd01724
Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 940-998 2.28e-07

Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits.


Pssm-ID: 212471  Cd Length: 92  Bit Score: 49.53  E-value: 2.28e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2074743980  940 VELKNGETYNGHLVNCDTWMNIHLREVICTSKdGDRFWRMPECYIRGNTIKYLRVPDEV 998
Cdd:cd01724     16 IELKNGTVVHGTITGVDVSMNTHLKNVKLTLK-GKNPVSLDTLSIRGNNIRYIILPDSL 73
MutL_Trans_MutL cd03482
MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 247-344 2.77e-07

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


Pssm-ID: 239564 [Multi-domain]  Cd Length: 123  Bit Score: 50.27  E-value: 2.77e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074743980  247 SDGCVVEGFVSKSGYGsgRNIGDRQFFFVNGRPV-DmpkvgKLVNELYRGANSK-----QYPIAIMNFSIPTQAYDVNVT 320
Cdd:cd03482     24 AGGLRLSGWIALPTFA--RSQADIQYFYVNGRMVrD-----KLISHAVRQAYSDvlhggRHPAYVLYLELDPAQVDVNVH 96

                           90       100
                   ....*....|....*....|....
gi 2074743980  321 PDKRKIFFSDENAILQSLREALEK 344
Cdd:cd03482     97 PAKHEVRFRDSRLVHDFIYHAVKK 120
LSm2 cd01725
Like-Sm protein 2; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 927-1000 6.72e-07

Like-Sm protein 2; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212472  Cd Length: 89  Bit Score: 48.35  E-value: 6.72e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074743980  927 LSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTskDGDRFWRM---PECYIRGNTIKYLRVPDEVID 1000
Cdd:cd01725      3 FSFFKTLVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNISVN--DPEKYPHLlsvKNCFIRGSVVRYVQLPADEVD 77
Sm_F cd01722
Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 935-993 6.60e-06

Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.


Pssm-ID: 212469  Cd Length: 69  Bit Score: 44.90  E-value: 6.60e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2074743980  935 GHPMLVELKNGETYNGHLVNCDTWMNIHLR---EVICTSKDGDrfwrMPECYIRGNTIKYLR 993
Cdd:cd01722     11 GKPVIVKLKWGMEYKGTLVSVDSYMNLQLAnteEYIDGKFTGN----LGEVLIRCNNVLYIR 68
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 926-991 1.14e-05

Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212473  Cd Length: 68  Bit Score: 44.05  E-value: 1.14e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2074743980  926 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHL---REVIctskDGDRFWRMPECYIRGNTIKY 991
Cdd:cd01726      2 PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLedtEEYV----DGQLVAKYGDAFIRGNNVLY 66
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
 31-77 3.88e-05

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: 43.90  E-value: 3.88e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2074743980   31 VILDLSSAVKELVENSLD--AGASSVEIALKDYGQDSFQVIDNGSGISP 77
Cdd:pfam02518    2 DELRLRQVLSNLLDNALKhaAKAGEITVTLSEGGELTLTVEDNGIGIPP 50
PRK04184 PRK04184
DNA topoisomerase VI subunit B; Validated
 39-77 2.45e-03

DNA topoisomerase VI subunit B; Validated


Pssm-ID: 235246 [Multi-domain]  Cd Length: 535  Bit Score: 41.80  E-value: 2.45e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2074743980   39 VKELVENSLDAGASS-------VEIALKDYGQDSFQVI--DNGSGISP 77
Cdd:PRK04184    41 VKELVDNSLDACEEAgilpdikIEIKRVDEGKDHYRVTveDNGPGIPP 88
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 35-77 9.02e-03

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


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 37.24  E-value: 9.02e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 2074743980    35 LSSAVKELVENSLDAGASSVEIAL---KDYGQDSFQVIDNGSGISP 77
Cdd:smart00387    6 LRQVLSNLLDNAIKYTPEGGRITVtleRDGDHVEITVEDNGPGIPP 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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