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Conserved domains on  [gi|2462574362|ref|XP_054198553|]
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PMS1 protein homolog 1 isoform X1 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
 1-279 1.35e-106

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: 331.53  E-value: 1.35e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362   1 MKQLPAATVRLLSSSQIITSVVSVVKELIENSLDAGATSVDVKLENYGFDKIEVRDNGEGIKAVDAPVMAMKYYTSKINS 80
Cdd:TIGR00585   3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362  81 HEDLENLTTYGFRGEALGSICCIAEVLITTRT-AADNFSTQYVLDGsGHILSQKPSHLGQGTTVTALRLFKNLPVRKQFy 159
Cdd:TIGR00585  83 FEDLERIETLGFRGEALASISSVSRLTITTKTsAADGLAYQALLEG-GMIESIKPAPRPVGTTVEVRDLFYNLPVRRKF- 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 160 stAKKCKDEIKKIQDLLMSFGILKPDLRIVFVHN-----------------------------------------KIYLS 198
Cdd:TIGR00585 161 --LKSPKKEFRKILDVLQRYALIHPDISFSLTHDgkkvlqlstkpnqstkenrirsvfgtavlrklipldewedlDLQLE 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 199 GFLPKCDADHSFTSLStperSFIFINSRPVHQKDILKLIRHHYNLKCLKEStrlYPVFFLKIDVPTADVDVNLTPDKSQV 278
Cdd:TIGR00585 239 GFISQPNVTRSRRSGW----QFLFINGRPVELKLLLKAIREVYHEYLPKGQ---YPVFVLNLEIDPELVDVNVHPDKKEV 311


                  .
gi 2462574362 279 L 279
Cdd:TIGR00585 312 R 312
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 532-603 9.99e-30

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


:

Pssm-ID: 438801 [Multi-domain]  Cd Length: 73  Bit Score: 112.25  E-value: 9.99e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462574362 532 IKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQE 603
Cdd:cd21985     2 IRKPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAAKDLERYNSQKKRAAEQP 73
 
Name Accession Description Interval E-value
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
 1-279 1.35e-106

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: 331.53  E-value: 1.35e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362   1 MKQLPAATVRLLSSSQIITSVVSVVKELIENSLDAGATSVDVKLENYGFDKIEVRDNGEGIKAVDAPVMAMKYYTSKINS 80
Cdd:TIGR00585   3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362  81 HEDLENLTTYGFRGEALGSICCIAEVLITTRT-AADNFSTQYVLDGsGHILSQKPSHLGQGTTVTALRLFKNLPVRKQFy 159
Cdd:TIGR00585  83 FEDLERIETLGFRGEALASISSVSRLTITTKTsAADGLAYQALLEG-GMIESIKPAPRPVGTTVEVRDLFYNLPVRRKF- 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 160 stAKKCKDEIKKIQDLLMSFGILKPDLRIVFVHN-----------------------------------------KIYLS 198
Cdd:TIGR00585 161 --LKSPKKEFRKILDVLQRYALIHPDISFSLTHDgkkvlqlstkpnqstkenrirsvfgtavlrklipldewedlDLQLE 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 199 GFLPKCDADHSFTSLStperSFIFINSRPVHQKDILKLIRHHYNLKCLKEStrlYPVFFLKIDVPTADVDVNLTPDKSQV 278
Cdd:TIGR00585 239 GFISQPNVTRSRRSGW----QFLFINGRPVELKLLLKAIREVYHEYLPKGQ---YPVFVLNLEIDPELVDVNVHPDKKEV 311


                  .
gi 2462574362 279 L 279
Cdd:TIGR00585 312 R 312
HATPase_MutL-MLH-PMS-like cd16926
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ...
 8-193 1.06e-77

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: 250.43  E-value: 1.06e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362   8 TVRLLSSSQIITSVVSVVKELIENSLDAGATSVDVKLENYGFDKIEVRDNGEGIKAVDAPVMAMKYYTSKINSHEDLENL 87
Cdd:cd16926     1 VVNKIAAGEVIERPASVVKELVENSIDAGATRIDVEIEEGGLKLIRVTDNGSGISREDLELAFERHATSKISSFEDLFSI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362  88 TTYGFRGEALGSICCIAEVLITTRTAADNFSTQYVLDGSGHILSQKPSHLGQGTTVTALRLFKNLPVRKQFYSTAKKckd 167
Cdd:cd16926    81 TTLGFRGEALASIASVSRLTITTRTADDDVGTRLVVDGGGIIEEVKPAAAPVGTTVTVRDLFYNTPARRKFLKSPKT--- 157

                         170       180
                  ....*....|....*....|....*.
gi 2462574362 168 EIKKIQDLLMSFGILKPDLRIVFVHN 193
Cdd:cd16926   158 ELSKILDLVQRLALAHPDVSFSLTHD 183
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
2-278 2.37e-59

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


Pssm-ID: 440092 [Multi-domain]  Cd Length: 515  Bit Score: 211.44  E-value: 2.37e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362   2 KQLPAATVrllssSQI-----ITSVVSVVKELIENSLDAGATSVDVKLENYGFDKIEVRDNGEGIKAVDAPvMA-MKYYT 75
Cdd:COG0323     5 RLLPDELA-----NQIaagevVERPASVVKELVENAIDAGATRIEVEIEEGGKSLIRVTDNGCGMSPEDLP-LAfERHAT 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362  76 SKINSHEDLENLTTYGFRGEALGSICCIAEVLITTRTAADNFSTQYVLDGsGHILSQKPSHLGQGTTVTALRLFKNLPVR 155
Cdd:COG0323    79 SKIRSAEDLFRIRTLGFRGEALASIASVSRLTLTTRTAGAELGTRIEVEG-GKVVEVEPAAAPKGTTVEVRDLFFNTPAR 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 156 KQFYSTAKKckdEIKKIQDLLMSFGILKPDLRIVFVHNK------------------IYLSGFLPK---CDADHSFTSL- 213
Cdd:COG0323   158 RKFLKSDAT---ELAHITDVVRRLALAHPDIAFTLIHNGrevfqlpgagdllqriaaIYGREFAENllpVEAEREGLRLs 234

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462574362 214 ---STPE--RS-----FIFINSRPVHQKDILKLIRHHYnlkclkeSTRL----YPVFFLKIDVPTADVDVNLTPDKSQV 278
Cdd:COG0323   235 gyiGKPEfsRSnrdyqYFFVNGRPVRDKLLSHAVREAY-------RDLLpkgrYPVAVLFLELDPELVDVNVHPTKTEV 306
mutL PRK00095
DNA mismatch repair endonuclease MutL;
2-286 9.77e-56

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 203.52  E-value: 9.77e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362   2 KQLPAATVrllssSQI-----ITSVVSVVKELIENSLDAGATSVDVKLENYGFDKIEVRDNGEGIKAVDAPVMAMKYYTS 76
Cdd:PRK00095    4 QLLPPQLA-----NQIaagevVERPASVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNGCGISKEDLALALARHATS 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362  77 KINSHEDLENLTTYGFRGEALGSICCIAEVLITTRTAADNFSTQYVLDGsGHILSQKPSHLGQGTTVTALRLFKNLPVRK 156
Cdd:PRK00095   79 KIASLDDLEAIRTLGFRGEALPSIASVSRLTLTSRTADAAEGWQIVYEG-GEIVEVKPAAHPVGTTIEVRDLFFNTPARR 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 157 QFYSTAKKckdEIKKIQDLLMSFGILKPDLRIVFVHN------------------KIYLSGFLPKC---DADHS------ 209
Cdd:PRK00095  158 KFLKSEKT---ELGHIDDVVNRLALAHPDVAFTLTHNgklvlqtrgagqllqrlaAILGREFAENAlpiDAEHGdlrlsg 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 210 FTSL-----STPERSFIFINSRPVHQKDILKLIRHHYnlkclkeSTRL----YPVFFLKIDVPTADVDVNLTPDKSQVLL 280
Cdd:PRK00095  235 YVGLptlsrANRDYQYLFVNGRYVRDKLLNHAIRQAY-------HDLLprgrYPAFVLFLELDPHQVDVNVHPAKHEVRF 307


                  ....*.
gi 2462574362 281 QNKESV 286
Cdd:PRK00095  308 RDERLV 313
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 532-603 9.99e-30

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


Pssm-ID: 438801 [Multi-domain]  Cd Length: 73  Bit Score: 112.25  E-value: 9.99e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462574362 532 IKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQE 603
Cdd:cd21985     2 IRKPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAAKDLERYNSQKKRAAEQP 73
DNA_mis_repair pfam01119
DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain ...
 186-292 3.17e-19

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: 84.09  E-value: 3.17e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 186 LRIVFVHNKIYLSGFLPKcdadHSFTSlSTPERSFIFINSRPVHQKDILKLIRHHYNLKclkESTRLYPVFFLKIDVPTA 265
Cdd:pfam01119  13 LPIEKEDDGLRLSGYISK----PTLSR-SNRDYQYLFVNGRPVRDKLLSHAIREAYRDL---LPKGRYPVAVLFLEIDPE 84

                          90       100
                  ....*....|....*....|....*..
gi 2462574362 266 DVDVNLTPDKSQVLLQNKESVLIALEN 292
Cdd:pfam01119  85 LVDVNVHPTKREVRFRDEREVYDFIKE 111
HMG smart00398
high mobility group;
531-598 5.93e-10

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 56.17  E-value: 5.93e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574362  531 VIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKR 598
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPE 68
HMG_box pfam00505
HMG (high mobility group) box;
532-598 4.70e-07

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 47.61  E-value: 4.70e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462574362 532 IKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKR 598
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPE 67
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
533-597 6.06e-05

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 45.24  E-value: 6.06e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462574362 533 KKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMK 597
Cdd:COG5648    72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKE 136
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 24-144 2.03e-03

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


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 38.78  E-value: 2.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362   24 VVKELIENSLDAGATS--VDVKLENYGFD-KIEVRDNGEGIKAVDAPVMAMKYYTSKINSHEdlenlttygFRGEALG-S 99
Cdd:smart00387   9 VLSNLLDNAIKYTPEGgrITVTLERDGDHvEITVEDNGPGIPPEDLEKIFEPFFRTDKRSRK---------IGGTGLGlS 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2462574362  100 ICciaevlittRTAADNFstqyvlDGSGHILSQkpshLGQGTTVT 144
Cdd:smart00387  80 IV---------KKLVELH------GGEISVESE----PGGGTTFT 105
 
Name Accession Description Interval E-value
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
 1-279 1.35e-106

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: 331.53  E-value: 1.35e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362   1 MKQLPAATVRLLSSSQIITSVVSVVKELIENSLDAGATSVDVKLENYGFDKIEVRDNGEGIKAVDAPVMAMKYYTSKINS 80
Cdd:TIGR00585   3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362  81 HEDLENLTTYGFRGEALGSICCIAEVLITTRT-AADNFSTQYVLDGsGHILSQKPSHLGQGTTVTALRLFKNLPVRKQFy 159
Cdd:TIGR00585  83 FEDLERIETLGFRGEALASISSVSRLTITTKTsAADGLAYQALLEG-GMIESIKPAPRPVGTTVEVRDLFYNLPVRRKF- 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 160 stAKKCKDEIKKIQDLLMSFGILKPDLRIVFVHN-----------------------------------------KIYLS 198
Cdd:TIGR00585 161 --LKSPKKEFRKILDVLQRYALIHPDISFSLTHDgkkvlqlstkpnqstkenrirsvfgtavlrklipldewedlDLQLE 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 199 GFLPKCDADHSFTSLStperSFIFINSRPVHQKDILKLIRHHYNLKCLKEStrlYPVFFLKIDVPTADVDVNLTPDKSQV 278
Cdd:TIGR00585 239 GFISQPNVTRSRRSGW----QFLFINGRPVELKLLLKAIREVYHEYLPKGQ---YPVFVLNLEIDPELVDVNVHPDKKEV 311


                  .
gi 2462574362 279 L 279
Cdd:TIGR00585 312 R 312
HATPase_MutL-MLH-PMS-like cd16926
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ...
 8-193 1.06e-77

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: 250.43  E-value: 1.06e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362   8 TVRLLSSSQIITSVVSVVKELIENSLDAGATSVDVKLENYGFDKIEVRDNGEGIKAVDAPVMAMKYYTSKINSHEDLENL 87
Cdd:cd16926     1 VVNKIAAGEVIERPASVVKELVENSIDAGATRIDVEIEEGGLKLIRVTDNGSGISREDLELAFERHATSKISSFEDLFSI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362  88 TTYGFRGEALGSICCIAEVLITTRTAADNFSTQYVLDGSGHILSQKPSHLGQGTTVTALRLFKNLPVRKQFYSTAKKckd 167
Cdd:cd16926    81 TTLGFRGEALASIASVSRLTITTRTADDDVGTRLVVDGGGIIEEVKPAAAPVGTTVTVRDLFYNTPARRKFLKSPKT--- 157

                         170       180
                  ....*....|....*....|....*.
gi 2462574362 168 EIKKIQDLLMSFGILKPDLRIVFVHN 193
Cdd:cd16926   158 ELSKILDLVQRLALAHPDVSFSLTHD 183
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
2-278 2.37e-59

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


Pssm-ID: 440092 [Multi-domain]  Cd Length: 515  Bit Score: 211.44  E-value: 2.37e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362   2 KQLPAATVrllssSQI-----ITSVVSVVKELIENSLDAGATSVDVKLENYGFDKIEVRDNGEGIKAVDAPvMA-MKYYT 75
Cdd:COG0323     5 RLLPDELA-----NQIaagevVERPASVVKELVENAIDAGATRIEVEIEEGGKSLIRVTDNGCGMSPEDLP-LAfERHAT 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362  76 SKINSHEDLENLTTYGFRGEALGSICCIAEVLITTRTAADNFSTQYVLDGsGHILSQKPSHLGQGTTVTALRLFKNLPVR 155
Cdd:COG0323    79 SKIRSAEDLFRIRTLGFRGEALASIASVSRLTLTTRTAGAELGTRIEVEG-GKVVEVEPAAAPKGTTVEVRDLFFNTPAR 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 156 KQFYSTAKKckdEIKKIQDLLMSFGILKPDLRIVFVHNK------------------IYLSGFLPK---CDADHSFTSL- 213
Cdd:COG0323   158 RKFLKSDAT---ELAHITDVVRRLALAHPDIAFTLIHNGrevfqlpgagdllqriaaIYGREFAENllpVEAEREGLRLs 234

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462574362 214 ---STPE--RS-----FIFINSRPVHQKDILKLIRHHYnlkclkeSTRL----YPVFFLKIDVPTADVDVNLTPDKSQV 278
Cdd:COG0323   235 gyiGKPEfsRSnrdyqYFFVNGRPVRDKLLSHAVREAY-------RDLLpkgrYPVAVLFLELDPELVDVNVHPTKTEV 306
mutL PRK00095
DNA mismatch repair endonuclease MutL;
2-286 9.77e-56

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 203.52  E-value: 9.77e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362   2 KQLPAATVrllssSQI-----ITSVVSVVKELIENSLDAGATSVDVKLENYGFDKIEVRDNGEGIKAVDAPVMAMKYYTS 76
Cdd:PRK00095    4 QLLPPQLA-----NQIaagevVERPASVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNGCGISKEDLALALARHATS 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362  77 KINSHEDLENLTTYGFRGEALGSICCIAEVLITTRTAADNFSTQYVLDGsGHILSQKPSHLGQGTTVTALRLFKNLPVRK 156
Cdd:PRK00095   79 KIASLDDLEAIRTLGFRGEALPSIASVSRLTLTSRTADAAEGWQIVYEG-GEIVEVKPAAHPVGTTIEVRDLFFNTPARR 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 157 QFYSTAKKckdEIKKIQDLLMSFGILKPDLRIVFVHN------------------KIYLSGFLPKC---DADHS------ 209
Cdd:PRK00095  158 KFLKSEKT---ELGHIDDVVNRLALAHPDVAFTLTHNgklvlqtrgagqllqrlaAILGREFAENAlpiDAEHGdlrlsg 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 210 FTSL-----STPERSFIFINSRPVHQKDILKLIRHHYnlkclkeSTRL----YPVFFLKIDVPTADVDVNLTPDKSQVLL 280
Cdd:PRK00095  235 YVGLptlsrANRDYQYLFVNGRYVRDKLLNHAIRQAY-------HDLLprgrYPAFVLFLELDPHQVDVNVHPAKHEVRF 307


                  ....*.
gi 2462574362 281 QNKESV 286
Cdd:PRK00095  308 RDERLV 313
MutL_Trans_hPMS_1_like cd03485
MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 194-299 2.14e-38

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: 139.33  E-value: 2.14e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 194 KIYLSGFLPKCDADHSFTslsTPERSFIFINSRPVHQ-KDILKLIRHHYNLKCLKESTRLYPVFFLKIDVPTADVDVNLT 272
Cdd:cd03485    29 QISLEGFLPKPGSDVSKT---KSDGKFISVNSRPVSLgKDIGKLLRQYYSSAYRKSSLRRYPVFFLNILCPPGLVDVNIE 105

                          90       100
                  ....*....|....*....|....*..
gi 2462574362 273 PDKSQVLLQNKESVLIALENLMTTCYG 299
Cdd:cd03485   106 PDKDDVLLQNKEAVLQAVENLLESLYG 132
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 532-603 9.99e-30

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


Pssm-ID: 438801 [Multi-domain]  Cd Length: 73  Bit Score: 112.25  E-value: 9.99e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462574362 532 IKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQE 603
Cdd:cd21985     2 IRKPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAAKDLERYNSQKKRAAEQP 73
MutL_Trans cd00782
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 186-298 5.65e-23

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: 94.92  E-value: 5.65e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 186 LRIVFVHNKIYLSGFLPKCDAdhsftSLSTPERSFIFINSRPVHQKDILKLIRHHYNLKCLKestRLYPVFFLKIDVPTA 265
Cdd:cd00782    18 IEVELESGDFRISGYISKPDF-----GRSSKDRQFLFVNGRPVRDKLLSKAINEAYRSYLPK---GRYPVFVLNLELPPE 89

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2462574362 266 DVDVNLTPDKSQVLLQNKESVLIALENLMTTCY 298
Cdd:cd00782    90 LVDVNVHPTKREVRFSDEEEVLELIREALRSAL 122
DNA_mis_repair pfam01119
DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain ...
 186-292 3.17e-19

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: 84.09  E-value: 3.17e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 186 LRIVFVHNKIYLSGFLPKcdadHSFTSlSTPERSFIFINSRPVHQKDILKLIRHHYNLKclkESTRLYPVFFLKIDVPTA 265
Cdd:pfam01119  13 LPIEKEDDGLRLSGYISK----PTLSR-SNRDYQYLFVNGRPVRDKLLSHAIREAYRDL---LPKGRYPVAVLFLEIDPE 84

                          90       100
                  ....*....|....*....|....*..
gi 2462574362 266 DVDVNLTPDKSQVLLQNKESVLIALEN 292
Cdd:pfam01119  85 LVDVNVHPTKREVRFRDEREVYDFIKE 111
MutL_Trans_hPMS_2_like cd03484
MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 190-292 1.60e-18

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


Pssm-ID: 239566 [Multi-domain]  Cd Length: 142  Bit Score: 82.70  E-value: 1.60e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 190 FVHNKIYLSGFLPKCDADHSFtslSTPERSFIFINSRPVHQKDILKLIR---HHYNlkclkesTRLYPVFFLKIDVPTAD 266
Cdd:cd03484    40 LADSEVKITGYISKPSHGCGR---SSSDRQFFYINGRPVDLKKVAKLINevyKSFN-------SRQYPFFILNISLPTSL 109

                          90       100
                  ....*....|....*....|....*.
gi 2462574362 267 VDVNLTPDKSQVLLQNKESVLIALEN 292
Cdd:cd03484   110 YDVNVTPDKRTVLLHDEDRLIDTLKT 135
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 192-279 6.52e-13

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: 65.75  E-value: 6.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 192 HNKIYLSGFLPKCDADHSftslsTPERSFIFINSRPVHQ-KDILKLIRHHYNLKCLKESTRLYPVFFLKIDVPTADVDVN 270
Cdd:cd00329    24 SDGFRVEGAISYPDSGRS-----SKDRQFSFVNGRPVREgGTHVKAVREAYTRALNGDDVRRYPVAVLSLKIPPSLVDVN 98


                  ....*....
gi 2462574362 271 LTPDKSQVL 279
Cdd:cd00329    99 VHPTKEEVR 107
HMG smart00398
high mobility group;
531-598 5.93e-10

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 56.17  E-value: 5.93e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574362  531 VIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKR 598
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPE 68
HMG_box pfam00505
HMG (high mobility group) box;
532-598 4.70e-07

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 47.61  E-value: 4.70e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462574362 532 IKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKR 598
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPE 67
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 533-601 8.81e-07

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


Pssm-ID: 438828 [Multi-domain]  Cd Length: 64  Bit Score: 46.90  E-value: 8.81e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462574362 533 KKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSeeeklkyeekaTKDLERYNSQMKRAIE 601
Cdd:cd22012     3 KRPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLD-----------ESEKEPYQEEYEKALE 60
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 534-597 1.25e-06

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


Pssm-ID: 438810 [Multi-domain]  Cd Length: 67  Bit Score: 46.52  E-value: 1.25e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462574362 534 KPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMK 597
Cdd:cd21994     1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMK 64
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
 24-144 1.91e-06

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


Pssm-ID: 460579 [Multi-domain]  Cd Length: 109  Bit Score: 47.36  E-value: 1.91e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362  24 VVKELIENSLD--AGATSVDVKLENYGFDKIEVRDNGEGIKAVDAPVMAMKYYTSKINSHEdlenlttygfrGEALG-SI 100
Cdd:pfam02518   9 VLSNLLDNALKhaAKAGEITVTLSEGGELTLTVEDNGIGIPPEDLPRIFEPFSTADKRGGG-----------GTGLGlSI 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2462574362 101 CciaevlittRTAADNFstqyvldgSGHIlsQKPSHLGQGTTVT 144
Cdd:pfam02518  78 V---------RKLVELL--------GGTI--TVESEPGGGTTVT 102
MutL_Trans_MLH3 cd03486
MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
 180-296 2.91e-06

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: 47.70  E-value: 2.91e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 180 GILKPDLRIV-FVHNKIYLSGFLPKCdadhsftslstPERS----FIFINSRPVHQKDILKLI----------------R 238
Cdd:cd03486    12 LVLAQKLKEVsAKFQEYEVSGYISSE-----------GHYSksfqFIYVNGRLYLKTRFHKLInklfrktsavaknkssP 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574362 239 HHYNLKCLKESTRLYPVFFLKIDVPTADVDVNLTPDKSQVLLQNKESVLIALENLMTT 296
Cdd:cd03486    81 QSKSSRRGKRSQESYPVFVLNITCPASEYDLSQEPSKTIIEFKDWKTLLPLILEVVKS 138
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 533-598 3.28e-06

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


Pssm-ID: 438792 [Multi-domain]  Cd Length: 81  Bit Score: 45.82  E-value: 3.28e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574362 533 KKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKR 598
Cdd:cd01390    15 KRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAAKDKKRYEEEKAA 80
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 534-592 2.32e-05

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


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 42.51  E-value: 2.32e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462574362 534 KPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERY 592
Cdd:cd00084     1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 533-592 3.79e-05

second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of HMGB family and functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory response. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. The family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa. It is a tumor suppressor that is a major constituent of the promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomeres lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, is a Drosophila HMG1 protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438795 [Multi-domain]  Cd Length: 71  Bit Score: 42.40  E-value: 3.79e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362 533 KKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERY 592
Cdd:cd21979     4 KRPPSAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKY 63
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
533-597 6.06e-05

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 45.24  E-value: 6.06e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462574362 533 KKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMK 597
Cdd:COG5648    72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKE 136
HMG-box_ABF2-like_rpt1 cd22010
first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 533-598 8.34e-05

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


Pssm-ID: 438826 [Multi-domain]  Cd Length: 68  Bit Score: 41.37  E-value: 8.34e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574362 533 KKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKR 598
Cdd:cd22010     2 KRPLSAYFLYFQEHRSDFVKENPDAKMTEISKIGGDKWKNLSADDKKKYEDDFQRELSEYQKAKAE 67
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 533-598 1.01e-04

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


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 41.24  E-value: 1.01e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574362 533 KKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKR 598
Cdd:pfam09011   5 KRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGT 70
HATPase_c_3 pfam13589
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents, additionally, ...
 23-112 2.57e-04

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


Pssm-ID: 433332 [Multi-domain]  Cd Length: 135  Bit Score: 41.93  E-value: 2.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362  23 SVVKELIENSLDAGATSVDVKLENY--GFDKIEVRDNGEGIKAVDApVMAMKYYTSKINSHEDLENLTTYGFrGEALGSI 100
Cdd:pfam13589   3 GALAELIDNSIDADATNIKIEVNKNrgGGTEIVIEDDGHGMSPEEL-INALRLATSAKEAKRGSTDLGRYGI-GLKLASL 80

                          90
                  ....*....|..
gi 2462574362 101 CCIAEVLITTRT 112
Cdd:pfam13589  81 SLGAKLTVTSKK 92
HMG-box_HMGB_rpt1 cd21978
first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 533-597 4.99e-04

first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian cells. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of the HMGB family that functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory responses. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. This family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa, is a tumor suppressor that is a major constituent of promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomere lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, binds preferentially to single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438794 [Multi-domain]  Cd Length: 69  Bit Score: 39.21  E-value: 4.99e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462574362 533 KKPMSASALFVQDHRPQFLIENPKTSLEDATL--QIEELWKTLSEEEKLKYEEKATKDLERYNSQMK 597
Cdd:cd21978     3 RGKMSSYAFFVQTCREEHKKKHPNESVNFSEFskKCSERWKTMSAKEKKKFEDMAKKDKARYEREMK 69
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 24-144 2.03e-03

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


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 38.78  E-value: 2.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574362   24 VVKELIENSLDAGATS--VDVKLENYGFD-KIEVRDNGEGIKAVDAPVMAMKYYTSKINSHEdlenlttygFRGEALG-S 99
Cdd:smart00387   9 VLSNLLDNAIKYTPEGgrITVTLERDGDHvEITVEDNGPGIPPEDLEKIFEPFFRTDKRSRK---------IGGTGLGlS 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2462574362  100 ICciaevlittRTAADNFstqyvlDGSGHILSQkpshLGQGTTVT 144
Cdd:smart00387  80 IV---------KKLVELH------GGEISVESE----PGGGTTFT 105
HATPase_TopVIB-like cd16933
Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family ...
 18-77 2.41e-03

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


Pssm-ID: 340410 [Multi-domain]  Cd Length: 203  Bit Score: 40.02  E-value: 2.41e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574362  18 ITSVVSVVKELIENSLDAGATS-------VDVKLENYGFDKIEVRDNGEGIKAVDAP-VMAMKYYTSK 77
Cdd:cd16933    17 IRSLYTTVRELVENSLDATEEAgilpdikVEIEEIGKDHYKVIVEDNGPGIPEEQIPkVFGKVLYGSK 84
PRK04184 PRK04184
DNA topoisomerase VI subunit B; Validated
 20-61 3.27e-03

DNA topoisomerase VI subunit B; Validated


Pssm-ID: 235246 [Multi-domain]  Cd Length: 535  Bit Score: 41.03  E-value: 3.27e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2462574362  20 SVVSVVKELIENSLDAGATS-------VDVKLENYGFD--KIEVRDNGEGI 61
Cdd:PRK04184   36 ALYTTVKELVDNSLDACEEAgilpdikIEIKRVDEGKDhyRVTVEDNGPGI 86
HMG-box_AtSSRP1 cd22013
high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and ...
 533-597 3.39e-03

high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and similar proteins; SSRP1, also called facilitates chromatin transcription complex subunit SSRP1, high mobility group B protein 8, nucleosome/chromatin assembly factor group D 08 (or D 8), protein NUCLEAR FUSION DEFECTIVE 8, or recombination signal sequence recognition protein 1, is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair. SSRP1 may bind specifically to double-stranded DNA. It is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. SSRP1 contains only one HMG-box domain.


Pssm-ID: 438829 [Multi-domain]  Cd Length: 80  Bit Score: 37.15  E-value: 3.39e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462574362 533 KKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMK 597
Cdd:cd22013    10 KRALSGFMFFSLMERENLKKEKPGISFGEVGKVLGEKWKNMSADDKAPYEAKAQVDKERYKKEMS 74
HATPase_DpiB-CitA-like cd16915
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
 21-81 4.93e-03

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


Pssm-ID: 340392 [Multi-domain]  Cd Length: 104  Bit Score: 37.27  E-value: 4.93e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574362  21 VVSVVKELIENSLDAGATS------VDVKLENYGFD-KIEVRDNGEGIKAVDAPVMAMKYYTSKINSH 81
Cdd:cd16915     1 LITIVGNLIDNALDALAATgapnkqVEVFLRDEGDDlVIEVRDTGPGIAPELRDKVFERGVSTKGQGE 68
HATPase_GyrB-like cd16928
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ...
 25-61 6.15e-03

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


Pssm-ID: 340405 [Multi-domain]  Cd Length: 180  Bit Score: 38.67  E-value: 6.15e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2462574362  25 VKELIENSLD---AG-ATSVDVKLENYGFdkIEVRDNGEGI 61
Cdd:cd16928     5 VWEIVDNSIDealAGyATEIEVTLHEDNS--ITVEDNGRGI 43
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 533-597 7.43e-03

high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; The HMG20 subfamily includes HMG20A and HMG20B. HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1, HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B. HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2, HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex. Both HMG20A and HMG20B contain one HMG-box.


Pssm-ID: 438796 [Multi-domain]  Cd Length: 81  Bit Score: 36.37  E-value: 7.43e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462574362 533 KKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMK 597
Cdd:cd21980     3 KAPLTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKERYVKELE 67
 
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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