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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184     1 MKALPPETVRLLCSSQVITSVLNVVKELIENSLDAGSSSLEVKLENYGLDRIEVRDNGSGIKATDVSVMAVKHYTSKISC 80
Cdd:TIGR00585   3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184    81 HEDLEQLETYGFRGEALASICAISEVIITTKT-ADDDFSIQYSVDhNGQIVSQKPSHLGQGTTVCAANLFKNLPVRRQYy 159
Cdd:TIGR00585  83 FEDLERIETLGFRGEALASISSVSRLTITTKTsAADGLAYQALLE-GGMIESIKPAPRPVGTTVEVRDLFYNLPVRRKF- 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184   160 snTKKCKDELKRVQNLLMAYAVIKPELRVTLSHN-KAVVWQKS-RVSDHR-TALMAVLGAASVANMLPVQHHQEQpEITI 236
Cdd:TIGR00585 161 --LKSPKKEFRKILDVLQRYALIHPDISFSLTHDgKKVLQLSTkPNQSTKeNRIRSVFGTAVLRKLIPLDEWEDL-DLQL 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184   237 DGFFPKPgsdlNSTSSSTTDKSFIFVNSRPVHHKEILKLIKQYYTSAQSNsesvsRRYPTFMMNITIPASTVDVNLTPDK 316
Cdd:TIGR00585 238 EGFISQP----NVTRSRRSGWQFLFINGRPVELKLLLKAIREVYHEYLPK-----GQYPVFVLNLEIDPELVDVNVHPDK 308

                  ....
gi 56912184   317 TEVM 320
Cdd:TIGR00585 309 KEVR 312

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184     1 MKALPPETVRLLCSSQVITSVLNVVKELIENSLDAGSSSLEVKLENYGLDRIEVRDNGSGIKATDVSVMAVKHYTSKISC 80
Cdd:TIGR00585   3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184    81 HEDLEQLETYGFRGEALASICAISEVIITTKT-ADDDFSIQYSVDhNGQIVSQKPSHLGQGTTVCAANLFKNLPVRRQYy 159
Cdd:TIGR00585  83 FEDLERIETLGFRGEALASISSVSRLTITTKTsAADGLAYQALLE-GGMIESIKPAPRPVGTTVEVRDLFYNLPVRRKF- 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184   160 snTKKCKDELKRVQNLLMAYAVIKPELRVTLSHN-KAVVWQKS-RVSDHR-TALMAVLGAASVANMLPVQHHQEQpEITI 236
Cdd:TIGR00585 161 --LKSPKKEFRKILDVLQRYALIHPDISFSLTHDgKKVLQLSTkPNQSTKeNRIRSVFGTAVLRKLIPLDEWEDL-DLQL 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184   237 DGFFPKPgsdlNSTSSSTTDKSFIFVNSRPVHHKEILKLIKQYYTSAQSNsesvsRRYPTFMMNITIPASTVDVNLTPDK 316
Cdd:TIGR00585 238 EGFISQP----NVTRSRRSGWQFLFINGRPVELKLLLKAIREVYHEYLPK-----GQYPVFVLNLEIDPELVDVNVHPDK 308

                  ....
gi 56912184   317 TEVM 320
Cdd:TIGR00585 309 KEVR 312

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184   4 LPPETVrllcsSQ-----VITSVLNVVKELIENSLDAGSSSLEVKLENYGLDRIEVRDNGSGIKATDVsVMAVK-HYTSK 77
Cdd:COG0323   7 LPDELA-----NQiaageVVERPASVVKELVENAIDAGATRIEVEIEEGGKSLIRVTDNGCGMSPEDL-PLAFErHATSK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184  78 ISCHEDLEQLETYGFRGEALASICAISEVIITTKTADDDFSIQYSVDhNGQIVSQKPSHLGQGTTVCAANLFKNLPVRRQ 157
Cdd:COG0323  81 IRSAEDLFRIRTLGFRGEALASIASVSRLTLTTRTAGAELGTRIEVE-GGKVVEVEPAAAPKGTTVEVRDLFFNTPARRK 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184 158 YY-SN---TKKCKDELKRvqnLLMAYavikPELRVTLSHNKAVVWQKSRVSDHRTALMAVLGAASVANMLPVQHhqEQPE 233
Cdd:COG0323 160 FLkSDateLAHITDVVRR---LALAH----PDIAFTLIHNGREVFQLPGAGDLLQRIAAIYGREFAENLLPVEA--EREG 230

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184 234 ITIDGFFPKPgsDLNstsssttdKS-----FIFVNSRPVHHKEILKLIKQYYtsaqsnsESV--SRRYPTFMMNITIPAS 306
Cdd:COG0323 231 LRLSGYIGKP--EFS--------RSnrdyqYFFVNGRPVRDKLLSHAVREAY-------RDLlpKGRYPVAVLFLELDPE 293

                       330       340
                ....*....|....*....|.
gi 56912184 307 TVDVNLTPDKTEVMLQNKDEV 327
Cdd:COG0323 294 LVDVNVHPTKTEVRFRDEREV 314

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56912184 525 SVRQPSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEKSLNAYNLQRKRAAEGG 597
Cdd:cd21985   1 GIRKPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAAKDLERYNSQKKRAAEQP 73

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56912184 527 RQPSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEKSLNAYNLQRK 591
Cdd:COG5648  72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKE 136

HMG (high mobility group) box;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 56912184   529 PSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEK 581
Cdd:pfam00505   4 PMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEK 56

DNA mismatch repair protein MutL; All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184     1 MKALPPETVRLLCSSQVITSVLNVVKELIENSLDAGSSSLEVKLENYGLDRIEVRDNGSGIKATDVSVMAVKHYTSKISC 80
Cdd:TIGR00585   3 IKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184    81 HEDLEQLETYGFRGEALASICAISEVIITTKT-ADDDFSIQYSVDhNGQIVSQKPSHLGQGTTVCAANLFKNLPVRRQYy 159
Cdd:TIGR00585  83 FEDLERIETLGFRGEALASISSVSRLTITTKTsAADGLAYQALLE-GGMIESIKPAPRPVGTTVEVRDLFYNLPVRRKF- 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184   160 snTKKCKDELKRVQNLLMAYAVIKPELRVTLSHN-KAVVWQKS-RVSDHR-TALMAVLGAASVANMLPVQHHQEQpEITI 236
Cdd:TIGR00585 161 --LKSPKKEFRKILDVLQRYALIHPDISFSLTHDgKKVLQLSTkPNQSTKeNRIRSVFGTAVLRKLIPLDEWEDL-DLQL 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184   237 DGFFPKPgsdlNSTSSSTTDKSFIFVNSRPVHHKEILKLIKQYYTSAQSNsesvsRRYPTFMMNITIPASTVDVNLTPDK 316
Cdd:TIGR00585 238 EGFISQP----NVTRSRRSGWQFLFINGRPVELKLLLKAIREVYHEYLPK-----GQYPVFVLNLEIDPELVDVNVHPDK 308

                  ....
gi 56912184   317 TEVM 320
Cdd:TIGR00585 309 KEVR 312

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184   4 LPPETVrllcsSQ-----VITSVLNVVKELIENSLDAGSSSLEVKLENYGLDRIEVRDNGSGIKATDVsVMAVK-HYTSK 77
Cdd:COG0323   7 LPDELA-----NQiaageVVERPASVVKELVENAIDAGATRIEVEIEEGGKSLIRVTDNGCGMSPEDL-PLAFErHATSK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184  78 ISCHEDLEQLETYGFRGEALASICAISEVIITTKTADDDFSIQYSVDhNGQIVSQKPSHLGQGTTVCAANLFKNLPVRRQ 157
Cdd:COG0323  81 IRSAEDLFRIRTLGFRGEALASIASVSRLTLTTRTAGAELGTRIEVE-GGKVVEVEPAAAPKGTTVEVRDLFFNTPARRK 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184 158 YY-SN---TKKCKDELKRvqnLLMAYavikPELRVTLSHNKAVVWQKSRVSDHRTALMAVLGAASVANMLPVQHhqEQPE 233
Cdd:COG0323 160 FLkSDateLAHITDVVRR---LALAH----PDIAFTLIHNGREVFQLPGAGDLLQRIAAIYGREFAENLLPVEA--EREG 230

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184 234 ITIDGFFPKPgsDLNstsssttdKS-----FIFVNSRPVHHKEILKLIKQYYtsaqsnsESV--SRRYPTFMMNITIPAS 306
Cdd:COG0323 231 LRLSGYIGKP--EFS--------RSnrdyqYFFVNGRPVRDKLLSHAVREAY-------RDLlpKGRYPVAVLFLELDPE 293

                       330       340
                ....*....|....*....|.
gi 56912184 307 TVDVNLTPDKTEVMLQNKDEV 327
Cdd:COG0323 294 LVDVNVHPTKTEVRFRDEREV 314

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184 205 DHRTALMAVLGAASVANMLPVQHHQEQPEITIDGFFPKPGSDLNSTSSsttDKSFIFVNSRPVHH-KEILKLIKQYYTSA 283
Cdd:cd03485   1 DHKEALARVLGTAVAANMVPVQSTDEDPQISLEGFLPKPGSDVSKTKS---DGKFISVNSRPVSLgKDIGKLLRQYYSSA 77

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 56912184 284 QSNSesVSRRYPTFMMNITIPASTVDVNLTPDKTEVMLQNKDEVLLSVETMLISLYG 340
Cdd:cd03485  78 YRKS--SLRRYPVFFLNILCPPGLVDVNIEPDKDDVLLQNKEAVLQAVENLLESLYG 132

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184 206 HRTALMAVLGAASVANMLPVQHhqEQPEITIDGFFPKPGSdlnstSSSTTDKSFIFVNSRPVHHKEILKLIKQYYTSAQS 285
Cdd:cd00782   1 LKDRIAQVYGKEVAKNLIEVEL--ESGDFRISGYISKPDF-----GRSSKDRQFLFVNGRPVRDKLLSKAINEAYRSYLP 73

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 56912184 286 NsesvsRRYPTFMMNITIPASTVDVNLTPDKTEVMLQNKDEVLLSVETMLISLY 339
Cdd:cd00782  74 K-----GRYPVFVLNLELPPELVDVNVHPTKREVRFSDEEEVLELIREALRSAL 122

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184 210 LMAVLGAASVANMLPV----------QHHQEQP-----EITIDGFFPKPGSDLNSTSSsttDKSFIFVNSRPVHHKEILK 274
Cdd:cd03484   6 IINVFGGKVIKGLIPInleldvnptkEELDSDEdladsEVKITGYISKPSHGCGRSSS---DRQFFYINGRPVDLKKVAK 82

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56912184 275 LIKQYYTSaqsnseSVSRRYPTFMMNITIPASTVDVNLTPDKTEVMLQNKDEVLLSVETMLISLYG 340
Cdd:cd03484  83 LINEVYKS------FNSRQYPFFILNISLPTSLYDVNVTPDKRTVLLHDEDRLIDTLKTSLSELFE 142

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56912184 529 PSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEKSLNAY 586
Cdd:cd00084   2 PLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56912184 527 RQPSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEKSLNAYNLQRKR 592
Cdd:cd22010   2 KRPLSAYFLYFQEHRSDFVKENPDAKMTEISKIGGDKWKNLSADDKKKYEDDFQRELSEYQKAKAE 67

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 (HMGB1) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB1, 2, 3, 4, 5, 7, 12 and 14. They bind preferentially to double-stranded DNA. HMGB1 modulates general plant growth and stress tolerance and confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. HMGB2 and HMGB5 confer sensitivity to salt and drought stresses. HMGB7 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily contain only one HMG-box domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 56912184 529 PSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEK 581
Cdd:cd22005   3 PPTAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAEK 55

HMG (high mobility group) box;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 56912184   529 PSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEK 581
Cdd:pfam00505   4 PMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEK 56

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56912184 529 PSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEKSLNAYNLQRK 591
Cdd:cd21994   2 PMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMK 64

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184 527 RQPSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEKSLNAY 586
Cdd:cd22008  11 KKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAVLMEKY 70

high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar proteins; This family includes class I members of the HMG-box superfamily of DNA-binding proteins, including Saccharomyces cerevisiae repressor ROX1, Schizosaccharomyces pombe mating-type M-specific polypeptide Mc (mat-Mc), Schizosaccharomyces pombe transcription factor ste11, Podospora anserina MAT+ sexual cell fertilization-promoting factor (FPR1), Podospora anserina sporulation minus regulator 2 (SMR2) and Candida albicans repressor of filamentous growth 1 (RFG1). These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. ROX1, also called heme-dependent repression factor, or hypoxic function repressor, is a transcription factor that represses the expression of HEM13, COX5B, ANB1, CYC7 or AAC3. It binds to the DNA sequence 5'-RRRTAACAAGAG-3'. mat-Mc belongs to the mating type protein family, which contains sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. mat-Mc is a positive regulator of MFM genes and is required for conjugation and efficient meiosis. Its HMG box recognizes the DNA sequence 5'-AACAAAG-3'. Ste11 is a key transcription factor for sexual development. It activates the transcription of the matp, matm, mei2, mfm, ste6 and rgs1 genes. It binds specifically to a DNA fragment carrying a 10-base motif 5'-TTCTTTGTTY-3'. FPR1 controls fertilization, probably by determining the mating type. SMR2 is a transcription factor that is required for post-fertilization events. It is required for the developmental events that occur in the female organ after fertilization. RFG1 is a transcription regulator that functions in both the positive and negative regulation of filamentous growth, depending upon environmental conditions.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 56912184 526 VRQPSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEK 581
Cdd:cd01389   1 IPRPPNAFILFRKEKHKQLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYKELAEE 56

high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family includes four members: TOX, TOX2, TOX3 and TOX4. TOX, also called thymus high mobility group box protein TOX, is a transcriptional regulator with a major role in neural stem cell commitment and corticogenesis as well as in lymphoid cell development and lymphoid tissue organogenesis. It binds to GC-rich DNA sequences in the proximity of transcription start sites and may alter chromatin structure, modifying access of transcription factors to DNA. TOX2, also called granulosa cell HMG box protein 1 (GCX-1), is a putative transcriptional activator involved in the hypothalamic-pituitary-gonadal system. TOX3, also called CAG trinucleotide repeat-containing gene F9 protein (CAGF9), or trinucleotide repeat-containing gene 9 protein (TNRC9), is a transcriptional coactivator of the p300/CBP-mediated transcription complex. It activates transactivation through cAMP response element (CRE) sites. It protects against cell death by inducing anti-apoptotic and repressing pro-apoptotic transcripts. TOX4, also called epidermal Langerhans cell protein LCP1, is a component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. All family members contain one HMG-box domain.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56912184 527 RQPSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAE-------KSLNAY 586
Cdd:cd21995   1 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLDEEQKQVYKKKTEaakkeylKALAAY 67

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 56912184 527 RQPSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEK 581
Cdd:cd21980   3 KAPLTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEK 57

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56912184    24 VVKELIENSLDAGS--SSLEVKLENYGLDRIEVRDNGSGIKATDVSVMavkhytskiscHEDLEQLETYGFRGEAL-ASI 100
Cdd:pfam02518   9 VLSNLLDNALKHAAkaGEITVTLSEGGELTLTVEDNGIGIPPEDLPRI-----------FEPFSTADKRGGGGTGLgLSI 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 56912184   101 C-AISEViittktadddfsiqysvdHNGQIvsQKPSHLGQGTTV 143
Cdd:pfam02518  78 VrKLVEL------------------LGGTI--TVESEPGGGTTV 101

fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins; UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the fourth one.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 56912184 529 PSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEKSLNAYN 587
Cdd:cd22001   6 PISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYE 64

high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) and similar proteins; NHP10, also called high mobility group protein 2, is probably involved in transcription regulation via its interaction with the INO80 complex, a chromatin remodeling complex.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56912184 529 PSSAFSLFEQDTRSQVL----QENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEKS 582
Cdd:cd22016  11 PANAFFLFCQEQREKVReeykEEHQEIDHHDLTKALAQAWRNLDAEDKKPYYELYEKD 68

high mobility group protein; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 56912184  531 SAFSLFEQDTRSQVLQENPKASpQDVTAAAK---ERWESLGEEDRKKYEGKAE 580
Cdd:PTZ00199  28 SAYMFFAKEKRAEIIAENPELA-KDVAAVGKmvgEAWNKLSEEEKAPYEKKAQ 79

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 56912184 529 PSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEKS 582
Cdd:cd21993   5 KKSGFQLWLEENRSSIEEENPELSEAEIIKLAMQRFRALPKEEKQKWNEKAKGD 58

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 15 (SOX15) and similar proteins; SOX-15, also called SOX-12, SOX-20, SOX-26, or SOX-27, is a crucial transcription factor involved in the regulation of embryonic development and in cell fate determination. It binds to the 5'-AACAAT-3' sequence. SOX-15 can be a tumor suppressor in multiple cancer types. SOX-5 is the only member of group G SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56912184 526 VRQPSSAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAeKSLNAYNLQ 589
Cdd:cd22035   8 VKRPMNAFMVWSSAQRRQMAQEHPKMHNSEISKRLGAAWKLLPEAEKRPFVEEA-KRLRARHMR 70

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 56912184 531 SAFSLFEQDTRSQVLQENPKASPQDVTAAAKERWESLGEEDRKKYEGKAEKSLNAY 586
Cdd:cd22013  14 SGFMFFSLMERENLKKEKPGISFGEVGKVLGEKWKNMSADDKAPYEAKAQVDKERY 69

DNA topoisomerase VI subunit B; Validated

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 56912184   20 SVLNVVKELIENSLDAGSSS-------LEVKLENYGLD--RIEVRDNGSGI 61
Cdd:PRK04184  36 ALYTTVKELVDNSLDACEEAgilpdikIEIKRVDEGKDhyRVTVEDNGPGI 86

high mobility group (HMG)-box found in group F SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxF transcription factors includes three members: Sox7, Sox17, and Sox18. They regulate endothelial cell fate as well as development and differentiation of the developing heart, blood cells, and lymphatic vessels.