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Conserved domains on  [gi|672070876|ref|XP_008766862|]
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HMG box transcription factor BBX isoform X4 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUF2028 super family cl09880
Domain of unknown function (DUF2028); This region of similarity is found in the vertebrate ...
 153-284 8.50e-50

Domain of unknown function (DUF2028); This region of similarity is found in the vertebrate homologs of the drosophila Bobby Sox.


The actual alignment was detected with superfamily member pfam09667:

Pssm-ID: 430742  Cd Length: 180  Bit Score: 173.56  E-value: 8.50e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672070876  153 EVPQLNFGMADPTQMGGLSMLLLAGEHAL----------------GTPEASSGTCRPDISESPELRQKSPLFQFAEISSR 216
Cdd:pfam09667   1 EMPQLNFGIADPTQMGGLSMLLLAGEHALtahgdhavtervehllSDHEVSSGICPLDASDFAEACQDSSLFQFAEISSN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672070876  217 TSHPD--APSKQCQASALFQFAEISSSTS--QLGGTEPVKRCGN---------------------------SALFQLAEM 265
Cdd:pfam09667  81 TSHPDdlAAAEQSEESALFQFAEISSDTSqtQINCPDPAKCCGKsalfqlaeissssshsdssalakqcgtSALFQLAEM 160

                         170
                  ....*....|....*....
gi 672070876  266 CLASEGVKMEGTELTKSKD 284
Cdd:pfam09667 161 CEASEAVKIEISRNVDTDD 179
HMG-box_SF super family cl00082
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 54-111 1.14e-33

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.


The actual alignment was detected with superfamily member cd21989:

Pssm-ID: 469606 [Multi-domain]  Cd Length: 69  Bit Score: 123.67  E-value: 1.14e-33
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 672070876  54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRW 111
Cdd:cd21989   12 KRHRSLVRERHPRLDNRGITKILGDWWAVLDPDEKQKYTDLAKQYKEAFMKANPNFKW 69
 
Name Accession Description Interval E-value
DUF2028 pfam09667
Domain of unknown function (DUF2028); This region of similarity is found in the vertebrate ...
 153-284 8.50e-50

Domain of unknown function (DUF2028); This region of similarity is found in the vertebrate homologs of the drosophila Bobby Sox.


Pssm-ID: 430742  Cd Length: 180  Bit Score: 173.56  E-value: 8.50e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672070876  153 EVPQLNFGMADPTQMGGLSMLLLAGEHAL----------------GTPEASSGTCRPDISESPELRQKSPLFQFAEISSR 216
Cdd:pfam09667   1 EMPQLNFGIADPTQMGGLSMLLLAGEHALtahgdhavtervehllSDHEVSSGICPLDASDFAEACQDSSLFQFAEISSN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672070876  217 TSHPD--APSKQCQASALFQFAEISSSTS--QLGGTEPVKRCGN---------------------------SALFQLAEM 265
Cdd:pfam09667  81 TSHPDdlAAAEQSEESALFQFAEISSDTSqtQINCPDPAKCCGKsalfqlaeissssshsdssalakqcgtSALFQLAEM 160

                         170
                  ....*....|....*....
gi 672070876  266 CLASEGVKMEGTELTKSKD 284
Cdd:pfam09667 161 CEASEAVKIEISRNVDTDD 179
HMG-box_HBP2 cd21989
high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar ...
 54-111 1.14e-33

high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar proteins; HBP2, also called HMG box transcription factor BBX, or Bobby sox homolog, is a transcription factor that is necessary for cell cycle progression from the G1 to S phase.


Pssm-ID: 438805 [Multi-domain]  Cd Length: 69  Bit Score: 123.67  E-value: 1.14e-33
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 672070876  54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRW 111
Cdd:cd21989   12 KRHRSLVRERHPRLDNRGITKILGDWWAVLDPDEKQKYTDLAKQYKEAFMKANPNFKW 69
HMG_box pfam00505
HMG (high mobility group) box;
56-109 3.02e-07

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 48.38  E-value: 3.02e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 672070876   56 HRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGY 109
Cdd:pfam00505  15 QRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
HMG smart00398
high mobility group;
54-110 1.90e-06

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 46.15  E-value: 1.90e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 672070876    54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYR 110
Cdd:smart00398  14 QENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
 
Name Accession Description Interval E-value
DUF2028 pfam09667
Domain of unknown function (DUF2028); This region of similarity is found in the vertebrate ...
 153-284 8.50e-50

Domain of unknown function (DUF2028); This region of similarity is found in the vertebrate homologs of the drosophila Bobby Sox.


Pssm-ID: 430742  Cd Length: 180  Bit Score: 173.56  E-value: 8.50e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672070876  153 EVPQLNFGMADPTQMGGLSMLLLAGEHAL----------------GTPEASSGTCRPDISESPELRQKSPLFQFAEISSR 216
Cdd:pfam09667   1 EMPQLNFGIADPTQMGGLSMLLLAGEHALtahgdhavtervehllSDHEVSSGICPLDASDFAEACQDSSLFQFAEISSN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672070876  217 TSHPD--APSKQCQASALFQFAEISSSTS--QLGGTEPVKRCGN---------------------------SALFQLAEM 265
Cdd:pfam09667  81 TSHPDdlAAAEQSEESALFQFAEISSDTSqtQINCPDPAKCCGKsalfqlaeissssshsdssalakqcgtSALFQLAEM 160

                         170
                  ....*....|....*....
gi 672070876  266 CLASEGVKMEGTELTKSKD 284
Cdd:pfam09667 161 CEASEAVKIEISRNVDTDD 179
HMG-box_HBP2 cd21989
high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar ...
 54-111 1.14e-33

high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar proteins; HBP2, also called HMG box transcription factor BBX, or Bobby sox homolog, is a transcription factor that is necessary for cell cycle progression from the G1 to S phase.


Pssm-ID: 438805 [Multi-domain]  Cd Length: 69  Bit Score: 123.67  E-value: 1.14e-33
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 672070876  54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRW 111
Cdd:cd21989   12 KRHRSLVRERHPRLDNRGITKILGDWWAVLDPDEKQKYTDLAKQYKEAFMKANPNFKW 69
HMG-box_CIC-like cd21990
high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a ...
 54-112 1.49e-20

high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a transcriptional repressor which plays a role in the development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, CIC is involved in brain development.


Pssm-ID: 438806 [Multi-domain]  Cd Length: 78  Bit Score: 86.36  E-value: 1.49e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 672070876  54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRWC 112
Cdd:cd21990   14 KRHRALVHQRHPNQDNRTVSKILGEWWYALGPEEKQKYHDLAFQVKEAHFKAHPDWKWC 72
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 54-102 2.81e-07

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: 48.28  E-value: 2.81e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 672070876  54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAF 102
Cdd:cd00084   11 KEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG_box pfam00505
HMG (high mobility group) box;
56-109 3.02e-07

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 48.38  E-value: 3.02e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 672070876   56 HRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGY 109
Cdd:pfam00505  15 QRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
HMG smart00398
high mobility group;
54-110 1.90e-06

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 46.15  E-value: 1.90e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 672070876    54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYR 110
Cdd:smart00398  14 QENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
HMG-box_ROX1-like cd01389
high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar ...
 54-113 2.81e-06

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.


Pssm-ID: 438791 [Multi-domain]  Cd Length: 72  Bit Score: 45.65  E-value: 2.81e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 672070876  54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRWCP 113
Cdd:cd01389   13 KEKHKQLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEEHKLKYPDYKYQP 72
HMG-box_SOX cd22004
high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family ...
 54-113 5.50e-06

high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family transcription factors; The SOX gene family of transcription factors are characterized by the evolutionarily conserved SRY-type HMG box, which is a DNA binding domain that binds the minor groove of DNA on a common consensus site, (A/T)(A/T)CAA(A/T)G but with different levels of efficiency. Members include SRY and its homologs identified in mammals that can be subdivided into 8 groups (A, B1, B2, C, D, E, F, G, H). They are involved in embryonic development, regulating processes such as cell differentiation, maintenance of stemness, sex determination, and development of the central nervous, haematopoietic and other organ systems. The SOX gene family has a crucial role in carcinogenesis and cancer progression.


Pssm-ID: 438820 [Multi-domain]  Cd Length: 75  Bit Score: 44.84  E-value: 5.50e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 672070876  54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRWCP 113
Cdd:cd22004   14 QQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEAERLREEHKKEYPDYKYRP 73
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 54-104 9.02e-06

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: 44.46  E-value: 9.02e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 672070876  54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMK 104
Cdd:cd21980   14 NERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKERYVK 64
HMG-box_SoxA_SoxB_SoxG cd22028
high mobility group (HMG)-box found in group A, group B and group G of SRY-related ...
 57-113 2.08e-05

high mobility group (HMG)-box found in group A, group B and group G of SRY-related high-mobility group (HMG) box (Sox) transcription factors; This subfamily includes SoxA, SoxB, and SoxG proteins. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors. SRY, also called testis-determining factor, is a transcriptional regulator that controls a genetic switch in male development. It promotes DNA bending and is also involved in pre-mRNA splicing. The SRY HMG box recognizes DNA by partial intercalation in the minor groove. It binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'. SoxB transcription factors play critical roles in the regulation of neurogenesis. They can be divided into two main subgroups, SoxB1 (Sox-1/Sox-2/Sox-3) and SoxB2 (SOX-14/SOX-21). SoxB1 proteins suppress neurogenesis by maintaining neural cells in an undifferentiated state. SoxB2 proteins may have the opposite activity and promote neuronal differentiation. SOX-5 is the only member of group G Sox transcription factors. It is also called SOX-12, SOX-20, SOX-26, or SOX-27. SOX-5 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.


Pssm-ID: 438837 [Multi-domain]  Cd Length: 76  Bit Score: 43.50  E-value: 2.08e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 672070876  57 RSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRWCP 113
Cdd:cd22028   17 RRKIAQENPKMHNSEISKRLGAEWKQLSEDEKRPFIDEAKRLRAQHMKEHPDYKYRP 73
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 54-104 8.80e-05

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.


Pssm-ID: 438817 [Multi-domain]  Cd Length: 66  Bit Score: 41.13  E-value: 8.80e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 672070876  54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMK 104
Cdd:cd22001   15 KEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYEK 65
HMG-box_HBP1 cd21988
high mobility group (HMG)-box found in HMG box-containing protein 1 (HBP1) and similar ...
 54-107 2.27e-04

high mobility group (HMG)-box found in HMG box-containing protein 1 (HBP1) and similar proteins; HBP1, also called HMG box transcription factor 1, or high mobility group box transcription factor 1, is a transcriptional repressor that binds to the promoter region of target genes. It plays a role in the regulation of the cell cycle and the Wnt pathway. HBP1 binds preferentially to the sequence 5'-TTCATTCATTCA-3'.


Pssm-ID: 438804 [Multi-domain]  Cd Length: 69  Bit Score: 40.14  E-value: 2.27e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 672070876  54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANP 107
Cdd:cd21988   12 KKYRVEYTQMHPGKDNRAISVILGDRWKKMKNEERRVYTLEAKALAEEHKRLHP 65
HMG-box_HMG20B cd22018
high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar ...
 57-104 2.60e-04

high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar proteins; 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 (HMGXB2), 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.


Pssm-ID: 438834 [Multi-domain]  Cd Length: 85  Bit Score: 40.73  E-value: 2.60e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 672070876  57 RSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMK 104
Cdd:cd22018   17 REQIRTQHPDLPFPEITKMLGAEWSKLQPHEKQRYLDEAERDKQQYMK 64
HMG-box_SoxG_SOX15 cd22035
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 15 (SOX15) and ...
 56-113 6.86e-04

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.


Pssm-ID: 438844 [Multi-domain]  Cd Length: 84  Bit Score: 39.29  E-value: 6.86e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 672070876  56 HRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRWCP 113
Cdd:cd22035   22 QRRQMAQEHPKMHNSEISKRLGAAWKLLPEAEKRPFVEEAKRLRARHMRDYPDYKYRP 79
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 54-102 7.26e-04

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: 38.81  E-value: 7.26e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 672070876  54 KRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDmakEYKDAF 102
Cdd:cd22012   14 KEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQE---EYEKAL 59
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 55-105 2.02e-03

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: 37.66  E-value: 2.02e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 672070876  55 RHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKA 105
Cdd:cd21994   12 ENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKA 62
HMG-box_SoxB cd01388
high mobility group (HMG)-box found in group B SRY-related high-mobility group (HMG) box (Sox) ...
 57-113 2.13e-03

high mobility group (HMG)-box found in group B SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxB transcription factors play critical roles in the regulation of neurogenesis. They can be divided into two main subgroups, SoxB1 (Sox-1/Sox-2/Sox-3) and SoxB2 (SOX-14/SOX-21). SoxB1 proteins suppress neurogenesis by maintaining neural cells in an undifferentiated state. SoxB2 proteins may have the opposite activity and promote neuronal differentiation. SOX-1 is involved in the regulation of embryonic development and cell fate determination. It also acts as a tumor suppressor that plays an anti-tumorigenicity role in different cells and its expression is inhibited in a variety of cancers. SOX-2 plays an important role in various phases of embryonic development, including cell fate and differentiation. Its overexpression and gene amplification may be associated with tumor aggression and metastasis in various cancer types, including breast, prostate, lung, ovarian and colon cancer. SOX-3 is required during the formation of the hypothalamic-pituitary axis. It plays a role in both normal neural development and carcinogenesis. SOX-14, also called SOX-28, acts as a negative regulator of transcription. It is mainly involved in the regulation of neural development. It can also promote proliferation and invasion capacity of cervical cancer cells by activating the Wnt/beta-catenin pathway. SOX-21, also called SOX-A, or SOX-25, promotes the progression of vertebrate neurogenesis.


Pssm-ID: 438790 [Multi-domain]  Cd Length: 80  Bit Score: 37.96  E-value: 2.13e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 672070876  57 RSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRWCP 113
Cdd:cd01388   18 RRKMAQENPKMHNSEISKRLGAEWKLLSEAEKRPFIDEAKRLRALHMKEHPDYKYRP 74
HMG-box_BHMG1 cd21977
high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing ...
 56-98 3.02e-03

high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing protein 1 (BHMG1) and similar proteins; BHMG1 is an uncharacterized HMG-box containing protein that contains a degenerate basic motif not likely to bind DNA.


Pssm-ID: 438793 [Multi-domain]  Cd Length: 66  Bit Score: 36.91  E-value: 3.02e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 672070876  56 HRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEY 98
Cdd:cd21977   15 NRKNYIDKHPGLASTELTKELGQLWRELSAEEKKPYCVRAREL 57
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 61-109 5.55e-03

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: 36.23  E-value: 5.55e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 672070876   61 RQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGY 109
Cdd:pfam09011  23 KRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGTY 71
 
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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