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Conserved domains on  [gi|13397837|emb|CAC34632|]
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upstream binding transcription factor, RNA polymerase I, partial [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HMG-box_UBF1_rpt1-like cd21998
first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 109-158 3.11e-25

first 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 first one. This model also includes the first HMG-box domain of upstream-binding factor 1-like protein 1 (UBTFL1), which contains two HMG-box domains.


:

Pssm-ID: 438814 [Multi-domain]  Cd Length: 77  Bit Score: 92.00  E-value: 3.11e-25
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 13397837 109 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd21998   1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKK 50
 
Name Accession Description Interval E-value
HMG-box_UBF1_rpt1-like cd21998
first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 109-158 3.11e-25

first 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 first one. This model also includes the first HMG-box domain of upstream-binding factor 1-like protein 1 (UBTFL1), which contains two HMG-box domains.


Pssm-ID: 438814 [Multi-domain]  Cd Length: 77  Bit Score: 92.00  E-value: 3.11e-25
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 13397837 109 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd21998   1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKK 50
HMG_box pfam00505
HMG (high mobility group) box;
112-158 3.41e-11

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 55.70  E-value: 3.41e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 13397837   112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEK 47
HMG smart00398
high mobility group;
112-158 8.39e-08

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 46.93  E-value: 8.39e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 13397837    112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEK 48
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
83-158 8.42e-05

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 41.00  E-value: 8.42e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13397837  83 RTLTELILDAQEHVKNPYKGKKLKKH------PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEK 156
Cdd:COG5648  36 TTLVELEKPLQQLLTKPRKKTKSKRLvrkkkdPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDE 115


                ..
gi 13397837 157 KK 158
Cdd:COG5648 116 EK 117
 
Name Accession Description Interval E-value
HMG-box_UBF1_rpt1-like cd21998
first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 109-158 3.11e-25

first 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 first one. This model also includes the first HMG-box domain of upstream-binding factor 1-like protein 1 (UBTFL1), which contains two HMG-box domains.


Pssm-ID: 438814 [Multi-domain]  Cd Length: 77  Bit Score: 92.00  E-value: 3.11e-25
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 13397837 109 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd21998   1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKK 50
HMG_box pfam00505
HMG (high mobility group) box;
112-158 3.41e-11

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 55.70  E-value: 3.41e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 13397837   112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEK 47
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 110-158 4.35e-11

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: 55.38  E-value: 4.35e-11
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 13397837 110 DFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22001   1 EKPKRPISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKK 49
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 114-158 3.77e-10

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: 52.52  E-value: 3.77e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 13397837 114 KPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd00084   1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEK 45
HMG smart00398
high mobility group;
112-158 8.39e-08

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 46.93  E-value: 8.39e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 13397837    112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEK 48
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 112-158 2.23e-07

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: 46.00  E-value: 2.23e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 13397837 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd21980   2 PKAPLTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEK 48
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 112-158 2.75e-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: 45.35  E-value: 2.75e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 13397837 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22012   2 PKRPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEK 48
HMG-box_ABF2-like_rpt1 cd22010
first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 112-158 3.09e-07

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: 45.22  E-value: 3.09e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 13397837 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22010   1 PKRPLSAYFLYFQEHRSDFVKENPDAKMTEISKIGGDKWKNLSADDK 47
HMG-box_NHP10-like cd22016
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) ...
 106-158 8.69e-07

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.


Pssm-ID: 438832 [Multi-domain]  Cd Length: 79  Bit Score: 44.25  E-value: 8.69e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 13397837 106 KKHPDFPKKPLTPYFRFFMEKR----AKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22016   2 EKDPNAPKRPANAFFLFCQEQRekvrEEYKEEHQEIDHHDLTKALAQAWRNLDAEDK 58
HMG-box_SMARCE1 cd21983
high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent ...
 109-158 1.10e-06

high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (SMARCE1) and similar proteins; SMARCE1, also called BRG1-associated factor 57 (BAF57), is a ubiquitously expressed protein involved in transcriptional activation and repression of select genes by chromatin remodeling. It is a component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. SMARCE1 has a single HMG domain that displays non-specific DNA-binding characteristics. It also contains a kinesin-like coiled-coil (KLCC) domain.


Pssm-ID: 438799 [Multi-domain]  Cd Length: 73  Bit Score: 43.82  E-value: 1.10e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 13397837 109 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd21983   2 PKPPEKPLMPYMRYSRKVWDQVKASNPDLKLWEIGKIIGQMWRELSDEEK 51
HMG-box_AtHMGB6-like_rpt3 cd22008
third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 103-158 3.56e-06

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.


Pssm-ID: 438824 [Multi-domain]  Cd Length: 78  Bit Score: 42.63  E-value: 3.56e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 13397837 103 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22008   1 KNKNVDPNKPKKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEK 56
HMG-box_HMG20A cd22017
high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar ...
 101-158 1.18e-05

high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar proteins; HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1 (HMGXB1), 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.


Pssm-ID: 438833 [Multi-domain]  Cd Length: 104  Bit Score: 41.86  E-value: 1.18e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 13397837 101 KGKKLKKHP---DFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22017   7 KGRKRKKPLrdsNAPKAPLTGYVRFMNERREQLRAERPDVPFPEITRMLGNEWSKLPAEEK 67
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 101-158 2.39e-05

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: 40.43  E-value: 2.39e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 13397837 101 KGKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd01390   3 KKGRKKKDPNAPKRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEK 60
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
83-158 8.42e-05

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 41.00  E-value: 8.42e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13397837  83 RTLTELILDAQEHVKNPYKGKKLKKH------PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEK 156
Cdd:COG5648  36 TTLVELEKPLQQLLTKPRKKTKSKRLvrkkkdPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDE 115


                ..
gi 13397837 157 KK 158
Cdd:COG5648 116 EK 117
HMG-box_HMG20B cd22018
high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar ...
 112-158 1.50e-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: 38.42  E-value: 1.50e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 13397837 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22018   2 PKAPVTGYVRFLNERREQIRTQHPDLPFPEITKMLGAEWSKLQPHEK 48
HMG-box_HMO1-like cd22015
high mobility group (HMG)-box found in Saccharomyces cerevisiae high mobility group protein 1 ...
 112-158 2.37e-04

high mobility group (HMG)-box found in Saccharomyces cerevisiae high mobility group protein 1 (HMO1) and similar proteins; HMO1, also called high spontaneous mutagenesis protein 2 (HSM2), is a DNA-binding protein that is probably part of the rDNA transcription apparatus. It acts synergetically with the RPA49 subunit of RNA polymerase I during rDNA transcription. It may participate in mutagenesis control.


Pssm-ID: 438831 [Multi-domain]  Cd Length: 68  Bit Score: 37.47  E-value: 2.37e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 13397837 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22015   1 PKKPLTPYFAFSNHVRPQLKAERPKASPTEIAEEISERWANLSDEEK 47
HMG-box_SOX cd22004
high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family ...
 113-158 4.30e-04

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: 37.14  E-value: 4.30e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 13397837 113 KKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22004   3 KRPMNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEK 48
HMG-box_TFAM_rpt1 cd21986
first high mobility group (HMG)-box found in mitochondrial transcription factor A (TFA) and ...
 112-158 5.21e-04

first high mobility group (HMG)-box found in mitochondrial transcription factor A (TFA) and similar proteins; TFA, also called TFAM, mitochondrial transcription factor 1 (TF1), transcription factor 6 (TCF-6), or transcription factor 6-like 2, binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. It is a component of the mitochondrial transcription initiation complex, composed of at least TFB2M, TFAM and POLRMT that is required for basal transcription of mitochondrial DNA. TFA is required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. It can unwind DNA. It bends the mitochondrial light strand promoter DNA into a U-turn shape via its HMG boxes. TFA is required for maintenance of normal levels of mitochondrial DNA and may play a role in organizing and compacting mitochondrial DNA. TFA contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438802 [Multi-domain]  Cd Length: 65  Bit Score: 36.76  E-value: 5.21e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 13397837 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSnLDLTKILSKKYKELPEKKK 158
Cdd:cd21986   1 PKRPLSPYLRFYREQLPSFPAQNPDAT-TDLSKRIGERWRELPDSQK 46
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 114-158 1.63e-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: 35.35  E-value: 1.63e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 13397837 114 KPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd21994   1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDK 45
HMG-box_AtSSRP1 cd22013
high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and ...
 104-158 1.78e-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: 35.60  E-value: 1.78e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 13397837 104 KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22013   1 KKKKDPNAPKRALSGFMFFSLMERENLKKEKPGISFGEVGKVLGEKWKNMSADDK 55
HMG-box_AtHMGB6-like_rpt2 cd22007
second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 112-158 2.58e-03

second 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 second one.


Pssm-ID: 438823 [Multi-domain]  Cd Length: 68  Bit Score: 34.92  E-value: 2.58e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 13397837 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22007   1 PKRPQSAYFLYANDRRAALKEENKNVKITEIAKMLGAEWKNLSDAKK 47
HMG-box_SoxA_SoxB_SoxG cd22028
high mobility group (HMG)-box found in group A, group B and group G of SRY-related ...
 113-158 3.14e-03

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: 34.64  E-value: 3.14e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 13397837 113 KKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22028   3 KRPMNAFMVWSREQRRKIAQENPKMHNSEISKRLGAEWKQLSEDEK 48
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 112-158 3.42e-03

first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; 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. Ixr1 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438827 [Multi-domain]  Cd Length: 75  Bit Score: 34.44  E-value: 3.42e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 13397837 112 PKKPLTPYFRFFMEKRAKY-AKLHPEMSNLDLTKILSKKYKELPEKKK 158
Cdd:cd22011   1 PKRPSSAYFLFSQEIRKNLkSQGSPEEKVPELSKRAAEQWRSLTLAEK 48
 
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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