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Conserved domains on  [gi|270132752|ref|NP_818774|]
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HMG box-containing protein 1 isoform 2 [Mus musculus]

Protein Classification

AXH and HMG-box_SF domain-containing protein( domain architecture ID 10650206)

AXH and HMG-box_SF domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AXH smart00536
domain in Ataxins and HMG containing proteins; unknown function
 224-350 2.99e-56

domain in Ataxins and HMG containing proteins; unknown function


:

Pssm-ID: 197779  Cd Length: 116  Bit Score: 182.69  E-value: 2.99e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270132752   224 CFLKGTRLCFHKESNKEWQDV--EDFARAASCDNEEEIQMGTHKGYGSDGLkllsheesvsfgESVLKLTFDPGtVEDGL 301
Cdd:smart00536   1 CFMKGTRLCLANGSNKKVEDLktEDFIRSAGCSNDEDLQMSTVKRIGSSGL------------PSVVTLTFDPG-VEDAL 67

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 270132752   302 LTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEIHIGDVCLPPGHP 350
Cdd:smart00536  68 LTVECQVEHPFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLSLTHN 116
HMG-box_SF super family cl00082
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 447-474 8.21e-17

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 cd21988:

Pssm-ID: 469606 [Multi-domain]  Cd Length: 69  Bit Score: 74.80  E-value: 8.21e-17
                         10        20
                 ....*....|....*....|....*...
gi 270132752 447 KRPMNAFMLFAKKYRVEYTQMYPGKDNR 474
Cdd:cd21988    1 KRPMNAFMLFAKKYRVEYTQMHPGKDNR 28
 
Name Accession Description Interval E-value
AXH smart00536
domain in Ataxins and HMG containing proteins; unknown function
 224-350 2.99e-56

domain in Ataxins and HMG containing proteins; unknown function


Pssm-ID: 197779  Cd Length: 116  Bit Score: 182.69  E-value: 2.99e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270132752   224 CFLKGTRLCFHKESNKEWQDV--EDFARAASCDNEEEIQMGTHKGYGSDGLkllsheesvsfgESVLKLTFDPGtVEDGL 301
Cdd:smart00536   1 CFMKGTRLCLANGSNKKVEDLktEDFIRSAGCSNDEDLQMSTVKRIGSSGL------------PSVVTLTFDPG-VEDAL 67

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 270132752   302 LTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEIHIGDVCLPPGHP 350
Cdd:smart00536  68 LTVECQVEHPFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLSLTHN 116
AXH pfam08517
Ataxin-1 and HBP1 module (AXH); AXH is a protein-protein and RNA binding motif found in ...
 225-349 4.97e-55

Ataxin-1 and HBP1 module (AXH); AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1). ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression.


Pssm-ID: 462505  Cd Length: 111  Bit Score: 179.28  E-value: 4.97e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270132752  225 FLKGTRLCFHKEsnkEWQDVEDFAraascdNEEEIQMGthkgYGSDGLKLLSHEESVSFGESVLKLTFDPGTvEDGLLTV 304
Cdd:pfam08517   1 FLKGTRIQLANG---ELKRVEDLR------TEDFLRSA----EGSDGLKLTESTVVRIFGSSVLLLTFSPGE-QKAQVTV 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 270132752  305 ECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEIHIGDVCLPPGH 349
Cdd:pfam08517  67 ECQVEHPFFVKGKGWSSCNPSLTVVRYGLPCQQLQVGDVCLPLTH 111
HMG-box_HBP1 cd21988
high mobility group (HMG)-box found in HMG box-containing protein 1 (HBP1) and similar ...
 447-474 8.21e-17

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: 74.80  E-value: 8.21e-17
                         10        20
                 ....*....|....*....|....*...
gi 270132752 447 KRPMNAFMLFAKKYRVEYTQMYPGKDNR 474
Cdd:cd21988    1 KRPMNAFMLFAKKYRVEYTQMHPGKDNR 28
 
Name Accession Description Interval E-value
AXH smart00536
domain in Ataxins and HMG containing proteins; unknown function
 224-350 2.99e-56

domain in Ataxins and HMG containing proteins; unknown function


Pssm-ID: 197779  Cd Length: 116  Bit Score: 182.69  E-value: 2.99e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270132752   224 CFLKGTRLCFHKESNKEWQDV--EDFARAASCDNEEEIQMGTHKGYGSDGLkllsheesvsfgESVLKLTFDPGtVEDGL 301
Cdd:smart00536   1 CFMKGTRLCLANGSNKKVEDLktEDFIRSAGCSNDEDLQMSTVKRIGSSGL------------PSVVTLTFDPG-VEDAL 67

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 270132752   302 LTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEIHIGDVCLPPGHP 350
Cdd:smart00536  68 LTVECQVEHPFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLSLTHN 116
AXH pfam08517
Ataxin-1 and HBP1 module (AXH); AXH is a protein-protein and RNA binding motif found in ...
 225-349 4.97e-55

Ataxin-1 and HBP1 module (AXH); AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1). ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression.


Pssm-ID: 462505  Cd Length: 111  Bit Score: 179.28  E-value: 4.97e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270132752  225 FLKGTRLCFHKEsnkEWQDVEDFAraascdNEEEIQMGthkgYGSDGLKLLSHEESVSFGESVLKLTFDPGTvEDGLLTV 304
Cdd:pfam08517   1 FLKGTRIQLANG---ELKRVEDLR------TEDFLRSA----EGSDGLKLTESTVVRIFGSSVLLLTFSPGE-QKAQVTV 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 270132752  305 ECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEIHIGDVCLPPGH 349
Cdd:pfam08517  67 ECQVEHPFFVKGKGWSSCNPSLTVVRYGLPCQQLQVGDVCLPLTH 111
HMG-box_HBP1 cd21988
high mobility group (HMG)-box found in HMG box-containing protein 1 (HBP1) and similar ...
 447-474 8.21e-17

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: 74.80  E-value: 8.21e-17
                         10        20
                 ....*....|....*....|....*...
gi 270132752 447 KRPMNAFMLFAKKYRVEYTQMYPGKDNR 474
Cdd:cd21988    1 KRPMNAFMLFAKKYRVEYTQMHPGKDNR 28
HMG-box_CIC-like cd21990
high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a ...
 447-474 4.95e-09

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: 52.84  E-value: 4.95e-09
                         10        20
                 ....*....|....*....|....*...
gi 270132752 447 KRPMNAFMLFAKKYRVEYTQMYPGKDNR 474
Cdd:cd21990    3 RRPMNAFMIFSKRHRALVHQRHPNQDNR 30
HMG-box_SOX cd22004
high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family ...
 447-473 1.27e-05

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: 42.92  E-value: 1.27e-05
                         10        20
                 ....*....|....*....|....*..
gi 270132752 447 KRPMNAFMLFAKKYRVEYTQMYPGKDN 473
Cdd:cd22004    3 KRPMNAFMVWSQQERKKIAKQNPKLHN 29
HMG-box_HBP2 cd21989
high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar ...
 447-474 6.71e-05

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: 40.85  E-value: 6.71e-05
                         10        20
                 ....*....|....*....|....*...
gi 270132752 447 KRPMNAFMLFAKKYRVEYTQMYPGKDNR 474
Cdd:cd21989    1 RRPMNAFLLFCKRHRSLVRERHPRLDNR 28
HMG-box_SoxH_SOX30 cd22033
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 30 (SOX30) and ...
 445-473 8.54e-04

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 30 (SOX30) and similar proteins; SOX-30 is a crucial transcription factor that controls the transition from a late meiotic to a post-meiotic gene expression program and subsequent round spermatid development. It specially prevents Wnt-signaling to suppress metastasis. SOX-30 binds to the DNA sequence 5'-ACAAT-3' and shows a preference for guanine residues surrounding this core motif. SOX-30 is the only member of the group H of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438842 [Multi-domain]  Cd Length: 75  Bit Score: 38.17  E-value: 8.54e-04
                         10        20
                 ....*....|....*....|....*....
gi 270132752 445 KCKRPMNAFMLFAKKYRVEYTQMYPGKDN 473
Cdd:cd22033    1 HIKRPMNAFMVWARIHRPALAKANPNANN 29
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 448-474 2.72e-03

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: 35.96  E-value: 2.72e-03
                         10        20
                 ....*....|....*....|....*..
gi 270132752 448 RPMNAFMLFAKKYRVEYTQMYPGKDNR 474
Cdd:cd00084    1 RPLSAYLLFSKEKRPKLKKENPDLSFT 27
HMG-box_EGL13-like cd22042
high mobility group (HMG)-box found in Caenorhabditis elegans protein egg laying defective 13 ...
 447-473 4.48e-03

high mobility group (HMG)-box found in Caenorhabditis elegans protein egg laying defective 13 (EGL-13) and similar proteins; EGL-13 may act as a transcription factor that is required for uterine cell fate decisions in Caenorhabditis elegans. It controls genes required for the specification and differentiation of O(2) and CO(2)-sensing neurons and for maintaining URX sensory neuronal cell fate.


Pssm-ID: 438848 [Multi-domain]  Cd Length: 78  Bit Score: 36.03  E-value: 4.48e-03
                         10        20
                 ....*....|....*....|....*..
gi 270132752 447 KRPMNAFMLFAKKYRVEYTQMYPGKDN 473
Cdd:cd22042    4 KRPMNAFMVWAKDERRKILKACPDMHN 30
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 447-469 4.75e-03

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: 35.72  E-value: 4.75e-03
                         10        20
                 ....*....|....*....|...
gi 270132752 447 KRPMNAFMLFAKKYRVEYTQMYP 469
Cdd:cd22012    3 KRPASAYFLFAKEVRPKLKEENP 25
HMG-box_ROX1-like cd01389
high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar ...
 447-474 9.42e-03

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: 34.87  E-value: 9.42e-03
                         10        20
                 ....*....|....*....|....*...
gi 270132752 447 KRPMNAFMLFAKKYRVEYTQMYPGKDNR 474
Cdd:cd01389    2 PRPPNAFILFRKEKHKQLRAQNPGLTNS 29
 
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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