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Conserved domains on  [gi|2519023674|pdb|7ZIE|A]
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Chain A, Gcf1p

Protein Classification

HMG-box domain-containing protein( domain architecture ID 228)

HMG (High Mobility Group)-box domain-containing protein binds DNA and may be a chromosomal protein or function as a transcription factor

CATH:  1.10.30.10
Gene Ontology:  GO:0003677|GO:0005515
PubMed:  23153957|17599239|8506143
SCOP:  4000788

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HMG-box_SF super family cl00082
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 160-223 2.22e-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.


The actual alignment was detected with superfamily member cd21987:

Pssm-ID: 469606 [Multi-domain]  Cd Length: 100  Bit Score: 47.80  E-value: 2.22e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
7ZIE_A      160 KPKLGANGFAKYVQENY--IRGDSLTETMKKLADEWNALSETEKQQY-QISKEDKEKYKKALEKWKE 223
Cdd:cd21987  20 KPKRPRSAFNIFVSEHFqeAKGDSPQEKLKTLKEEWKNLSSSQKQLYiQLAEDDKIRYENEMKSWEE 86
 
Name Accession Description Interval E-value
HMG-box_TFAM_rpt2 cd21987
second high mobility group (HMG)-box found in mitochondrial transcription factor A (TFA) and ...
 160-223 2.22e-07

second 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 second one.


Pssm-ID: 438803 [Multi-domain]  Cd Length: 100  Bit Score: 47.80  E-value: 2.22e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
7ZIE_A      160 KPKLGANGFAKYVQENY--IRGDSLTETMKKLADEWNALSETEKQQY-QISKEDKEKYKKALEKWKE 223
Cdd:cd21987  20 KPKRPRSAFNIFVSEHFqeAKGDSPQEKLKTLKEEWKNLSSSQKQLYiQLAEDDKIRYENEMKSWEE 86
HMG smart00398
high mobility group;
160-222 6.70e-03

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 34.60  E-value: 6.70e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7ZIE_A         160 KPKLGANGFAKYVQENYIR------GDSLTETMKKLADEWNALSETEKQQY-QISKEDKEKYKKALEKWK 222
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKikaenpDLSNAEISKKLGERWKLLSEEEKAPYeEKAKKDKERYEEEMPEYK 70
 
Name Accession Description Interval E-value
HMG-box_TFAM_rpt2 cd21987
second high mobility group (HMG)-box found in mitochondrial transcription factor A (TFA) and ...
 160-223 2.22e-07

second 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 second one.


Pssm-ID: 438803 [Multi-domain]  Cd Length: 100  Bit Score: 47.80  E-value: 2.22e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
7ZIE_A      160 KPKLGANGFAKYVQENY--IRGDSLTETMKKLADEWNALSETEKQQY-QISKEDKEKYKKALEKWKE 223
Cdd:cd21987  20 KPKRPRSAFNIFVSEHFqeAKGDSPQEKLKTLKEEWKNLSSSQKQLYiQLAEDDKIRYENEMKSWEE 86
HMG-box_AtHMGB9-like cd22009
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 ...
 161-221 4.65e-06

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 (HMGB9) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB9, 10, 11, and 15. They are DNA-binding proteins containing both HMG-box and AT-rich interaction domains. They bind preferentially to DNA with A/T-rich content. HMGB9 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 have only one HMG-box domain.


Pssm-ID: 438825 [Multi-domain]  Cd Length: 67  Bit Score: 43.22  E-value: 4.65e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
7ZIE_A      161 PKLGANGFAKYVQENYIRGDSL-----TETMKKLADEWNALSETEKQQYQ-ISKEDKEKYKKALEKW 221
Cdd:cd22009   1 PKPNRSGYNFFFAEQHARLKALypgkdREISKMIGEMWSNLTEEEKEVYQdKGVEDKERYKREMEEY 67
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 179-222 1.65e-05

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: 41.51  E-value: 1.65e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
7ZIE_A      179 GDSLTETMKKLADEWNALSETEKQQY-QISKEDKEKYKKALEKWK 222
Cdd:cd21994  23 GISVTEISKKAGEIWKELDEEDKEKWeQKAEKAKERYDKAMKEYK 67
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 161-223 1.57e-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: 1.57e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
7ZIE_A      161 PKLGANGFAKYVQENY------IRGDSLTETMKKLADEWNALSETEKQQYQiskedkEKYKKALEKWKE 223
Cdd:cd22012   2 PKRPASAYFLFAKEVRpklkeeNPNEKYTDITKLISEKWRSLDESEKEPYQ------EEYEKALEEYEE 64
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 181-222 1.75e-04

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: 39.07  E-value: 1.75e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
7ZIE_A      181 SLTETMKKLADEWNALSETEKQQY-QISKEDKEKYKKALEKWK 222
Cdd:cd21980  28 SFPEITKILGAEWSSLSAEEKQKYlDEAEKDKERYVKELEAYQ 70
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 166-214 3.49e-04

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: 37.88  E-value: 3.49e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
7ZIE_A      166 NGFAKYVQENYIR------GDSLTETMKKLADEWNALSETEKQQYQ-ISKEDKEKY 214
Cdd:cd00084   4 SAYLLFSKEKRPKlkkenpDLSFTEISKLLGERWKELSEEEKQPYEeKAKEDKERY 59
HMG smart00398
high mobility group;
160-222 6.70e-03

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 34.60  E-value: 6.70e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7ZIE_A         160 KPKLGANGFAKYVQENYIR------GDSLTETMKKLADEWNALSETEKQQY-QISKEDKEKYKKALEKWK 222
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKikaenpDLSNAEISKKLGERWKLLSEEEKAPYeEKAKKDKERYEEEMPEYK 70
HMG-box_UBF1_rpt6-like cd22003
sixth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 166-223 9.21e-03

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


Pssm-ID: 438819 [Multi-domain]  Cd Length: 86  Bit Score: 34.58  E-value: 9.21e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
7ZIE_A      166 NGFAKYVQE----NYIRGDSLTETMKKLADEWNALSETEKQQYQISKED-KEKYKKALEKWKE 223
Cdd:cd22003   9 SGYQLFSQEmlknGELVHLSLKERMVEIAKRWKRLSESEKDKYKKKAEElQKQYKKKLDKYLK 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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