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Conserved domains on  [gi|223998917|ref|XP_002289131|]
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predicted protein [Thalassiosira pseudonana CCMP1335]

Protein Classification

HMG-box domain-containing protein( domain architecture ID 10647823)

HMG (High Mobility Group)-box domain-containing protein binds DNA and may be a chromosomal protein or function as a transcription factor; similar to Schizosaccharomyces pombe mating-type P-specific polypeptide Pc required for conjugation and efficient meiosis

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 smart00398
high mobility group;
55-144 3.03e-08

high mobility group;


:

Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 50.01  E-value: 3.03e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917    55 HPLRPRSSYNFFFTMQRqaiikqqqkqplvvhkstrNKHRIgKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKE 134
Cdd:smart00398   1 KPKRPMSAFMLFSQENR-------------------AKIKA-ENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60

                           90
                   ....*....|
gi 223998917   135 RYERELMDWN 144
Cdd:smart00398  61 RYEEEMPEYK 70
 
Name Accession Description Interval E-value
HMG smart00398
high mobility group;
55-144 3.03e-08

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 50.01  E-value: 3.03e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917    55 HPLRPRSSYNFFFTMQRqaiikqqqkqplvvhkstrNKHRIgKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKE 134
Cdd:smart00398   1 KPKRPMSAFMLFSQENR-------------------AKIKA-ENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60

                           90
                   ....*....|
gi 223998917   135 RYERELMDWN 144
Cdd:smart00398  61 RYEEEMPEYK 70
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 58-136 5.20e-08

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: 49.05  E-value: 5.20e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 223998917  58 RPRSSYNFFFtmqrqaiikqqqkqplvvhKSTRNKHRiGKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKERY 136
Cdd:cd00084    1 RPLSAYLLFS-------------------KEKRPKLK-KENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 56-144 5.33e-07

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: 46.63  E-value: 5.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917   56 PLRPRSSYNFFFtmqrqaiikqqqkqplvvhKSTRNKHRiGKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKER 135
Cdd:pfam09011   4 PKRARNAYAFFV-------------------QEMIPEHK-RQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNR 63


                  ....*....
gi 223998917  136 YERELMDWN 144
Cdd:pfam09011  64 YDREMGTYD 72
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
35-174 4.14e-06

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 47.16  E-value: 4.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917  35 SKPTKTSKIPT-TSKKGDEEGhPLRPRSSYNFFFTMQRQAIikqqqkqplvvhKSTRNKHRigkhanvgFANLAKIIGEQ 113
Cdd:COG5648   50 TKPRKKTKSKRlVRKKKDPNG-PKRPLSAYFLYSAENRDEI------------RKENPKLT--------FGEVGKLLSEK 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 223998917 114 WRKADPAMKKEMKRRAKLDKERYERELMDWNAKKKGVAMI---KKDTAASATVITPDNKVSTVI 174
Cdd:COG5648  109 WKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNKAPIgpfIENEPKIRPKVEGPSPDKALV 172
PTZ00199 PTZ00199
high mobility group protein; Provisional
 104-144 2.82e-05

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 42.53  E-value: 2.82e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 223998917 104 ANLAKIIGEQWRKADPAMKKEMKRRAKLDKERYERELMDWN 144
Cdd:PTZ00199  53 AAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA 93
 
Name Accession Description Interval E-value
HMG smart00398
high mobility group;
55-144 3.03e-08

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 50.01  E-value: 3.03e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917    55 HPLRPRSSYNFFFTMQRqaiikqqqkqplvvhkstrNKHRIgKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKE 134
Cdd:smart00398   1 KPKRPMSAFMLFSQENR-------------------AKIKA-ENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60

                           90
                   ....*....|
gi 223998917   135 RYERELMDWN 144
Cdd:smart00398  61 RYEEEMPEYK 70
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 58-136 5.20e-08

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: 49.05  E-value: 5.20e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 223998917  58 RPRSSYNFFFtmqrqaiikqqqkqplvvhKSTRNKHRiGKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKERY 136
Cdd:cd00084    1 RPLSAYLLFS-------------------KEKRPKLK-KENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 42-139 7.27e-08

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: 49.29  E-value: 7.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917  42 KIPTTSKKGDEEGhPLRPRSSYNFFFTMQRQAIIKqqqkqplvvhkstrnkhrigKHANVGFANLAKIIGEQWRKADPAM 121
Cdd:cd01390    1 KKKKGRKKKDPNA-PKRGLSAYMFFSQDNREKVKE--------------------ENPDATFGEVGKLLGEKWKELSEEE 59

                         90
                 ....*....|....*...
gi 223998917 122 KKEMKRRAKLDKERYERE 139
Cdd:cd01390   60 KAPYEEKAAKDKKRYEEE 77
HMG-box_HMGB_rpt1 cd21978
first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 56-141 9.13e-08

first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian cells. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of the HMGB family that functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory responses. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. This family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa, is a tumor suppressor that is a major constituent of promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomere lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, binds preferentially to single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438794 [Multi-domain]  Cd Length: 69  Bit Score: 48.84  E-value: 9.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917  56 PLRPRSSYNFFFtmqrqaiikqqqkqplvvhKSTRNKH-RIGKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKE 134
Cdd:cd21978    2 PRGKMSSYAFFV-------------------QTCREEHkKKHPNESVNFSEFSKKCSERWKTMSAKEKKKFEDMAKKDKA 62


                 ....*..
gi 223998917 135 RYERELM 141
Cdd:cd21978   63 RYEREMK 69
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 56-144 5.33e-07

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: 46.63  E-value: 5.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917   56 PLRPRSSYNFFFtmqrqaiikqqqkqplvvhKSTRNKHRiGKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKER 135
Cdd:pfam09011   4 PKRARNAYAFFV-------------------QEMIPEHK-RQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNR 63


                  ....*....
gi 223998917  136 YERELMDWN 144
Cdd:pfam09011  64 YDREMGTYD 72
HMG-box_AtHMGB9-like cd22009
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 ...
 56-143 1.91e-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: 45.15  E-value: 1.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917  56 PLRPRSSYNFFFTMQRQAIIkqqqkqPLVVHKSTrnkhrigkhanvgfaNLAKIIGEQWRKADPAMKKEMKRRAKLDKER 135
Cdd:cd22009    1 PKPNRSGYNFFFAEQHARLK------ALYPGKDR---------------EISKMIGEMWSNLTEEEKEVYQDKGVEDKER 59


                 ....*...
gi 223998917 136 YERELMDW 143
Cdd:cd22009   60 YKREMEEY 67
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
35-174 4.14e-06

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 47.16  E-value: 4.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917  35 SKPTKTSKIPT-TSKKGDEEGhPLRPRSSYNFFFTMQRQAIikqqqkqplvvhKSTRNKHRigkhanvgFANLAKIIGEQ 113
Cdd:COG5648   50 TKPRKKTKSKRlVRKKKDPNG-PKRPLSAYFLYSAENRDEI------------RKENPKLT--------FGEVGKLLSEK 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 223998917 114 WRKADPAMKKEMKRRAKLDKERYERELMDWNAKKKGVAMI---KKDTAASATVITPDNKVSTVI 174
Cdd:COG5648  109 WKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNKAPIgpfIENEPKIRPKVEGPSPDKALV 172
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 90-144 5.67e-06

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: 43.44  E-value: 5.67e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 223998917  90 RNKHRIGK-HANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKERYERELMDWN 144
Cdd:cd21994   12 ENREKIKKeNPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKEYK 67
HMG-box_AtHMGB6-like_rpt2 cd22007
second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 96-140 1.27e-05

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: 42.63  E-value: 1.27e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 223998917  96 GKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKERYEREL 140
Cdd:cd22007   21 EENKNVKITEIAKMLGAEWKNLSDAKKKPYEEKAKKLKEAYLQEM 65
HMG_box pfam00505
HMG (high mobility group) box;
56-143 1.46e-05

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 42.60  E-value: 1.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917   56 PLRPRSSYNFFFTMQRqaiikqqqkqplvvhkstrnKHRIGKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKER 135
Cdd:pfam00505   1 PKRPMSAFFLFSKEQR--------------------AKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKAR 60


                  ....*...
gi 223998917  136 YERELMDW 143
Cdd:pfam00505  61 YEKEHPEY 68
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 97-140 2.07e-05

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: 42.53  E-value: 2.07e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 223998917  97 KHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKERYEREL 140
Cdd:cd21980   23 ENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKERYVKEL 66
PTZ00199 PTZ00199
high mobility group protein; Provisional
 104-144 2.82e-05

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 42.53  E-value: 2.82e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 223998917 104 ANLAKIIGEQWRKADPAMKKEMKRRAKLDKERYERELMDWN 144
Cdd:PTZ00199  53 AAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA 93
HMG-box_AtSSRP1 cd22013
high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and ...
 48-144 5.10e-05

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: 41.38  E-value: 5.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917  48 KKGDEEGHPLRPRSSYNFFFTMQRQAIikqqqkqplvvhKSTrnkhrigkHANVGFANLAKIIGEQWRKADPAMKKEMKR 127
Cdd:cd22013    1 KKKKDPNAPKRALSGFMFFSLMERENL------------KKE--------KPGISFGEVGKVLGEKWKNMSADDKAPYEA 60

                         90
                 ....*....|....*..
gi 223998917 128 RAKLDKERYERELMDWN 144
Cdd:cd22013   61 KAQVDKERYKKEMSGYK 77
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 96-143 1.78e-03

second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of HMGB family and functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory response. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. The family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa. It is a tumor suppressor that is a major constituent of the promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomeres lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, is a Drosophila HMG1 protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438795 [Multi-domain]  Cd Length: 71  Bit Score: 36.62  E-value: 1.78e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 223998917  96 GKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKERYERELMDW 143
Cdd:cd21979   23 GEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEKDIAAY 70
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 56-146 2.41e-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: 36.36  E-value: 2.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223998917  56 PLRPRSSYNFFFTMQRqaiikqqqkqplvvhkstRNKHRIGKhANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKER 135
Cdd:cd22011    1 PKRPSSAYFLFSQEIR------------------KNLKSQGS-PEEKVPELSKRAAEQWRSLTLAEKQPYYDEVEVLKKQ 61

                         90
                 ....*....|.
gi 223998917 136 YERELMDWNAK 146
Cdd:cd22011   62 YDVEKEEYEKE 72
HMG-box_HMG20B cd22018
high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar ...
 90-143 2.79e-03

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: 36.49  E-value: 2.79e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 223998917  90 RNKHRIGKHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKERYERELMDW 143
Cdd:cd22018   16 RREQIRTQHPDLPFPEITKMLGAEWSKLQPHEKQRYLDEAERDKQQYMKELREY 69
HMG-box_HMG20A cd22017
high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar ...
 97-140 4.55e-03

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: 36.46  E-value: 4.55e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 223998917  97 KHANVGFANLAKIIGEQWRKADPAMKKEMKRRAKLDKERYEREL 140
Cdd:cd22017   42 ERPDVPFPEITRMLGNEWSKLPAEEKQRYLDEAEKDKERYMKEL 85
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 97-145 5.43e-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: 34.95  E-value: 5.43e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 223998917  97 KHANVGFANLAKIIGEQWRKADPAMKKEMkrrakldKERYERELMDWNA 145
Cdd:cd22012   23 ENPNEKYTDITKLISEKWRSLDESEKEPY-------QEEYEKALEEYEE 64
 
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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