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Conserved domains on  [gi|1826601731|ref|NP_001366230|]
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high mobility group protein B4 isoform 1 [Homo sapiens]

Protein Classification

high mobility group protein B( domain architecture ID 17777591)

high mobility group protein B (HMGB) is multifunctional protein with various roles in different cellular compartments

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_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 91-161 3.61e-36

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: 120.59  E-value: 3.61e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826601731  91 QEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYR 161
Cdd:cd21979     1 NAPKRPPSAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEKDIAAYR 71
HMG-box_HMGB_rpt1 cd21978
first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 8-76 5.60e-27

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: 96.99  E-value: 5.60e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1826601731   8 KPKANVSSYVHFLLNYRNKFKEQQPNTYVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMM 76
Cdd:cd21978     1 KPRGKMSSYAFFVQTCREEHKKKHPNESVNFSEFSKKCSERWKTMSAKEKKKFEDMAKKDKARYEREMK 69
 
Name Accession Description Interval E-value
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 91-161 3.61e-36

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: 120.59  E-value: 3.61e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826601731  91 QEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYR 161
Cdd:cd21979     1 NAPKRPPSAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEKDIAAYR 71
HMG-box_HMGB_rpt1 cd21978
first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 8-76 5.60e-27

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: 96.99  E-value: 5.60e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1826601731   8 KPKANVSSYVHFLLNYRNKFKEQQPNTYVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMM 76
Cdd:cd21978     1 KPRGKMSSYAFFVQTCREEHKKKHPNESVNFSEFSKKCSERWKTMSAKEKKKFEDMAKKDKARYEREMK 69
HMG_box pfam00505
HMG (high mobility group) box;
93-160 9.08e-14

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 63.01  E-value: 9.08e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1826601731  93 PRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELY 160
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 8-78 1.19e-13

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: 62.81  E-value: 1.19e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826601731   8 KPKANVSSYVHFLLNYRNKFKEQQPntYVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:pfam09011   3 KPKRARNAYAFFVQEMIPEHKRQNP--VIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGTY 71
HMG smart00398
high mobility group;
93-161 1.78e-12

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 59.64  E-value: 1.78e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1826601731   93 PRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYR 161
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
HMG smart00398
high mobility group;
8-78 6.87e-10

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 53.09  E-value: 6.87e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826601731    8 KPKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPD--LSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
89-162 5.37e-09

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 53.33  E-value: 5.37e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1826601731  89 DPQEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYRK 162
Cdd:COG5648    67 DPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNK 140
PTZ00199 PTZ00199
high mobility group protein; Provisional
 89-162 2.60e-08

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 49.47  E-value: 2.60e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731  89 DPQEPRRPPSSFLLFCQDHYAQLKRENPNWS--VVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYRK 162
Cdd:PTZ00199   19 DPNAPKRALSAYMFFAKEKRAEIIAENPELAkdVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94
PTZ00199 PTZ00199
high mobility group protein; Provisional
 3-78 1.64e-03

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 36.37  E-value: 1.64e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731   3 KEIQLKPKANVSSYVHFLLNYRNKFKEQQPNTYVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:PTZ00199   17 KKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEY 92
 
Name Accession Description Interval E-value
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 91-161 3.61e-36

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: 120.59  E-value: 3.61e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826601731  91 QEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYR 161
Cdd:cd21979     1 NAPKRPPSAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEKDIAAYR 71
HMG-box_HMGB_rpt1 cd21978
first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 8-76 5.60e-27

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: 96.99  E-value: 5.60e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1826601731   8 KPKANVSSYVHFLLNYRNKFKEQQPNTYVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMM 76
Cdd:cd21978     1 KPRGKMSSYAFFVQTCREEHKKKHPNESVNFSEFSKKCSERWKTMSAKEKKKFEDMAKKDKARYEREMK 69
HMG_box pfam00505
HMG (high mobility group) box;
93-160 9.08e-14

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 63.01  E-value: 9.08e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1826601731  93 PRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELY 160
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 8-78 1.19e-13

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: 62.81  E-value: 1.19e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826601731   8 KPKANVSSYVHFLLNYRNKFKEQQPntYVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:pfam09011   3 KPKRARNAYAFFVQEMIPEHKRQNP--VIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGTY 71
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 95-153 6.15e-13

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: 60.61  E-value: 6.15e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1826601731  95 RPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKY 153
Cdd:cd00084     1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_AtSSRP1 cd22013
high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and ...
 9-78 1.44e-12

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: 60.26  E-value: 1.44e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd22013     9 PKRALSGFMFFSLMERENLKKEKPG--ISFGEVGKVLGEKWKNMSADDKAPYEAKAQVDKERYKKEMSGY 76
HMG smart00398
high mobility group;
93-161 1.78e-12

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 59.64  E-value: 1.78e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1826601731   93 PRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYR 161
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
HMG-box_AtHMGB1-like cd22005
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 ...
 95-153 9.59e-12

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 (HMGB1) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB1, 2, 3, 4, 5, 7, 12 and 14. They bind preferentially to double-stranded DNA. HMGB1 modulates general plant growth and stress tolerance and confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. HMGB2 and HMGB5 confer sensitivity to salt and drought stresses. HMGB7 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 contain only one HMG-box domain.


Pssm-ID: 438821 [Multi-domain]  Cd Length: 60  Bit Score: 57.70  E-value: 9.59e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1826601731  95 RPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKY 153
Cdd:cd22005     2 RPPTAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAEKEKAEY 60
HMG-box_AtHMGB6-like_rpt2 cd22007
second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 93-160 2.39e-11

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: 56.88  E-value: 2.39e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1826601731  93 PRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELY 160
Cdd:cd22007     1 PKRPQSAYFLYANDRRAALKEENKNVKITEIAKMLGAEWKNLSDAKKKPYEEKAKKLKEAYLQEMEEY 68
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 89-160 6.91e-11

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: 55.84  E-value: 6.91e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1826601731  89 DPQEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELY 160
Cdd:cd01390    10 DPNAPKRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAAKDKKRYEEEKAAY 81
HMG_box pfam00505
HMG (high mobility group) box;
9-78 3.96e-10

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 53.38  E-value: 3.96e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNTYVGfkEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNA--EISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 14-78 6.27e-10

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: 53.07  E-value: 6.27e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1826601731  14 SSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd21994     4 SAYMLWLNENREKIKKENPG--ISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKEY 66
HMG smart00398
high mobility group;
8-78 6.87e-10

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 53.09  E-value: 6.87e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826601731    8 KPKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPD--LSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 9-78 9.27e-10

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: 52.76  E-value: 9.27e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd01390    14 PKRGLSAYMFFSQDNREKVKEENPD--ATFGEVGKLLGEKWKELSEEEKAPYEEKAAKDKKRYEEEKAAY 81
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 9-78 1.03e-09

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: 52.55  E-value: 1.03e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd21980     2 PKAPLTGYVRFLNERREKLRAENPD--LSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKERYVKELEAY 69
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 93-162 1.32e-09

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: 51.90  E-value: 1.32e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731  93 PRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRvallrakYFEELELYRK 162
Cdd:cd22012     2 PKRPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQEE-------YEKALEEYEE 64
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 14-71 1.34e-09

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: 51.75  E-value: 1.34e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1826601731  14 SSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARY 71
Cdd:cd00084     4 SAYLLFSKEKRPKLKKENPD--LSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_AtHMGB6-like_rpt1 cd22006
first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 94-168 2.15e-09

first 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 first one.


Pssm-ID: 438822 [Multi-domain]  Cd Length: 68  Bit Score: 51.68  E-value: 2.15e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQrvallraKYFEELELYRKQCNARK 168
Cdd:cd22006     1 KKPKTAYFLWCKDQREEVKKENPNADFSEVSKILGAKWKNLSEEEKKPYEE-------KYKEEKEKYLKVVGEEK 68
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 95-161 2.29e-09

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: 51.53  E-value: 2.29e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1826601731  95 RPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYR 161
Cdd:cd21994     1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKEYK 67
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
89-162 5.37e-09

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 53.33  E-value: 5.37e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1826601731  89 DPQEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYRK 162
Cdd:COG5648    67 DPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNK 140
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
9-159 1.91e-08

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 51.79  E-value: 1.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNYVGKRkkrrkr 88
Cdd:COG5648    71 PKRPLSAYFLYSAENRDEIRKENPK--LTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKL------ 142

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826601731  89 dpqEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELEL 159
Cdd:COG5648   143 ---PNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYPE 210
PTZ00199 PTZ00199
high mobility group protein; Provisional
 89-162 2.60e-08

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 49.47  E-value: 2.60e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731  89 DPQEPRRPPSSFLLFCQDHYAQLKRENPNWS--VVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYRK 162
Cdd:PTZ00199   19 DPNAPKRALSAYMFFAKEKRAEIIAENPELAkdVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94
HMG-box_ABF2-like_rpt1 cd22010
first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 93-160 2.92e-08

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: 48.69  E-value: 2.92e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1826601731  93 PRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELY 160
Cdd:cd22010     1 PKRPLSAYFLYFQEHRSDFVKENPDAKMTEISKIGGDKWKNLSADDKKKYEDDFQRELSEYQKAKAEF 68
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 93-162 7.31e-08

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: 47.53  E-value: 7.31e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826601731  93 PRRPPSSFLLFCQDHYAQLKRENPNWS-VVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYRK 162
Cdd:cd22011     1 PKRPSSAYFLFSQEIRKNLKSQGSPEEkVPELSKRAAEQWRSLTLAEKQPYYDEVEVLKKQYDVEKEEYEK 71
HMG-box_SMARCE1 cd21983
high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent ...
 89-160 7.44e-08

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: 47.68  E-value: 7.44e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1826601731  89 DPQEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELY 160
Cdd:cd21983     1 PPKPPEKPLMPYMRYSRKVWDQVKASNPDLKLWEIGKIIGQMWRELSDEEKQEYIEEYEAEKVEYEEQMKAY 72
HMG-box_ROX1-like cd01389
high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar ...
 93-152 1.54e-07

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: 46.81  E-value: 1.54e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731  93 PRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAK 152
Cdd:cd01389     1 IPRPPNAFILFRKEKHKQLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEE 60
HMG-box_AtHMGB1-like cd22005
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 ...
 14-71 1.77e-07

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 (HMGB1) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB1, 2, 3, 4, 5, 7, 12 and 14. They bind preferentially to double-stranded DNA. HMGB1 modulates general plant growth and stress tolerance and confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. HMGB2 and HMGB5 confer sensitivity to salt and drought stresses. HMGB7 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 contain only one HMG-box domain.


Pssm-ID: 438821 [Multi-domain]  Cd Length: 60  Bit Score: 46.15  E-value: 1.77e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1826601731  14 SSYVHFLLNYRNKFKEQQPNTyvGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARY 71
Cdd:cd22005     5 TAFFLFLADFRKTYKKKNPDK--SVKAVGKAAGEKWKSMSDEEKAPYVEKAEKEKAEY 60
HMG-box_AtHMGB6-like_rpt3 cd22008
third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 89-161 2.56e-07

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: 46.48  E-value: 2.56e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1826601731  89 DPQEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYR 161
Cdd:cd22008     6 DPNKPKKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAVLMEKYKKEVEEYN 78
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 93-172 2.90e-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: 2.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731  93 PRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYrKQCNARKKYRM 172
Cdd:cd21980     2 PKAPLTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKERYVKELEAY-QQTEAYKAFLK 80
HMG-box_HBP2 cd21989
high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar ...
 94-142 5.66e-07

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: 45.09  E-value: 5.66e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPY 142
Cdd:cd21989     1 RRPMNAFLLFCKRHRSLVRERHPRLDNRGITKILGDWWAVLDPDEKQKY 49
HMG-box_AtSSRP1 cd22013
high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and ...
 89-162 2.23e-06

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: 43.69  E-value: 2.23e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1826601731  89 DPQEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYRK 162
Cdd:cd22013     5 DPNAPKRALSGFMFFSLMERENLKKEKPGISFGEVGKVLGEKWKNMSADDKAPYEAKAQVDKERYKKEMSGYKN 78
HMG-box_NHP10-like cd22016
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) ...
 89-160 3.24e-06

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: 43.48  E-value: 3.24e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731  89 DPQEPRRPPSSFLLFCQDH----YAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELY 160
Cdd:cd22016     4 DPNAPKRPANAFFLFCQEQrekvREEYKEEHQEIDHHDLTKALAQAWRNLDAEDKKPYYELYEKDKERYEKEMEEY 79
HMG-box_TOX-like cd21995
high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family ...
 94-161 3.29e-06

high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family includes four members: TOX, TOX2, TOX3 and TOX4. TOX, also called thymus high mobility group box protein TOX, is a transcriptional regulator with a major role in neural stem cell commitment and corticogenesis as well as in lymphoid cell development and lymphoid tissue organogenesis. It binds to GC-rich DNA sequences in the proximity of transcription start sites and may alter chromatin structure, modifying access of transcription factors to DNA. TOX2, also called granulosa cell HMG box protein 1 (GCX-1), is a putative transcriptional activator involved in the hypothalamic-pituitary-gonadal system. TOX3, also called CAG trinucleotide repeat-containing gene F9 protein (CAGF9), or trinucleotide repeat-containing gene 9 protein (TNRC9), is a transcriptional coactivator of the p300/CBP-mediated transcription complex. It activates transactivation through cAMP response element (CRE) sites. It protects against cell death by inducing anti-apoptotic and repressing pro-apoptotic transcripts. TOX4, also called epidermal Langerhans cell protein LCP1, is a component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. All family members contain one HMG-box domain.


Pssm-ID: 438811 [Multi-domain]  Cd Length: 70  Bit Score: 43.23  E-value: 3.29e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYR 161
Cdd:cd21995     1 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLDEEQKQVYKKKTEAAKKEYLKALAAYR 68
HMG-box_HMG20B cd22018
high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar ...
 9-78 5.41e-06

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: 43.04  E-value: 5.41e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd22018     2 PKAPVTGYVRFLNERREQIRTQHPD--LPFPEITKMLGAEWSKLQPHEKQRYLDEAERDKQQYMKELREY 69
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 90-156 5.56e-06

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: 42.39  E-value: 5.56e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1826601731  90 PQEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEE 156
Cdd:pfam09011   1 PNKPKRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDRE 67
HMG-box_CMB1-like cd22014
high mobility group (HMG)-box found in Schizosaccharomyces pombe mismatch-binding protein cmb1 ...
 93-157 5.59e-06

high mobility group (HMG)-box found in Schizosaccharomyces pombe mismatch-binding protein cmb1 and similar proteins; Cmb1 binds to cytosines in base mismatches and opposite chemically altered guanines. It contains only one HMG-box domain.


Pssm-ID: 438830 [Multi-domain]  Cd Length: 62  Bit Score: 42.36  E-value: 5.59e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1826601731  93 PRRPPSSFLLFCQDHYAQLKRENPnwsVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEEL 157
Cdd:cd22014     1 PKRPPSPFLLFMEEFRRNEDNGKN---LVELSRIAAEAWKNMSEDEKQPYIDRAKELLEEYKKQL 62
HMG-box_MAEL cd21992
high mobility group (HMG)-box found in protein maelstrom (MAEL) and similar proteins; MAEL is ...
 15-70 8.23e-06

high mobility group (HMG)-box found in protein maelstrom (MAEL) and similar proteins; MAEL is an RNA-binding protein that has evolved from an ancient nuclease active in protists. It plays a central role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons.


Pssm-ID: 438808 [Multi-domain]  Cd Length: 61  Bit Score: 41.84  E-value: 8.23e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731  15 SYVHFLLNYRNKFkEQQPNTYVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKAR 70
Cdd:cd21992     6 AFYFFMLELKPEL-ERKGKNFPGMAEAAPLASPKWKSLSPEEKEPYEEMAKEEKEN 60
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 9-78 9.50e-06

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: 42.01  E-value: 9.50e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNTYVGfkEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd21979     3 PKRPPSAFFLFCSEHRPKIKGEHPGLSIG--DVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEKDIAAY 70
HMG-box_HMG20A cd22017
high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar ...
 9-78 9.74e-06

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: 42.63  E-value: 9.74e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd22017    21 PKAPLTGYVRFMNERREQLRAERPD--VPFPEITRMLGNEWSKLPAEEKQRYLDEAEKDKERYMKELEQY 88
HMG-box_AtHMGB6-like_rpt3 cd22008
third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 8-78 9.93e-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: 41.86  E-value: 9.93e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826601731   8 KPKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd22008     9 KPKKPASSYLLFGKEYRKKLQEERPG--ANNATVTALISLKWKELGEEEKQVYNDKAAVLMEKYKKEVEEY 77
HMG-box_NSD2 cd21991
high mobility group (HMG)-box found in nuclear SET domain-containing protein 2 (NSD2) and ...
 94-147 9.98e-06

high mobility group (HMG)-box found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins; NSD2, also called multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), acts as a histone-lysine N-methyltransferase with histone H3 'Lys-36' (H3K36me) methyltransferase activity. NSD2 has been shown to mediate di- and trimethylation of H3K36 and dimethylation of H4K20 in different systems and has been characterized as a transcriptional repressor interacting with histone deacetylase HDAC1 and histone demethylase LSD1. NSD2 mediates constitutive NF-kappaB signaling for cancer cell proliferation, survival and tumor growth. It is highly overexpressed in several types of human cancers, including small-cell lung cancers, neuroblastoma, carcinomas of stomach and colon, and bladder cancers, and its overexpression tends to be associated with tumor aggressiveness.


Pssm-ID: 438807 [Multi-domain]  Cd Length: 62  Bit Score: 41.53  E-value: 9.98e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVA 147
Cdd:cd21991     3 KVKKGQFEVFCQKHREEVAQEHPDLSEEEIEEYLKKQWNNMSEKQRARYKSKFA 56
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 93-156 1.38e-05

fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins; UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the fourth one.


Pssm-ID: 438817 [Multi-domain]  Cd Length: 66  Bit Score: 41.13  E-value: 1.38e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1826601731  93 PRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEE 156
Cdd:cd22001     3 PKRPISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYEKK 66
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 94-166 1.90e-05

high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; PMS1, also called DNA mismatch repair protein PMS1, is probably involved in the repair of mismatches in DNA.


Pssm-ID: 438801 [Multi-domain]  Cd Length: 73  Bit Score: 40.99  E-value: 1.90e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVAllrakyfEELELYRKQCNA 166
Cdd:cd21985     3 RKPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAA-------KDLERYNSQKKR 68
HMG-box_SoxF_SOX17 cd22047
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and ...
 94-161 3.23e-05

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and similar proteins; SOX-17 is a developmental transcription regulator involved in endoderm formation, angiogenesis, and carcinogenesis. It acts as a tumor suppressor and modulates WNT signaling. SOX-17 binds target promoter DNA and bends the DNA. It binds to the sequences 5'-AACAAT-'3 or 5'-AACAAAG-3'. SOX-17 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438850 [Multi-domain]  Cd Length: 81  Bit Score: 40.84  E-value: 3.23e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYR 161
Cdd:cd22047     8 RRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK 75
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 9-79 3.53e-05

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: 40.60  E-value: 3.53e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNTyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNYV 79
Cdd:cd22011     1 PKRPSSAYFLFSQEIRKNLKSQGSPE-EKVPELSKRAAEQWRSLTLAEKQPYYDEVEVLKKQYDVEKEEYE 70
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 10-66 4.02e-05

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 39.92  E-value: 4.02e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1826601731  10 KANVSSYVHFLLNYRNKFKEQQPNTyvGFKEFSRKCSEKWRSISKHEKAKYEALAKL 66
Cdd:cd21984     1 KRNPSGYILFSSEVRKSIKAENPDY--SFGEISRLVGTEWRNLPAEKKAEYEERAQK 55
HMG-box_ROX1-like cd01389
high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar ...
 19-78 4.14e-05

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: 40.26  E-value: 4.14e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731  19 FLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd01389    11 FRKEKHKQLRAQNPG--LTNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEEHKLKYPDY 68
HMG-box_CMB1-like cd22014
high mobility group (HMG)-box found in Schizosaccharomyces pombe mismatch-binding protein cmb1 ...
 9-75 4.61e-05

high mobility group (HMG)-box found in Schizosaccharomyces pombe mismatch-binding protein cmb1 and similar proteins; Cmb1 binds to cytosines in base mismatches and opposite chemically altered guanines. It contains only one HMG-box domain.


Pssm-ID: 438830 [Multi-domain]  Cd Length: 62  Bit Score: 39.66  E-value: 4.61e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNTyvgfkEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEM 75
Cdd:cd22014     1 PKRPPSPFLLFMEEFRRNEDNGKNLV-----ELSRIAAEAWKNMSEDEKQPYIDRAKELLEEYKKQL 62
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 9-78 1.01e-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: 1.01e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYealakldKARYQEEMMNY 78
Cdd:cd22012     2 PKRPASAYFLFAKEVRPKLKEENPN--EKYTDITKLISEKWRSLDESEKEPY-------QEEYEKALEEY 62
HMG-box_SoxF_SOX7 cd22046
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar ...
 94-169 1.09e-04

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar proteins; SOX-7 is an endothelial-associated transcription factor that acts as a tumor suppressor in a number of cancer types. It binds the DNA sequence 5'-AACAAT-3'. SOX-7 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438849 [Multi-domain]  Cd Length: 88  Bit Score: 39.29  E-value: 1.09e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYRKQCNARKK 169
Cdd:cd22046    13 RRPMNAFMVWAKDERKRLAVQNPDLHNAELSKMLGKSWKALTPSQKRPYVEEAERLRVQHMQDYPNYKYRPRRKKQ 88
HMG-box_SOX cd22004
high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family ...
 94-156 1.32e-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: 38.68  E-value: 1.32e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEE 156
Cdd:cd22004     3 KRPMNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEAERLREEHKKE 65
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 10-75 2.35e-04

high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; PMS1, also called DNA mismatch repair protein PMS1, is probably involved in the repair of mismatches in DNA.


Pssm-ID: 438801 [Multi-domain]  Cd Length: 73  Bit Score: 38.29  E-value: 2.35e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731  10 KANVSSYVHFLLNYRNKFKEQQPNTYVgfKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEM 75
Cdd:cd21985     3 RKPMSASALFEQETRPQFLAENPKASL--QDITLKIEERWKNLSEEEKKKYEEKAAKDLERYNSQK 66
HMG-box_AtHMGB9-like cd22009
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 ...
 9-78 3.92e-04

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: 37.45  E-value: 3.92e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNTYvgfKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd22009     1 PKPNRSGYNFFFAEQHARLKALYPGKD---REISKMIGEMWSNLTEEEKEVYQDKGVEDKERYKREMEEY 67
HMG-box_SoxF_SOX18 cd22048
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 18 (SOX18) and ...
 94-169 4.64e-04

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 18 (SOX18) and similar proteins; SOX-18 is a transcription factor involved in the development of cardiovascular and lymphatic vessels during embryonic development. It binds to the consensus sequence 5'-AACAAAG-3' and is able to trans-activate transcription via this site. SOX-18 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438851 [Multi-domain]  Cd Length: 80  Bit Score: 37.36  E-value: 4.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYRKQCNARKK 169
Cdd:cd22048     5 RRPMNAFMVWAKDERKRLAQQNPDLHNAVLSKMLGQSWKSLSAAEKRPFVEEAERLRVQHLQDHPNYKYRPRRKKQ 80
HMG-box_AtHMGB6-like_rpt2 cd22007
second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 9-78 4.80e-04

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: 37.23  E-value: 4.80e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd22007     1 PKRPQSAYFLYANDRRAALKEENKN--VKITEIAKMLGAEWKNLSDAKKKPYEEKAKKLKEAYLQEMEEY 68
HMG-box_AtHMGB6-like_rpt1 cd22006
first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 8-75 5.04e-04

first 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 first one.


Pssm-ID: 438822 [Multi-domain]  Cd Length: 68  Bit Score: 37.05  E-value: 5.04e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1826601731   8 KPKanvSSYVHFLLNYRNKFKEQQPNTyvGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEM 75
Cdd:cd22006     2 KPK---TAYFLWCKDQREEVKKENPNA--DFSEVSKILGAKWKNLSEEEKKPYEEKYKEEKEKYLKVV 64
HMG-box_NHP10-like cd22016
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) ...
 9-78 5.43e-04

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: 37.31  E-value: 5.43e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKE--QQPNTYVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:cd22016     8 PKRPANAFFLFCQEQREKVREeyKEEHQEIDHHDLTKALAQAWRNLDAEDKKPYYELYEKDKERYEKEMEEY 79
HMG-box_SoxA_SRY cd22034
high mobility group (HMG)-box found in sex-determining region Y protein (SRY) and similar ...
 94-169 1.24e-03

high mobility group (HMG)-box found in sex-determining region Y protein (SRY) and similar proteins; 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'. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438843 [Multi-domain]  Cd Length: 85  Bit Score: 36.54  E-value: 1.24e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYRKQCNARKK 169
Cdd:cd22034     6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAK 81
HMG-box_SoxG_SOX15 cd22035
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 15 (SOX15) and ...
 90-161 1.63e-03

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 15 (SOX15) and similar proteins; SOX-15, also called SOX-12, SOX-20, SOX-26, or SOX-27, is a crucial transcription factor involved in the regulation of embryonic development and in cell fate determination. It binds to the 5'-AACAAT-3' sequence. SOX-15 can be a tumor suppressor in multiple cancer types. SOX-5 is the only member of group G SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438844 [Multi-domain]  Cd Length: 84  Bit Score: 36.21  E-value: 1.63e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1826601731  90 PQEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYR 161
Cdd:cd22035     5 LEKVKRPMNAFMVWSSAQRRQMAQEHPKMHNSEISKRLGAAWKLLPEAEKRPFVEEAKRLRARHMRDYPDYK 76
PTZ00199 PTZ00199
high mobility group protein; Provisional
 3-78 1.64e-03

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 36.37  E-value: 1.64e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731   3 KEIQLKPKANVSSYVHFLLNYRNKFKEQQPNTYVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEEMMNY 78
Cdd:PTZ00199   17 KKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEY 92
HMG-box_TFAM_rpt1 cd21986
first high mobility group (HMG)-box found in mitochondrial transcription factor A (TFA) and ...
 9-74 3.10e-03

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: 34.84  E-value: 3.10e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731   9 PKANVSSYVHFLLNYRNKFKEQQPNTYVgfkEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEE 74
Cdd:cd21986     1 PKRPLSPYLRFYREQLPSFPAQNPDATT---DLSKRIGERWRELPDSQKKKYQDAYKAEWQKYKEE 63
HMG-box_HMG20A cd22017
high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar ...
 80-177 4.57e-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: 35.31  E-value: 4.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731  80 GKRKKRRKRDPQEPRRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELEL 159
Cdd:cd22017     8 GRKRKKPLRDSNAPKAPLTGYVRFMNERREQLRAERPDVPFPEITRMLGNEWSKLPAEEKQRYLDEAEKDKERYMKELEQ 87

                          90
                  ....*....|....*...
gi 1826601731 160 YrKQCNARKKYRMSARNR 177
Cdd:cd22017    88 Y-QKTEAYKLFSRKAQDR 104
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 94-149 7.12e-03

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 33.75  E-value: 7.12e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALL 149
Cdd:cd21984     1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQ 56
HMG-box_SoxF cd22032
high mobility group (HMG)-box found in group F SRY-related high-mobility group (HMG) box (Sox) ...
 94-161 7.29e-03

high mobility group (HMG)-box found in group F SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxF transcription factors includes three members: Sox7, Sox17, and Sox18. They regulate endothelial cell fate as well as development and differentiation of the developing heart, blood cells, and lymphatic vessels.


Pssm-ID: 438841 [Multi-domain]  Cd Length: 76  Bit Score: 33.93  E-value: 7.29e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYR 161
Cdd:cd22032     3 RRPMNAFMVWAKDERKRLADENPDLHNAELSKMLGKKWKSLSLAEKRPFVEEAERLRVQHMQDYPNYK 70
HMG-box_SoxE cd22031
high mobility group (HMG)-box found in group E SRY-related high-mobility group (HMG) box (Sox) ...
 94-163 8.35e-03

high mobility group (HMG)-box found in group E SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxE transcription factors includes three members: Sox8, Sox9, and Sox10. They function as important transcriptional regulators of neural differentiation and nervous system development. They regulate mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. SOX-8 is specifically expressed by M cells in the intestinal epithelium. It acts as a transcription factor necessary for the maintenance of spermatogenesis. It may play a role in central nervous system, limb and facial development. SOX-9 is involved in cell differentiation, sex determination, and tumorigenesis. It plays a role in chondrocyte differentiation and skeletal development. SOX-10 plays a central role in the development of melanocytes and glial cells from neural crest precursors.


Pssm-ID: 438840 [Multi-domain]  Cd Length: 75  Bit Score: 33.90  E-value: 8.35e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826601731  94 RRPPSSFLLFCQDHYAQLKRENPNWSVVQVAKATGKMWSTATDLEKHPYEQRVALLRAKYFEELELYRKQ 163
Cdd:cd22031     3 KRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLSESEKRPFIEEAERLRVQHKKDHPDYKYQ 72
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 8-74 9.50e-03

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: 33.42  E-value: 9.50e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1826601731   8 KPKANVSSYVHFLLNYRNKFKEQQPNtyVGFKEFSRKCSEKWRSISKHEKAKYEALAKLDKARYQEE 74
Cdd:cd22001     2 KPKRPISAMFIYSKEKRSKLKKKHPE--LSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYEKK 66
 
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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