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Conserved domains on  [gi|1487549048|ref|NP_001353430|]
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HMG domain-containing protein 3 isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HMG-box_HMGXB3 cd21981
high mobility group (HMG)-box found in HMG domain-containing protein 3 (HMGXB3) and similar ...
 6-105 1.05e-46

high mobility group (HMG)-box found in HMG domain-containing protein 3 (HMGXB3) and similar proteins; HMGXB3, also called HMG box-containing protein 3, or protein SMF, is involved in DNA-damage repair and cell-cycle regulation.


:

Pssm-ID: 438797 [Multi-domain]  Cd Length: 105  Bit Score: 162.35  E-value: 1.05e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048    6 DGTEVTVVMEEIEEAYCYTSPGPPKKKKKYKIH---GEKTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRL 82
Cdd:cd21981      1 DGTEITVVTEEIEGCYTYTSPVPPKKKKKSKEQaeqGEKAKKPRSAYLLYYYDIHLKVQQEFPHLPQSEINKKISESWKL 80

                           90       100
                   ....*....|....*....|...
gi 1487549048   83 LSVAERSYYLEKAKLEKEGLDPD 105
Cdd:cd21981     81 LSVAEKSYYLEKAKLEKEGLDPN 103
CxC4 pfam18717
CxC4 like cysteine cluster associated with KDZ transposases; A predicted Zinc chelating domain ...
 577-697 1.11e-10

CxC4 like cysteine cluster associated with KDZ transposases; A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain.


:

Pssm-ID: 408494  Cd Length: 129  Bit Score: 60.42  E-value: 1.11e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048  577 ESPSTQCLL--CSSPLFKGGQNSLAGP---QECWLLTASRLQTVTAQVKMClnPHCLalHSFID---IYTGLFNVGNKLL 648
Cdd:pfam18717    3 ELSAPPFLLalCLSRCPCGTTWDPAGPelwQDCTVYTLTGSQEVRVEVQPC--PACA--VRFIGpdlRELGLFNWNNRTL 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1487549048  649 VSLDLLFAIRNQIKLGEDPRVSINVVLKSVQEQTEKTLTSEELSQLQEL 697
Cdd:pfam18717   79 FTHELLDLYLSAFTRSETPFSAWVSAVRRRYTPSGRSFLSEETFRRAWF 127
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 276-424 1.96e-03

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 42.62  E-value: 1.96e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048  276 PVVKSGVQPEVTLGTTDNDSPGADVPTPSEGTSTSSPLPAPkkPTGADLLTPGSRAPELKGRARGkPSLLAAARPMRail 355
Cdd:PHA03247  2804 PADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPG--PPPPSLPLGGSVAPGGDVRRRP-PSRSPAAKPAA--- 2877

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1487549048  356 PAPVNVGRGSSMGLPRARQAFSLSD------KTPSVRTCGLKPSTLKQLGQPIQQPSGPGEVKLPSGPSNRTSQV 424
Cdd:PHA03247  2878 PARPPVRRLARPAVSRSTESFALPPdqperpPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGA 2952
 
Name Accession Description Interval E-value
HMG-box_HMGXB3 cd21981
high mobility group (HMG)-box found in HMG domain-containing protein 3 (HMGXB3) and similar ...
 6-105 1.05e-46

high mobility group (HMG)-box found in HMG domain-containing protein 3 (HMGXB3) and similar proteins; HMGXB3, also called HMG box-containing protein 3, or protein SMF, is involved in DNA-damage repair and cell-cycle regulation.


Pssm-ID: 438797 [Multi-domain]  Cd Length: 105  Bit Score: 162.35  E-value: 1.05e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048    6 DGTEVTVVMEEIEEAYCYTSPGPPKKKKKYKIH---GEKTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRL 82
Cdd:cd21981      1 DGTEITVVTEEIEGCYTYTSPVPPKKKKKSKEQaeqGEKAKKPRSAYLLYYYDIHLKVQQEFPHLPQSEINKKISESWKL 80

                           90       100
                   ....*....|....*....|...
gi 1487549048   83 LSVAERSYYLEKAKLEKEGLDPD 105
Cdd:cd21981     81 LSVAEKSYYLEKAKLEKEGLDPN 103
CxC4 pfam18717
CxC4 like cysteine cluster associated with KDZ transposases; A predicted Zinc chelating domain ...
 577-697 1.11e-10

CxC4 like cysteine cluster associated with KDZ transposases; A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain.


Pssm-ID: 408494  Cd Length: 129  Bit Score: 60.42  E-value: 1.11e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048  577 ESPSTQCLL--CSSPLFKGGQNSLAGP---QECWLLTASRLQTVTAQVKMClnPHCLalHSFID---IYTGLFNVGNKLL 648
Cdd:pfam18717    3 ELSAPPFLLalCLSRCPCGTTWDPAGPelwQDCTVYTLTGSQEVRVEVQPC--PACA--VRFIGpdlRELGLFNWNNRTL 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1487549048  649 VSLDLLFAIRNQIKLGEDPRVSINVVLKSVQEQTEKTLTSEELSQLQEL 697
Cdd:pfam18717   79 FTHELLDLYLSAFTRSETPFSAWVSAVRRRYTPSGRSFLSEETFRRAWF 127
HMG smart00398
high mobility group;
41-100 2.15e-10

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 57.71  E-value: 2.15e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048    41 KTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:smart00398    1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 41-100 1.97e-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: 46.63  E-value: 1.97e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048   41 KTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:pfam09011    3 KPKRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKN 62
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
43-100 1.62e-03

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 41.00  E-value: 1.62e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1487549048   43 KKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:COG5648     72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRE 129
PHA03247 PHA03247
large tegument protein UL36; Provisional
 276-424 1.96e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 42.62  E-value: 1.96e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048  276 PVVKSGVQPEVTLGTTDNDSPGADVPTPSEGTSTSSPLPAPkkPTGADLLTPGSRAPELKGRARGkPSLLAAARPMRail 355
Cdd:PHA03247  2804 PADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPG--PPPPSLPLGGSVAPGGDVRRRP-PSRSPAAKPAA--- 2877

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1487549048  356 PAPVNVGRGSSMGLPRARQAFSLSD------KTPSVRTCGLKPSTLKQLGQPIQQPSGPGEVKLPSGPSNRTSQV 424
Cdd:PHA03247  2878 PARPPVRRLARPAVSRSTESFALPPdqperpPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGA 2952
 
Name Accession Description Interval E-value
HMG-box_HMGXB3 cd21981
high mobility group (HMG)-box found in HMG domain-containing protein 3 (HMGXB3) and similar ...
 6-105 1.05e-46

high mobility group (HMG)-box found in HMG domain-containing protein 3 (HMGXB3) and similar proteins; HMGXB3, also called HMG box-containing protein 3, or protein SMF, is involved in DNA-damage repair and cell-cycle regulation.


Pssm-ID: 438797 [Multi-domain]  Cd Length: 105  Bit Score: 162.35  E-value: 1.05e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048    6 DGTEVTVVMEEIEEAYCYTSPGPPKKKKKYKIH---GEKTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRL 82
Cdd:cd21981      1 DGTEITVVTEEIEGCYTYTSPVPPKKKKKSKEQaeqGEKAKKPRSAYLLYYYDIHLKVQQEFPHLPQSEINKKISESWKL 80

                           90       100
                   ....*....|....*....|...
gi 1487549048   83 LSVAERSYYLEKAKLEKEGLDPD 105
Cdd:cd21981     81 LSVAEKSYYLEKAKLEKEGLDPN 103
CxC4 pfam18717
CxC4 like cysteine cluster associated with KDZ transposases; A predicted Zinc chelating domain ...
 577-697 1.11e-10

CxC4 like cysteine cluster associated with KDZ transposases; A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain.


Pssm-ID: 408494  Cd Length: 129  Bit Score: 60.42  E-value: 1.11e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048  577 ESPSTQCLL--CSSPLFKGGQNSLAGP---QECWLLTASRLQTVTAQVKMClnPHCLalHSFID---IYTGLFNVGNKLL 648
Cdd:pfam18717    3 ELSAPPFLLalCLSRCPCGTTWDPAGPelwQDCTVYTLTGSQEVRVEVQPC--PACA--VRFIGpdlRELGLFNWNNRTL 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1487549048  649 VSLDLLFAIRNQIKLGEDPRVSINVVLKSVQEQTEKTLTSEELSQLQEL 697
Cdd:pfam18717   79 FTHELLDLYLSAFTRSETPFSAWVSAVRRRYTPSGRSFLSEETFRRAWF 127
HMG smart00398
high mobility group;
41-100 2.15e-10

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 57.71  E-value: 2.15e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048    41 KTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:smart00398    1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 59-100 5.42e-08

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 50.21  E-value: 5.42e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1487549048   59 KVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:cd00084     16 KLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKE 57
HMG-box_ROX1-like cd01389
high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar ...
 59-100 4.09e-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: 48.35  E-value: 4.09e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1487549048   59 KVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:cd01389     18 QLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYKELAEEEKE 59
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 41-100 1.97e-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: 46.63  E-value: 1.97e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048   41 KTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:pfam09011    3 KPKRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKN 62
HMG-box_SoxG_SOX15 cd22035
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 15 (SOX15) and ...
 40-96 4.05e-06

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: 45.84  E-value: 4.05e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1487549048   40 EKTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAK 96
Cdd:cd22035      6 EKVKRPMNAFMVWSSAQRRQMAQEHPKMHNSEISKRLGAAWKLLPEAEKRPFVEEAK 62
HMG_box pfam00505
HMG (high mobility group) box;
42-100 8.99e-06

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 44.52  E-value: 8.99e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1487549048   42 TKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:pfam00505    1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKA 59
HMG-box_AtHMGB6-like_rpt3 cd22008
third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 41-105 6.57e-05

third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the third one.


Pssm-ID: 438824 [Multi-domain]  Cd Length: 78  Bit Score: 42.25  E-value: 6.57e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1487549048   41 KTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKEGLDPD 105
Cdd:cd22008      9 KPKKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAVLMEKYKKE 73
HMG-box_SoxB cd01388
high mobility group (HMG)-box found in group B SRY-related high-mobility group (HMG) box (Sox) ...
 40-96 3.16e-04

high mobility group (HMG)-box found in group B SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxB transcription factors play critical roles in the regulation of neurogenesis. They can be divided into two main subgroups, SoxB1 (Sox-1/Sox-2/Sox-3) and SoxB2 (SOX-14/SOX-21). SoxB1 proteins suppress neurogenesis by maintaining neural cells in an undifferentiated state. SoxB2 proteins may have the opposite activity and promote neuronal differentiation. SOX-1 is involved in the regulation of embryonic development and cell fate determination. It also acts as a tumor suppressor that plays an anti-tumorigenicity role in different cells and its expression is inhibited in a variety of cancers. SOX-2 plays an important role in various phases of embryonic development, including cell fate and differentiation. Its overexpression and gene amplification may be associated with tumor aggression and metastasis in various cancer types, including breast, prostate, lung, ovarian and colon cancer. SOX-3 is required during the formation of the hypothalamic-pituitary axis. It plays a role in both normal neural development and carcinogenesis. SOX-14, also called SOX-28, acts as a negative regulator of transcription. It is mainly involved in the regulation of neural development. It can also promote proliferation and invasion capacity of cervical cancer cells by activating the Wnt/beta-catenin pathway. SOX-21, also called SOX-A, or SOX-25, promotes the progression of vertebrate neurogenesis.


Pssm-ID: 438790 [Multi-domain]  Cd Length: 80  Bit Score: 40.66  E-value: 3.16e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1487549048   40 EKTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAK 96
Cdd:cd01388      1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSEAEKRPFIDEAK 57
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 40-100 3.23e-04

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: 39.97  E-value: 3.23e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1487549048   40 EKTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:cd22001      1 EKPKRPISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKA 61
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 43-94 5.91e-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: 39.19  E-value: 5.91e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1487549048   43 KKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEK 94
Cdd:cd22012      3 KRPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQEE 54
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 59-100 8.46e-04

high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; The HMG20 subfamily includes HMG20A and HMG20B. HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1, HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B. HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2, HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex. Both HMG20A and HMG20B contain one HMG-box.


Pssm-ID: 438796 [Multi-domain]  Cd Length: 81  Bit Score: 39.07  E-value: 8.46e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1487549048   59 KVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:cd21980     19 KLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKE 60
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
43-100 1.62e-03

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 41.00  E-value: 1.62e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1487549048   43 KKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:COG5648     72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRE 129
HMG-box_AtHMGB6-like_rpt1 cd22006
first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 43-100 1.83e-03

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: 37.82  E-value: 1.83e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1487549048   43 KKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:cd22006      1 KKPKTAYFLWCKDQREEVKKENPNADFSEVSKILGAKWKNLSEEEKKPYEEKYKEEKE 58
PHA03247 PHA03247
large tegument protein UL36; Provisional
 276-424 1.96e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 42.62  E-value: 1.96e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048  276 PVVKSGVQPEVTLGTTDNDSPGADVPTPSEGTSTSSPLPAPkkPTGADLLTPGSRAPELKGRARGkPSLLAAARPMRail 355
Cdd:PHA03247  2804 PADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPG--PPPPSLPLGGSVAPGGDVRRRP-PSRSPAAKPAA--- 2877

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1487549048  356 PAPVNVGRGSSMGLPRARQAFSLSD------KTPSVRTCGLKPSTLKQLGQPIQQPSGPGEVKLPSGPSNRTSQV 424
Cdd:PHA03247  2878 PARPPVRRLARPAVSRSTESFALPPdqperpPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGA 2952
HMG-box_SoxA_SoxB_SoxG cd22028
high mobility group (HMG)-box found in group A, group B and group G of SRY-related ...
 59-96 2.12e-03

high mobility group (HMG)-box found in group A, group B and group G of SRY-related high-mobility group (HMG) box (Sox) transcription factors; This subfamily includes SoxA, SoxB, and SoxG proteins. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors. SRY, also called testis-determining factor, is a transcriptional regulator that controls a genetic switch in male development. It promotes DNA bending and is also involved in pre-mRNA splicing. The SRY HMG box recognizes DNA by partial intercalation in the minor groove. It binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'. SoxB transcription factors play critical roles in the regulation of neurogenesis. They can be divided into two main subgroups, SoxB1 (Sox-1/Sox-2/Sox-3) and SoxB2 (SOX-14/SOX-21). SoxB1 proteins suppress neurogenesis by maintaining neural cells in an undifferentiated state. SoxB2 proteins may have the opposite activity and promote neuronal differentiation. SOX-5 is the only member of group G Sox transcription factors. It is also called SOX-12, SOX-20, SOX-26, or SOX-27. SOX-5 is a crucial transcription factor involved in the regulation of embryonic development and in cell fate determination. It binds to the 5'-AACAAT-3' sequence. SOX-15 can be a tumor suppressor in multiple cancer types.


Pssm-ID: 438837 [Multi-domain]  Cd Length: 76  Bit Score: 38.10  E-value: 2.12e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1487549048   59 KVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAK 96
Cdd:cd22028     19 KIAQENPKMHNSEISKRLGAEWKQLSEDEKRPFIDEAK 56
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 44-100 3.47e-03

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.


Pssm-ID: 438810 [Multi-domain]  Cd Length: 67  Bit Score: 37.28  E-value: 3.47e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1487549048   44 KPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:cd21994      1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKE 57
PRK07788 PRK07788
acyl-CoA synthetase; Validated
 286-359 4.68e-03

acyl-CoA synthetase; Validated


Pssm-ID: 236097 [Multi-domain]  Cd Length: 549  Bit Score: 41.07  E-value: 4.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549048  286 VTLGTTDNDSP-GADVPTPSE--GTSTSSPLPAPKKPTGADLLTPG-SRAPelKGRARGKPSLLAAAR------PMRA-- 353
Cdd:PRK07788   172 AWGGNPDDDEPsGSTDETLDDliAGSSTAPLPKPPKPGGIVILTSGtTGTP--KGAPRPEPSPLAPLAgllsrvPFRAge 249


                   ....*...
gi 1487549048  354 --ILPAPV 359
Cdd:PRK07788   250 ttLLPAPM 257
HMG-box_SoxF_SOX17 cd22047
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and ...
 41-96 4.86e-03

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: 37.37  E-value: 4.86e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1487549048   41 KTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAK 96
Cdd:cd22047      6 RIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAE 61
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 43-100 5.75e-03

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: 36.96  E-value: 5.75e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1487549048   43 KKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAKLEKE 100
Cdd:cd01390     15 KRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAAKDKK 72
HMG-box_SOX cd22004
high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family ...
 59-96 6.27e-03

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: 36.75  E-value: 6.27e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1487549048   59 KVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAK 96
Cdd:cd22004     19 KIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEAE 56
HMG-box_SoxA_SRY cd22034
high mobility group (HMG)-box found in sex-determining region Y protein (SRY) and similar ...
 40-96 6.49e-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: 36.92  E-value: 6.49e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1487549048   40 EKTKKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKAK 96
Cdd:cd22034      3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQ 59
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 43-95 8.74e-03

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: 36.37  E-value: 8.74e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1487549048   43 KKPRSAYLLYYYDIYLKVQQELPHLPQSEINKKISESWRLLSVAERSYYLEKA 95
Cdd:cd21985      3 RKPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKA 55
 
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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