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Conserved domains on  [gi|1002276650|ref|XP_015642670|]
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nuclear transcription factor Y subunit B-10-like [Oryza sativa Japonica Group]

Protein Classification

nuclear transcription factor Y subunit beta( domain architecture ID 19223195)

NF-YB, also called CAAT box DNA-binding protein subunit B, or nuclear transcription factor Y subunit B, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y), which specifically recognizes the 5'-CCAAT-3' box motif found in the promoters of its target genes

CATH:  1.10.20.10
Gene Ontology:  GO:0003677|GO:0003700|GO:0046982|GO:0016602|GO:0006357|GO:0140297
PubMed:  1549471|23332751
SCOP:  4000797

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_NFYB cd22907
histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar ...
 29-119 1.56e-59

histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar proteins; NF-YB, also called CAAT box DNA-binding protein subunit B, or nuclear transcription factor Y subunit B, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y), which specifically recognizes the 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding.


:

Pssm-ID: 467032  Cd Length: 91  Bit Score: 183.14  E-value: 1.56e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002276650  29 VREQDRLMPIANVIRIMRRVLPPHAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAMDRLGFDDYV 108
Cdd:cd22907     1 LREQDRLLPIANIARIMKKALPPNAKISKDAKETMQECVSEFISFVTSEASERCQREKRKTITGDDILWAMSTLGFDNYV 80

                          90
                  ....*....|.
gi 1002276650 109 PPLTAYLRRMR 119
Cdd:cd22907    81 EPLKIYLQKYR 91
 
Name Accession Description Interval E-value
HFD_NFYB cd22907
histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar ...
 29-119 1.56e-59

histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar proteins; NF-YB, also called CAAT box DNA-binding protein subunit B, or nuclear transcription factor Y subunit B, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y), which specifically recognizes the 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding.


Pssm-ID: 467032  Cd Length: 91  Bit Score: 183.14  E-value: 1.56e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002276650  29 VREQDRLMPIANVIRIMRRVLPPHAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAMDRLGFDDYV 108
Cdd:cd22907     1 LREQDRLLPIANIARIMKKALPPNAKISKDAKETMQECVSEFISFVTSEASERCQREKRKTITGDDILWAMSTLGFDNYV 80

                          90
                  ....*....|.
gi 1002276650 109 PPLTAYLRRMR 119
Cdd:cd22907    81 EPLKIYLQKYR 91
CBFD_NFYB_HMF pfam00808
Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes ...
 34-99 7.65e-25

Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes archaebacterial histones and histone like transcription factors from eukaryotes.


Pssm-ID: 395650  Cd Length: 65  Bit Score: 93.44  E-value: 7.65e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002276650  34 RLMPIANVIRIMRRVlPPHAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAM 99
Cdd:pfam00808   1 AELPIARVKRIMKSD-PDAGRISQDAKELIAECVEEFIEFVASEAAEICNKAGRKTINPEHIKQAV 65
COG5150 COG5150
Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];
36-122 3.38e-14

Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];


Pssm-ID: 227479  Cd Length: 148  Bit Score: 67.68  E-value: 3.38e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002276650  36 MPIANVIRIMRRVLPPHAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAMDRLGFDDYVPPLTAYL 115
Cdd:COG5150    12 LPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIESCMEEH 91


                  ....*..
gi 1002276650 116 RRMREYE 122
Cdd:COG5150    92 ENYKSYQ 98
 
Name Accession Description Interval E-value
HFD_NFYB cd22907
histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar ...
 29-119 1.56e-59

histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar proteins; NF-YB, also called CAAT box DNA-binding protein subunit B, or nuclear transcription factor Y subunit B, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y), which specifically recognizes the 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding.


Pssm-ID: 467032  Cd Length: 91  Bit Score: 183.14  E-value: 1.56e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002276650  29 VREQDRLMPIANVIRIMRRVLPPHAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAMDRLGFDDYV 108
Cdd:cd22907     1 LREQDRLLPIANIARIMKKALPPNAKISKDAKETMQECVSEFISFVTSEASERCQREKRKTITGDDILWAMSTLGFDNYV 80

                          90
                  ....*....|.
gi 1002276650 109 PPLTAYLRRMR 119
Cdd:cd22907    81 EPLKIYLQKYR 91
CBFD_NFYB_HMF pfam00808
Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes ...
 34-99 7.65e-25

Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes archaebacterial histones and histone like transcription factors from eukaryotes.


Pssm-ID: 395650  Cd Length: 65  Bit Score: 93.44  E-value: 7.65e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002276650  34 RLMPIANVIRIMRRVlPPHAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAM 99
Cdd:pfam00808   1 AELPIARVKRIMKSD-PDAGRISQDAKELIAECVEEFIEFVASEAAEICNKAGRKTINPEHIKQAV 65
HFD_POLE3_DPB4 cd22928
histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; ...
 35-117 4.00e-22

histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; POLE3, also called arsenic-transactivated protein (AsTP), chromatin accessibility complex 17 kDa protein (CHRAC-17), DNA polymerase II subunit 3, or DNA polymerase epsilon subunit p17, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex, which consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. It forms a complex with CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1. In fungi, POLE3 has been named as DNA polymerase epsilon subunit D (DPB4, also known as DNA polymerase II subunit D). DPB4 acts as an accessory component of the DNA polymerase epsilon (DNA polymerase II) that consists of POL2, DPB2, DPB3 and DPB4, and participates in chromosomal DNA replication. It also functions as a component of the ISW2 complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA.


Pssm-ID: 467053  Cd Length: 87  Bit Score: 86.80  E-value: 4.00e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002276650  35 LMPIANVIRIMRRVLPPHAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAMDRLGFDDYVPPLTAY 114
Cdd:cd22928     4 ELPRAVITRIIKEALPEGVQVSKDARLALSRAATVFILYLTAAANEIAKSNKRKTISADDVLKALEELEFDEFVPPLKEE 83


                  ...
gi 1002276650 115 LRR 117
Cdd:cd22928    84 LEA 86
HFD_Dr1 cd22905
histone-fold domain found in protein Dr1 and similar proteins; Dr1, also called down-regulator ...
 31-122 6.37e-20

histone-fold domain found in protein Dr1 and similar proteins; Dr1, also called down-regulator of transcription 1 or negative cofactor 2-beta (NC2-beta), is a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. It forms a heterodimer with DRAP1. The association of the Dr1/DRAP1 heterodimer with TBP results in functional repression of both activated and basal transcription of class II genes. Dr1 can bind to DNA on its own. Dr1 is a component of the ADA2A-containing complex (ATAC) that has histone acetyltransferase activity on histones H3 and H4.


Pssm-ID: 467030  Cd Length: 129  Bit Score: 82.62  E-value: 6.37e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002276650  31 EQDRLMPIANVIRIMRRVLPPHAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAMDRLGFDDYVPP 110
Cdd:cd22905     1 DDDLSLPKATVNKLIKEVLPPDMRVSKDTRELILECCTEFIHLISSEANEICEKEKKKTISPEHVLKALENLGFGEYIEE 80

                          90
                  ....*....|..
gi 1002276650 111 LTAYLRRMREYE 122
Cdd:cd22905    81 VEEALEDHKEEA 92
COG5150 COG5150
Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];
36-122 3.38e-14

Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];


Pssm-ID: 227479  Cd Length: 148  Bit Score: 67.68  E-value: 3.38e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002276650  36 MPIANVIRIMRRVLPPHAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAMDRLGFDDYVPPLTAYL 115
Cdd:COG5150    12 LPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIESCMEEH 91


                  ....*..
gi 1002276650 116 RRMREYE 122
Cdd:COG5150    92 ENYKSYQ 98
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 37-100 3.35e-06

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


Pssm-ID: 467021  Cd Length: 63  Bit Score: 43.36  E-value: 3.35e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002276650  37 PIANVIRIMRRVLPphAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAMD 100
Cdd:cd00076     2 LRSAVARILKSAGF--DSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 37-94 8.91e-06

histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription regulators and similar proteins; The family includes many archaeal histone-fold proteins and histone-like transcription regulators, which may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. They can increase the resistance of DNA to thermal denaturation.


Pssm-ID: 467034  Cd Length: 64  Bit Score: 42.15  E-value: 8.91e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1002276650  37 PIANVIRIMRRVlppHAK-ISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAED 94
Cdd:cd22909     3 PKAPVKRIIKKA---GAErVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAED 58
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
37-94 6.48e-05

Archaeal histone H3/H4 [Chromatin structure and dynamics];


Pssm-ID: 441639  Cd Length: 67  Bit Score: 39.81  E-value: 6.48e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002276650  37 PIANVIRIMR-----RVlpphakiSDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAED 94
Cdd:COG2036     3 PVAPVDRIIKkagaeRV-------SEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAED 58
HFD_CENP-T cd22920
histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also ...
 36-121 1.36e-03

histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also called interphase centromere complex protein 22 (ICEN22), is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in the assembly of kinetochore proteins, mitotic progression, and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. CENP-T is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENPA. Moreover, CENP-T is a component of the heterotetrameric CENP-T-W-S-X complex that binds and supercoils DNA, and plays an important role in kinetochore assembly. CENP-T has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. It is required for normal chromosome organization and normal progress through mitosis.


Pssm-ID: 467045  Cd Length: 94  Bit Score: 37.15  E-value: 1.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002276650  36 MPIANVIRIMRRVLPPhaKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAMDRLGFDDYVPPLTAYL 115
Cdd:cd22920     3 LPKSLVKKLFKHFLKR--RVSKEALEALEEISEEFFEQLSDDLEAYADHAGRKTINEKDVELLMKRQRLVTDKQSLESLA 80


                  ....*...
gi 1002276650 116 RRM--REY 121
Cdd:cd22920    81 RKYlpLEL 88
HFD_Dpb3-like cd23645
histone-fold domain found in Schizosaccharomyces pombe DNA polymerase epsilon subunit C (Dpb3) ...
 36-104 3.08e-03

histone-fold domain found in Schizosaccharomyces pombe DNA polymerase epsilon subunit C (Dpb3) and similar proteins; Schizosaccharomyces pombe Dpb3 is an accessory component of the DNA polymerase epsilon (DNA polymerase II) that is a heterotetramer consisting of cdc20/Pol2, Dpb2, Dpb3, and Dpb4, and participates in chromosomal DNA replication. Dpb3 is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. The Dpb3-Dpb4 dimer associates with histone deacetylases, chromatin remodelers, and histones and plays a crucial role in the inheritance of histone hypoacetylation and H3K9 methylation in heterochromatin. The Dpb3-Dpb4 dimer is also required for the recruitment of sir2 to heterochromatin.


Pssm-ID: 467059 [Multi-domain]  Cd Length: 78  Bit Score: 35.67  E-value: 3.08e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002276650  36 MPIANVIRIMRRVlPPHAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAM---DRLGF 104
Cdd:cd23645     3 LPLARVKRIIKAD-KDVKICSKDAVFLISKATELFIEYLAEQAYELAKLEKRKTVQYKDLAKAVkrdDNLEF 73
 
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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