SUPERFAMILY 1.75 HMM library and genome assignments server

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TATA-box binding protein-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   TBP-like [ 55944] (11)
Superfamily:   TATA-box binding protein-like [ 55945] (2)
Families:   TATA-box binding protein (TBP), C-terminal domain [ 55946]
  DNA repair glycosylase, N-terminal domain [ 55952] (2)


Superfamily statistics
Genomes (1,376) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 4,210 19,025 43
Proteins 2,812 14,243 30


Functional annotation
General category Information
Detailed category Transcription

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0.0000344Least InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases0.00000000000007799InformativeDirect
Enzyme Commission (EC)DNA-(apurinic or apyrimidinic site) lyase0.00000000000004672Highly InformativeDirect

Document: EC annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)pollen0Moderately InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)M germinated pollen stage0InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0.000008711Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.1103Least InformativeInherited
Enzyme Commission (EC)Carbon-oxygen lyases0.00000005336Moderately InformativeDirect
Enzyme Commission (EC)Glycosylases0.0000456Moderately InformativeDirect
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0.0000002269InformativeDirect
Enzyme Commission (EC)DNA-(apurinic or apyrimidinic site) lyase0Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR012294 SSF55945 Protein matches
Abstract

Transcription factor TFIID (also known as TATA-binding protein, TBP) is a general factor that plays a central role in the activation of eukaryotic genes transcribed by RNA polymerase II [PubMed2374612, PubMed2197561]. TFIID binds specifically to the TATA-box promoter element, which lies close to the position of transcription initiation. The C-terminal domain (~180 residues) of eukaryotic TFIID sequences is highly conserved and is involved in TATA-box binding. The most striking feature of the domain is the presence of 2 conserved 77 amino-acid repeats. The symmetrical disposition of these features generates a saddle-shaped structure that straddles the DNA [PubMed1436073].

DNA glycosylases are involved in the repair of damaged bases in DNA, acting to cleave the bond between the damaged, modified base and the deoxyribose sugar backbone of the DNA. These DNA repair activities are conserved from bacteria to man. Different DNA glycosylases can have different overall folds, even though many of them work by a common mechanism, involving bending the DNA and clamping on to the damaged base to excise it. This entry is represented by 3-methyladenine DNA glycosylase II (AlkA) from Escherichia coli and human 8-oxoguanine glycosylase , whose N-terminal domains display a beta-alpha-beta(4)-alpha fold similar to that found in the C-terminal domain of TFIID. However, unlike TFIID, which contains a duplication of this fold, these DNA glycosylases carry only a single copy of this fold [PubMed15102448, PubMed11554308].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 15 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a TATA-box binding protein-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 15 hidden Markov models representing the TATA-box binding protein-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]