D-I-TASSER Q12962

D-I-TASSER results for Q12962

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Summary of the Protein

Uniprot ID: Q12962
Protein Name: Transcription initiation factor TFIID subunit 10
Gene Name: TAF10

Input Sequence in FASTA format

>Q12962 (218 residues)
MSCSGSGADPEAAPASAASAPGPAPPVSAPAALPSSTAAENKASPAGTAGGPGAGAAAGG
TGPLAARAGEPAERRGAAPVSAGGAAPPEGAISNGVYVLPSAANGDVKPVVSSTPLVDFL
MQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIANDALQHCKMKGTA
SGSSRSKSKDRKYTLTMEDLTPALSEYGINVKKPHYFT

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q12962-D1	1-218	218		MSCSGSGADPEAAPASAASAPGPAPPVSAPAALPSSTAAENKASPAGTAGGPGAGAAAGGTGPLAARAGEPAERRGAAPVSAGGAAPPEGAISNGVYVLPSAANGDVKPVVSSTPLVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIANDALQHCKMKGTASGSSRSKSKDRKYTLTMEDLTPALSEYGINVKKPHYFT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5787

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	7d4fA	0.47	5.52	0.045	0.798	model1_7d4fA.pdb.gz
2	1g8xA	0.46	5.26	0.037	0.761	model1_1g8xA.pdb.gz
3	6nurA2	0.46	5.65	0.050	0.798	model1_6nurA2.pdb.gz
4	4f91B	0.46	5.97	0.041	0.807	model1_4f91B.pdb.gz
5	2nyfA	0.45	5.60	0.056	0.743	model1_2nyfA.pdb.gz
6	1y2mB	0.45	5.60	0.065	0.739	model1_1y2mB.pdb.gz
7	5yz0A	0.45	5.78	0.051	0.784	model1_5yz0A.pdb.gz
8	1o1dA	0.39	5.67	0.067	0.688	model1_1o1dA.pdb.gz
9	2bkiA1	0.39	5.63	0.039	0.628	model1_2bkiA1.pdb.gz
10	1dceA	0.34	5.48	0.036	0.555	model1_1dceA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003700	0.92	transcription factor activity, sequence-specific DNA binding
GO:0003824	0.80	catalytic activity
GO:0016740	0.78	transferase activity
GO:0004402	0.75	histone acetyltransferase activity
GO:0003712	0.67	transcription cofactor activity
GO:0003713	0.66	transcription coactivator activity
GO:0070063	0.65	RNA polymerase binding
GO:0030331	0.65	estrogen receptor binding
GO:1901363	0.55	heterocyclic compound binding
GO:0097159	0.55	organic cyclic compound binding
GO:0003676	0.50	nucleic acid binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	0.95	cellular process
GO:0044260	0.91	cellular macromolecule metabolic process
GO:0044238	0.91	primary metabolic process
GO:0016070	0.90	RNA metabolic process
GO:0032774	0.89	RNA biosynthetic process
GO:0065007	0.80	biological regulation
GO:0006367	0.80	transcription initiation from RNA polymerase II promoter
GO:0050789	0.79	regulation of biological process
GO:0016043	0.79	cellular component organization
GO:0050794	0.78	regulation of cellular process
GO:0006325	0.78	chromatin organization
GO:0006464	0.77	cellular protein modification process
GO:0018205	0.76	peptidyl-lysine modification
GO:0016570	0.76	histone modification
GO:0016573	0.75	histone acetylation
GO:0043966	0.69	histone H3 acetylation
GO:0065003	0.68	macromolecular complex assembly
GO:0006461	0.62	protein complex assembly
GO:0016579	0.61	protein deubiquitination
GO:0051260	0.60	protein homooligomerization
GO:0016578	0.60	histone deubiquitination
GO:0044699	0.51	single-organism process
GO:0019222	0.50	regulation of metabolic process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	1.00	intracellular part
GO:0044446	0.94	intracellular organelle part
GO:0043226	0.94	organelle
GO:0044428	0.93	nuclear part
GO:0032991	0.93	macromolecular complex
GO:0005634	0.93	nucleus
GO:0043234	0.92	protein complex
GO:0044451	0.91	nucleoplasm part
GO:1990234	0.89	transferase complex
GO:0000123	0.87	histone acetyltransferase complex
GO:0044798	0.80	nuclear transcription factor complex
GO:0090575	0.79	RNA polymerase II transcription factor complex
GO:0070461	0.79	SAGA-type complex
GO:0005669	0.78	transcription factor TFIID complex
GO:0005737	0.71	cytoplasm
GO:0044444	0.65	cytoplasmic part
GO:0048471	0.54	perinuclear region of cytoplasm
GO:0033276	0.54	transcription factor TFTC complex
GO:0030914	0.54	STAGA complex
GO:0000125	0.54	PCAF complex

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2nyfA	0.450	5.50	0.042	0.734	4.3.1.5	NA
2	0.060	1gpeA	0.400	5.87	0.053	0.702	1.1.3.4	NA
3	0.060	1jxaA	0.387	5.68	0.054	0.674	2.6.1.16	NA
4	0.060	3ialB	0.401	5.53	0.047	0.674	6.1.1.15	67
5	0.060	2zciA	0.422	6.07	0.038	0.771	4.1.1.32	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	2o7eA	0.390	6.00	0.084	0.651	0.19	PMI	complex1.pdb.gz	155,158,208
2	0.01	2rjsB	0.449	5.65	0.065	0.734	0.13	296	complex2.pdb.gz	143,208,210
3	0.01	1r1jA	0.428	5.84	0.043	0.748	0.14	OIR	complex3.pdb.gz	132,137,138,141,142
4	0.01	2x9hA	0.371	5.69	0.041	0.606	0.16	KI9	complex4.pdb.gz	144,158,159,206
5	0.01	1mmdA	0.367	5.55	0.067	0.615	0.15	UUU	complex5.pdb.gz	144,145,146,150
6	0.01	1d0zA	0.364	6.49	0.052	0.697	0.21	PNQ	complex6.pdb.gz	134,136,137,138,139
7	0.01	1mmnA	0.364	5.05	0.038	0.550	0.14	ANP	complex7.pdb.gz	143,144,145
8	0.01	2o7dB	0.389	5.99	0.079	0.647	0.16	DHC	complex8.pdb.gz	143,155,156
9	0.01	1w9jA	0.370	5.82	0.041	0.610	0.12	UUU	complex9.pdb.gz	133,136,137,138,139,156

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.