D-I-TASSER P23511

D-I-TASSER results for P23511

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

Summary of the Protein

Uniprot ID: P23511
Protein Name: Nuclear transcription factor Y subunit alpha
Gene Name: NFYA

Input Sequence in FASTA format

>P23511 (347 residues)
MEQYTANSNSSTEQIVVQAGQIQQQQQGGVTAVQLQTEAQVASASGQQVQTLQVVQGQPL
MVQVSGGQLITSTGQPIMVQAVPGGQGQTIMQVPVSGTQGLQQIQLVPPGQIQIQGGQAV
QVQGQQGQTQQIIIQQPQTAVTAGQTQTQQQIAVQGQQVAQTAEGQTIVYQPVNADGTIL
QQVTVPVSGMITIPAASLAGAQIVQTGANTNTTSSGQGTVTVTLPVAGNVVNSGGMVMMV
PGAGSVPAIQRIPLPGAEMLEEEPLYVNAKQYHRILKRRQARAKLEAEGKIPKERRKYLH
ESRHRHAMARKRGEGGRFFSPKEKDSPHMQDPNQADEEAMTQIIRVS

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	P23511-D1	1-106	106		MEQYTANSNSSTEQIVVQAGQIQQQQQGGVTAVQLQTEAQVASASGQQVQTLQVVQGQPLMVQVSGGQLITSTGQPIMVQAVPGGQGQTIMQVPVSGTQGLQQIQL
2	P23511-D2	107-266	160		VPPGQIQIQGGQAVQVQGQQGQTQQIIIQQPQTAVTAGQTQTQQQIAVQGQQVAQTAEGQTIVYQPVNADGTILQQVTVPVSGMITIPAASLAGAQIVQTGANTNTTSSGQGTVTVTLPVAGNVVNSGGMVMMVPGAGSVPAIQRIPLPGAEMLEEEPLY
3	P23511-D3	267-347	81		VNAKQYHRILKRRQARAKLEAEGKIPKERRKYLHESRHRHAMARKRGEGGRFFSPKEKDSPHMQDPNQADEEAMTQIIRVS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.44

(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	3a0fA	0.43	6.68	0.060	0.723	model1_3a0fA.pdb.gz
2	6hpdA	0.43	6.60	0.037	0.715	model1_6hpdA.pdb.gz
3	5k6lA	0.42	6.96	0.057	0.726	model1_5k6lA.pdb.gz
4	7bwmA	0.42	6.19	0.049	0.663	model1_7bwmA.pdb.gz
5	6rutB1	0.41	6.31	0.056	0.660	model1_6rutB1.pdb.gz
6	6p2kA	0.41	6.70	0.047	0.703	model1_6p2kA.pdb.gz
7	7emfW2	0.41	6.81	0.046	0.703	model1_7emfW2.pdb.gz
8	5amqA	0.41	6.49	0.043	0.666	model1_5amqA.pdb.gz
9	5mz61	0.41	6.27	0.054	0.663	model1_5mz61.pdb.gz
10	7enjW3	0.41	6.75	0.035	0.697	model1_7enjW3.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:1901363	0.91	heterocyclic compound binding
GO:0097159	0.91	organic cyclic compound binding
GO:0003676	0.90	nucleic acid binding
GO:0003677	0.88	DNA binding
GO:0044212	0.61	transcription regulatory region DNA binding
GO:0000976	0.60	transcription regulatory region sequence-specific DNA binding
GO:0001047	0.56	core promoter binding
GO:0001046	0.55	core promoter sequence-specific DNA binding
GO:0003700	0.50	transcription factor activity, sequence-specific DNA 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:0065007	0.96	biological regulation
GO:0006355	0.95	regulation of transcription, DNA-templated
GO:0009987	0.78	cellular process
GO:0008152	0.68	metabolic process
GO:0071704	0.66	organic substance metabolic process
GO:0044238	0.66	primary metabolic process
GO:0044237	0.65	cellular metabolic process
GO:0044260	0.63	cellular macromolecule metabolic process
GO:1901576	0.61	organic substance biosynthetic process
GO:1901360	0.61	organic cyclic compound metabolic process
GO:0048522	0.61	positive regulation of cellular process
GO:0046483	0.61	heterocycle metabolic process
GO:0044249	0.61	cellular biosynthetic process
GO:0034641	0.61	cellular nitrogen compound metabolic process
GO:0006725	0.61	cellular aromatic compound metabolic process
GO:0090304	0.60	nucleic acid metabolic process
GO:0045935	0.60	positive regulation of nucleobase-containing compound metabolic process
GO:0010557	0.60	positive regulation of macromolecule biosynthetic process
GO:0045893	0.59	positive regulation of transcription, DNA-templated
GO:0044271	0.59	cellular nitrogen compound biosynthetic process
GO:0016070	0.59	RNA metabolic process
GO:0009059	0.59	macromolecule biosynthetic process
GO:0032774	0.58	RNA biosynthetic process
GO:0034645	0.57	cellular macromolecule biosynthetic process
GO:0006351	0.56	transcription, DNA-templated

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:0044428	0.97	nuclear part
GO:0043229	0.83	intracellular organelle
GO:0043231	0.81	intracellular membrane-bounded organelle
GO:0005634	0.80	nucleus
GO:0043234	0.78	protein complex
GO:0090575	0.75	RNA polymerase II transcription factor complex
GO:0016602	0.74	CCAAT-binding factor 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	1y4wA	0.370	6.73	0.034	0.625	3.2.1.80	NA
2	0.060	2aryA	0.241	7.06	0.033	0.421	3.4.22.52	NA
3	0.060	2qf7B	0.271	6.43	0.033	0.438	6.4.1.1	NA
4	0.060	2wtzB	0.375	6.68	0.092	0.637	6.3.2.13	NA
5	0.060	3ecqB	0.380	7.03	0.056	0.669	3.2.1.97	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	1c3oA	0.377	7.18	0.055	0.677	0.26	GLN	complex1.pdb.gz	267,268,314,316
2	0.01	1a9xA	0.380	6.88	0.051	0.660	0.14	PO4	complex2.pdb.gz	311,313,315
3	0.01	1sqj0	0.398	6.79	0.049	0.683	0.19	III	complex3.pdb.gz	265,266,313,317
4	0.01	1bxrA	0.404	7.09	0.039	0.712	0.13	ANP	complex4.pdb.gz	308,310,314,315,316,319
5	0.01	1ce8C	0.402	7.09	0.056	0.700	0.18	ADP	complex5.pdb.gz	306,307,308,313,317,318
6	0.01	1a9xA	0.380	6.88	0.051	0.660	0.21	ADP	complex6.pdb.gz	268,275,313
7	0.01	3tw6C	0.276	7.97	0.020	0.559	0.21	ADP	complex7.pdb.gz	276,306,307,308,313
8	0.01	1a9x0	0.380	6.88	0.051	0.660	0.20	III	complex8.pdb.gz	273,276,277
9	0.01	2qf7A	0.405	6.94	0.059	0.692	0.21	SAP	complex9.pdb.gz	313,316,341
10	0.01	1a9xA	0.380	6.88	0.051	0.660	0.14	ADP	complex10.pdb.gz	269,306,317,318,322

	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.