D-I-TASSER Q9HAW0

D-I-TASSER results for Q9HAW0

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

Summary of the Protein

Uniprot ID: Q9HAW0
Protein Name: Transcription factor IIIB 50 kDa subunit
Gene Name: BRF2

Input Sequence in FASTA format

>Q9HAW0 (419 residues)
MPGRGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTG
ENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYRHSGIRAARLQKKEVLVGC
CVLITCRQHNWPLTMGAICTLLYADLDVFSSTYMQIVKLLGLDVPSLCLAELVKTYCSSF
KLFQASPSVPAKYVEDKEKMLSRTMQLVELANETWLVTGRHPLPVITAATFLAWQSLQPA
DRLSCSLARFCKLANVDLPYPASSRLQELLAVLLRMAEQLAWLRVLRLDKRSVVKHIGDL
LQHRQSLVRSAFRDGTAEVETREKEPPGWGQGQGEGEVGNNSLGLPQGKRPASPALLLPP
CMLKSPKRICPVPPVSTVTGDENISDSEIEQYLRTPQEVRDFQRAQAARQAATSVPNPP

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	Q9HAW0-D1	1-419	419		MPGRGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTGENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYRHSGIRAARLQKKEVLVGCCVLITCRQHNWPLTMGAICTLLYADLDVFSSTYMQIVKLLGLDVPSLCLAELVKTYCSSFKLFQASPSVPAKYVEDKEKMLSRTMQLVELANETWLVTGRHPLPVITAATFLAWQSLQPADRLSCSLARFCKLANVDLPYPASSRLQELLAVLLRMAEQLAWLRVLRLDKRSVVKHIGDLLQHRQSLVRSAFRDGTAEVETREKEPPGWGQGQGEGEVGNNSLGLPQGKRPASPALLLPPCMLKSPKRICPVPPVSTVTGDENISDSEIEQYLRTPQEVRDFQRAQAARQAATSVPNPP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.692

(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	4rocA	0.69	1.53	0.977	0.718	model1_4rocA.pdb.gz
2	6cnbR	0.66	3.55	0.139	0.752	model1_6cnbR.pdb.gz
3	6eu0Z	0.64	3.24	0.158	0.730	model1_6eu0Z.pdb.gz
4	5iy7M	0.52	3.48	0.179	0.611	model1_5iy7M.pdb.gz
5	4v1nM	0.51	3.45	0.166	0.590	model1_4v1nM.pdb.gz
6	6gykM	0.51	3.30	0.173	0.587	model1_6gykM.pdb.gz
7	1d3uB	0.44	2.16	0.206	0.470	model1_1d3uB.pdb.gz
8	3k7aM	0.29	4.00	0.196	0.358	model1_3k7aM.pdb.gz
9	1zp2A	0.23	3.14	0.085	0.258	model1_1zp2A.pdb.gz
10	1aisB1	0.22	1.49	0.237	0.232	model1_1aisB1.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	0.78	heterocyclic compound binding
GO:0097159	0.78	organic cyclic compound binding
GO:0003676	0.75	nucleic acid binding
GO:0003677	0.72	DNA binding
GO:0046872	0.71	metal ion binding
GO:0008134	0.71	transcription factor binding
GO:0008270	0.63	zinc ion binding
GO:0000988	0.60	transcription factor activity, protein binding
GO:0070063	0.58	RNA polymerase binding
GO:0000990	0.58	transcription factor activity, core RNA polymerase binding
GO:0000989	0.58	transcription factor activity, transcription factor binding
GO:0043175	0.56	RNA polymerase core enzyme binding
GO:0001132	0.53	RNA polymerase II transcription factor activity, TBP-class protein binding
GO:0001099	0.53	basal RNA polymerase II transcription machinery binding
GO:0044877	0.52	macromolecular complex binding
GO:0000991	0.52	transcription factor activity, core RNA polymerase II binding
GO:0032403	0.51	protein complex 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	0.94	cellular process
GO:0071704	0.88	organic substance metabolic process
GO:0044237	0.88	cellular metabolic process
GO:1901360	0.87	organic cyclic compound metabolic process
GO:0065007	0.87	biological regulation
GO:0044260	0.87	cellular macromolecule metabolic process
GO:0044238	0.87	primary metabolic process
GO:0034641	0.87	cellular nitrogen compound metabolic process
GO:0016070	0.86	RNA metabolic process
GO:0032774	0.85	RNA biosynthetic process
GO:0050789	0.84	regulation of biological process
GO:0050794	0.83	regulation of cellular process
GO:0010468	0.82	regulation of gene expression
GO:2001141	0.80	regulation of RNA biosynthetic process
GO:2000112	0.79	regulation of cellular macromolecule biosynthetic process
GO:0006355	0.78	regulation of transcription, DNA-templated
GO:0006351	0.72	transcription, DNA-templated
GO:0065009	0.65	regulation of molecular function
GO:0006352	0.63	DNA-templated transcription, initiation
GO:0016043	0.61	cellular component organization
GO:0044093	0.60	positive regulation of molecular function
GO:0006367	0.57	transcription initiation from RNA polymerase II promoter
GO:0051098	0.55	regulation of binding
GO:0043933	0.55	macromolecular complex subunit organization
GO:0065004	0.54	protein-DNA complex assembly
GO:0070897	0.53	DNA-templated transcriptional preinitiation complex assembly
GO:0001112	0.53	DNA-templated transcriptional open complex formation
GO:0051101	0.52	regulation of DNA binding
GO:0001173	0.52	DNA-templated transcriptional start site selection
GO:0031325	0.51	positive regulation of cellular metabolic process
GO:0010604	0.51	positive regulation of macromolecule metabolic process
GO:2000677	0.50	regulation of transcription regulatory region DNA binding
GO:1902680	0.50	positive regulation of RNA biosynthetic process
GO:0043388	0.50	positive regulation of DNA binding
GO:0010628	0.50	positive regulation of gene expression

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	0.85	intracellular organelle part
GO:0044428	0.84	nuclear part
GO:0043226	0.78	organelle
GO:0043229	0.77	intracellular organelle
GO:0043227	0.76	membrane-bounded organelle
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0005634	0.74	nucleus
GO:0005654	0.60	nucleoplasm

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	2ckjA	0.344	6.83	0.040	0.556	1.17.1.4 1.17.3.2	NA
2	0.060	2e1qA	0.361	6.46	0.052	0.563	1.17.3.2 1.17.1.4	NA
3	0.060	2uv8G	0.382	7.07	0.034	0.640	2.3.1.86	NA
4	0.060	1q78A	0.344	6.62	0.044	0.546	2.7.7.19	NA
5	0.060	1peuA	0.330	6.86	0.058	0.527	1.17.4.1	90,121

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.02	1d3uB	0.439	2.16	0.206	0.470	0.43	QNA	complex1.pdb.gz	219,220,221
	2	0.02	1c9bE	0.428	2.66	0.155	0.468	0.61	QNA	complex2.pdb.gz	68,97,118

	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.