D-I-TASSER Q9HAC8

D-I-TASSER results for Q9HAC8

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

Summary of the Protein

Uniprot ID: Q9HAC8
Protein Name: Ubiquitin domain-containing protein 1
Gene Name: UBTD1

Input Sequence in FASTA format

>Q9HAC8 (227 residues)
MGNCVGRQRRERPAAPGHPRKRAGRNEPLKKERLKWKSDYPMTDGQLRSKRDEFWDTAPA
FEGRKEIWDALKAAAYAAEANDHELAQAILDGASITLPHGTLCECYDELGNRYQLPIYCL
SPPVNLLLEHTEEESLEPPEPPPSVRREFPLKVRLSTGKDVRLSASLPDTVGQLKRQLHA
QEGIEPSWQRWFFSGKLLTDRTRLQETKIQKDFVIQVIINQPPPPQD

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	Q9HAC8-D1	1-227	227		MGNCVGRQRRERPAAPGHPRKRAGRNEPLKKERLKWKSDYPMTDGQLRSKRDEFWDTAPAFEGRKEIWDALKAAAYAAEANDHELAQAILDGASITLPHGTLCECYDELGNRYQLPIYCLSPPVNLLLEHTEEESLEPPEPPPSVRREFPLKVRLSTGKDVRLSASLPDTVGQLKRQLHAQEGIEPSWQRWFFSGKLLTDRTRLQETKIQKDFVIQVIINQPPPPQD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.678

(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	5bn3A	0.43	5.68	0.074	0.731	model1_5bn3A.pdb.gz
2	4xc6A	0.43	6.05	0.059	0.762	model1_4xc6A.pdb.gz
3	3j9tA	0.43	5.83	0.062	0.727	model1_3j9tA.pdb.gz
4	4cvuA	0.42	5.57	0.050	0.705	model1_4cvuA.pdb.gz
5	3i4lA	0.42	5.85	0.080	0.723	model1_3i4lA.pdb.gz
6	6um1A	0.42	5.75	0.032	0.696	model1_6um1A.pdb.gz
7	6lvfB	0.42	5.89	0.041	0.740	model1_6lvfB.pdb.gz
8	2uvcG	0.41	6.24	0.050	0.753	model1_2uvcG.pdb.gz
9	2veaA	0.41	5.83	0.045	0.718	model1_2veaA.pdb.gz
10	5uj6A	0.41	5.48	0.059	0.674	model1_5uj6A.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:0003824	0.72	catalytic activity
GO:1901363	0.66	heterocyclic compound binding
GO:0097159	0.66	organic cyclic compound binding
GO:0035639	0.56	purine ribonucleoside triphosphate binding
GO:0032559	0.56	adenyl ribonucleotide binding
GO:0032550	0.56	purine ribonucleoside binding
GO:0016787	0.53	hydrolase activity
GO:0044769	0.52	ATPase activity, coupled to transmembrane movement of ions, rotational mechanism
GO:0015078	0.52	hydrogen ion transmembrane transporter activity

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	0.97	cellular process
GO:0071704	0.92	organic substance metabolic process
GO:0044238	0.91	primary metabolic process
GO:0044237	0.91	cellular metabolic process
GO:0043170	0.81	macromolecule metabolic process
GO:0044260	0.80	cellular macromolecule metabolic process
GO:0065007	0.73	biological regulation
GO:0034641	0.73	cellular nitrogen compound metabolic process
GO:0019538	0.73	protein metabolic process
GO:0050789	0.72	regulation of biological process
GO:0044699	0.72	single-organism process
GO:0006139	0.72	nucleobase-containing compound metabolic process
GO:0044763	0.68	single-organism cellular process
GO:0050794	0.67	regulation of cellular process
GO:1901576	0.64	organic substance biosynthetic process
GO:0044271	0.64	cellular nitrogen compound biosynthetic process
GO:0051179	0.63	localization
GO:0034654	0.62	nucleobase-containing compound biosynthetic process
GO:0051234	0.61	establishment of localization
GO:0006464	0.60	cellular protein modification process
GO:1901564	0.58	organonitrogen compound metabolic process
GO:0044710	0.57	single-organism metabolic process
GO:0006796	0.57	phosphate-containing compound metabolic process
GO:0006810	0.56	transport
GO:1901566	0.55	organonitrogen compound biosynthetic process
GO:0046034	0.55	ATP metabolic process
GO:0044711	0.54	single-organism biosynthetic process
GO:0034220	0.54	ion transmembrane transport
GO:0090662	0.52	ATP hydrolysis coupled transmembrane transport
GO:0046129	0.52	purine ribonucleoside biosynthetic process
GO:0015988	0.52	energy coupled proton transmembrane transport, against electrochemical gradient
GO:0009206	0.52	purine ribonucleoside triphosphate biosynthetic process
GO:0009168	0.52	purine ribonucleoside monophosphate biosynthetic process
GO:0009152	0.52	purine ribonucleotide biosynthetic 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:0032991	0.95	macromolecular complex
GO:0043234	0.91	protein complex
GO:0033178	0.86	proton-transporting two-sector ATPase complex, catalytic domain
GO:0016020	0.81	membrane
GO:0044446	0.76	intracellular organelle part
GO:0044444	0.76	cytoplasmic part
GO:0043229	0.72	intracellular organelle
GO:0043227	0.70	membrane-bounded organelle
GO:0043231	0.69	intracellular membrane-bounded organelle
GO:0045261	0.53	proton-transporting ATP synthase complex, catalytic core F(1)
GO:0005829	0.52	cytosol
GO:0005886	0.51	plasma membrane

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	1z45A	0.392	5.63	0.054	0.670	5.1.3.2 5.1.3.3	164
2	0.060	3c2wC	0.389	5.92	0.060	0.683	2.7.13.3	NA
3	0.060	1b0pA	0.388	6.09	0.065	0.692	1.2.7.1	NA
4	0.060	3gvuA	0.215	5.54	0.021	0.339	2.7.10.2	NA
5	0.060	2ztgA	0.385	5.97	0.031	0.687	6.1.1.7	183

	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	0.01	3fksX	0.383	5.58	0.034	0.643	0.45	PO4	complex1.pdb.gz	171,172,174,175,176
	2	0.01	1h8eE	0.394	6.10	0.087	0.683	0.42	ADP	complex2.pdb.gz	176,177,178,217

	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.