D-I-TASSER Q9H832

D-I-TASSER results for Q9H832

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

Summary of the Protein

Uniprot ID: Q9H832
Protein Name: Ubiquitin-conjugating enzyme E2 Z
Gene Name: UBE2Z

Input Sequence in FASTA format

>Q9H832 (354 residues)
MAESPTEEAATAGAGAAGPGASSVAGVVGVSGSGGGFGPPFLPDVWAAAAAAGGAGGPGS
GLAPLPGLPPSAAAHGAALLSHWDPTLSSDWDGERTAPQCLLRIKRDIMSIYKEPPPGMF
VVPDTVDMTKIHALITGPFDTPYEGGFFLFVFRCPPDYPIHPPRVKLMTTGNNTVRFNPN
FYRNGKVCLSILGTWTGPAWSPAQSISSVLISIQSLMTENPYHNEPGFEQERHPGDSKNY
NECIRHETIRVAVCDMMEGKCPCPEPLRGVMEKSFLEYYDFYEVACKDRLHLQGQTMQDP
FGEKRGHFDYQSLLMRLGLIRQKVLERLHNENAEMDSDSSSSGTETDLHGSLRV

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	Q9H832-D1	1-61	61		MAESPTEEAATAGAGAAGPGASSVAGVVGVSGSGGGFGPPFLPDVWAAAAAAGGAGGPGSG
2	Q9H832-D2	62-232	171		LAPLPGLPPSAAAHGAALLSHWDPTLSSDWDGERTAPQCLLRIKRDIMSIYKEPPPGMFVVPDTVDMTKIHALITGPFDTPYEGGFFLFVFRCPPDYPIHPPRVKLMTTGNNTVRFNPNFYRNGKVCLSILGTWTGPAWSPAQSISSVLISIQSLMTENPYHNEPGFEQER
3	Q9H832-D3	233-354	122		HPGDSKNYNECIRHETIRVAVCDMMEGKCPCPEPLRGVMEKSFLEYYDFYEVACKDRLHLQGQTMQDPFGEKRGHFDYQSLLMRLGLIRQKVLERLHNENAEMDSDSSSSGTETDLHGSLRV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.63

(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	5a4pA	0.62	1.21	1.000	0.641	model1_5a4pA.pdb.gz
2	3cegA	0.62	3.16	0.284	0.703	model1_3cegA.pdb.gz
3	2dqmA	0.44	6.43	0.049	0.723	model1_2dqmA.pdb.gz
4	3se6A	0.43	6.58	0.084	0.712	model1_3se6A.pdb.gz
5	5nz7A	0.42	7.11	0.067	0.749	model1_5nz7A.pdb.gz
6	1ylaA	0.42	3.39	0.236	0.483	model1_1ylaA.pdb.gz
7	4kx7A	0.42	6.82	0.027	0.709	model1_4kx7A.pdb.gz
8	1l8nA2	0.41	6.80	0.067	0.709	model1_1l8nA2.pdb.gz
9	2ediA	0.41	2.82	0.223	0.452	model1_2ediA.pdb.gz
10	2xdtA2	0.40	6.83	0.063	0.698	model1_2xdtA2.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	0.85	heterocyclic compound binding
GO:0097159	0.85	organic cyclic compound binding
GO:0035639	0.82	purine ribonucleoside triphosphate binding
GO:0032555	0.82	purine ribonucleotide binding
GO:0032550	0.82	purine ribonucleoside binding
GO:0030554	0.82	adenyl nucleotide binding
GO:0003824	0.82	catalytic activity
GO:0005524	0.81	ATP binding
GO:0016740	0.78	transferase activity
GO:0004842	0.77	ubiquitin-protein transferase activity
GO:0019899	0.75	enzyme binding
GO:0061631	0.74	ubiquitin conjugating enzyme activity
GO:0061630	0.74	ubiquitin protein ligase activity
GO:0031625	0.74	ubiquitin protein ligase 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	0.82	cellular process
GO:0008152	0.73	metabolic process
GO:0071704	0.72	organic substance metabolic process
GO:0044238	0.72	primary metabolic process
GO:0044237	0.71	cellular metabolic process
GO:0043170	0.71	macromolecule metabolic process
GO:0044260	0.70	cellular macromolecule metabolic process
GO:0019538	0.66	protein metabolic process
GO:0065007	0.64	biological regulation
GO:0050789	0.63	regulation of biological process
GO:0006464	0.63	cellular protein modification process
GO:0050794	0.62	regulation of cellular process
GO:0070647	0.61	protein modification by small protein conjugation or removal
GO:0016567	0.60	protein ubiquitination
GO:0044699	0.56	single-organism process
GO:0042787	0.56	protein ubiquitination involved in ubiquitin-dependent protein catabolic process
GO:0006139	0.56	nucleobase-containing compound metabolic process
GO:0090304	0.55	nucleic acid metabolic process
GO:0048518	0.54	positive regulation of biological process
GO:0016043	0.54	cellular component organization
GO:0006508	0.54	proteolysis
GO:0080090	0.53	regulation of primary metabolic process
GO:0060255	0.53	regulation of macromolecule metabolic process
GO:0051603	0.53	proteolysis involved in cellular protein catabolic process
GO:0050896	0.53	response to stimulus
GO:0048583	0.53	regulation of response to stimulus
GO:0048523	0.53	negative regulation of cellular process
GO:0048522	0.53	positive regulation of cellular process
GO:0034645	0.53	cellular macromolecule biosynthetic process
GO:0031323	0.53	regulation of cellular metabolic process
GO:0009057	0.53	macromolecule catabolic process
GO:1903047	0.52	mitotic cell cycle process
GO:0044763	0.52	single-organism cellular process
GO:0009966	0.52	regulation of signal transduction
GO:0006259	0.52	DNA metabolic process
GO:1902531	0.51	regulation of intracellular signal transduction
GO:0051716	0.51	cellular response to stimulus
GO:0051128	0.51	regulation of cellular component organization
GO:0042981	0.51	regulation of apoptotic process
GO:0010033	0.51	response to organic substance
GO:0009968	0.51	negative regulation of signal transduction
GO:0000209	0.51	protein polyubiquitination
GO:1902532	0.50	negative regulation of intracellular signal transduction
GO:1901216	0.50	positive regulation of neuron death
GO:0090083	0.50	regulation of inclusion body assembly
GO:0071345	0.50	cellular response to cytokine stimulus
GO:0051130	0.50	positive regulation of cellular component organization
GO:0044843	0.50	cell cycle G1/S phase transition
GO:0044772	0.50	mitotic cell cycle phase transition
GO:0044089	0.50	positive regulation of cellular component biogenesis
GO:0043949	0.50	regulation of cAMP-mediated signaling
GO:0043523	0.50	regulation of neuron apoptotic process
GO:0043065	0.50	positive regulation of apoptotic process
GO:0035456	0.50	response to interferon-beta
GO:0010498	0.50	proteasomal protein catabolic process
GO:0006996	0.50	organelle organization
GO:0006261	0.50	DNA-dependent DNA replication

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:0043231	0.96	intracellular membrane-bounded organelle
GO:0005737	0.82	cytoplasm
GO:0005634	0.80	nucleus
GO:0044446	0.68	intracellular organelle part
GO:0044444	0.59	cytoplasmic part
GO:0044428	0.57	nuclear part

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	0.385	3cegB	0.622	3.16	0.293	0.701	6.3.2.19	162,186,190,192,194,205,215,224
2	0.084	1yh2A	0.395	2.31	0.327	0.424	6.3.2.19	185,188,192,212,214,216,219
3	0.060	2hcsA	0.335	6.51	0.045	0.556	2.7.7.48 3.4.21.91	NA
4	0.060	3d9dA	0.397	5.96	0.042	0.602	1.7.3.1	146
5	0.060	3ebgA	0.408	7.17	0.056	0.715	3.4.11.-	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	0.05	3eb62	0.382	2.00	0.378	0.404	1.18	III	complex1.pdb.gz	102,103,106,107,110,113,160,199,201,203
2	0.04	3h8kA	0.390	2.17	0.311	0.418	1.24	III	complex2.pdb.gz	108,115,116,119,120,121,122,125,132,134,136,139,144,145,147,249
3	0.04	3fshB	0.397	2.18	0.318	0.427	1.11	III	complex3.pdb.gz	108,120,136,145,147
4	0.04	3bzh0	0.396	1.87	0.305	0.415	1.16	III	complex4.pdb.gz	97,126,127,128,129,156,167,168,169,170,183,184,250,251
5	0.03	1yla0	0.419	3.39	0.236	0.483	0.90	III	complex5.pdb.gz	112,117,120,145,147,149,249,250,251,252

	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.