D-I-TASSER Q9UHD9

D-I-TASSER results for Q9UHD9

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

Summary of the Protein

Uniprot ID: Q9UHD9
Protein Name: Ubiquilin-2
Gene Name: UBQLN2

Input Sequence in FASTA format

>Q9UHD9 (624 residues)
MAENGESSGPPRPSRGPAAAQGSAAAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEA
ISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKSQNRPQGQSTQPSNAAG
TNTTSASTPRSNSTPISTNSNPFGLGSLGGLAGLSSLGLSSTNFSELQSQMQQQLMASPE
MMIQIMENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARN
PAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQEPMLNAAQEQFGGNPFASVGSSSS
SGEGTQPSRTENRDPLPNPWAPPPATQSSATTSTTTSTGSGSGNSSSNATGNTVAAANYV
ASIFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLSQNPDLAAQMMLNSPLFTANP
QLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFTPGV
GVGVLGTAIGPVGPVTPIGPIGPIVPFTPIGPIGPIGPTGPAAPPGSTGSGGPTGPTVSS
AAPSETTSPTSESGPNQQFIQQMVQALAGANAPQLPNPEVRFQQQLEQLNAMGFLNREAN
LQALIATGGDINAAIERLLGSQPS

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	Q9UHD9-D1	1-109	109		MAENGESSGPPRPSRGPAAAQGSAAAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKSQNRPQ
2	Q9UHD9-D2	110-480,554-624	442		GQSTQPSNAAGTNTTSASTPRSNSTPISTNSNPFGLGSLGGLAGLSSLGLSSTNFSELQSQMQQQLMASPEMMIQIMENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQEPMLNAAQEQFGGNPFASVGSSSSSGEGTQPSRTENRDPLPNPWAPPPATQSSATTSTTTSTGSGSGNSSSNATGNTVAAANYVASIFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLSQNPDLAAQMMLNSPLFTANPQLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFTPGVGPNQQFIQQMVQALAGANAPQLPNPEVRFQQQLEQLNAMGFLNREANLQALIATGGDINAAIERLLGSQPS
3	Q9UHD9-D3	481-553	73		GVGVLGTAIGPVGPVTPIGPIGPIVPFTPIGPIGPIGPTGPAAPPGSTGSGGPTGPTVSSAAPSETTSPTSES

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.37

(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

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	5t8vA	0.36	7.92	0.035	0.587	model1_5t8vA.pdb.gz
2	7abiA	0.35	7.78	0.044	0.550	model1_7abiA.pdb.gz
3	6ar6A	0.35	8.22	0.034	0.588	model1_6ar6A.pdb.gz
4	7lhtA	0.33	8.41	0.040	0.559	model1_7lhtA.pdb.gz
5	5f0oA	0.32	7.65	0.063	0.514	model1_5f0oA.pdb.gz
6	5nrlA	0.32	8.25	0.036	0.538	model1_5nrlA.pdb.gz
7	6z2wE	0.32	8.11	0.036	0.534	model1_6z2wE.pdb.gz
8	6yufD	0.32	7.99	0.028	0.511	model1_6yufD.pdb.gz
9	7luvC	0.32	8.04	0.060	0.516	model1_7luvC.pdb.gz
10	6um1A	0.31	8.30	0.022	0.530	model1_6um1A.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:0043130	0.63	ubiquitin binding
GO:0031593	0.62	polyubiquitin 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	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0080090	0.92	regulation of primary metabolic process
GO:0060255	0.92	regulation of macromolecule metabolic process
GO:0048519	0.92	negative regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0042176	0.91	regulation of protein catabolic process
GO:0031323	0.90	regulation of cellular metabolic process
GO:0009987	0.90	cellular process
GO:0032434	0.89	regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0008152	0.89	metabolic process
GO:0071704	0.87	organic substance metabolic process
GO:0044238	0.87	primary metabolic process
GO:0043170	0.86	macromolecule metabolic process
GO:0044237	0.84	cellular metabolic process
GO:0019538	0.84	protein metabolic process
GO:0044260	0.82	cellular macromolecule metabolic process
GO:1901575	0.76	organic substance catabolic process
GO:0006508	0.76	proteolysis
GO:0006511	0.75	ubiquitin-dependent protein catabolic process
GO:0048518	0.72	positive regulation of biological process
GO:0048522	0.71	positive regulation of cellular process
GO:0010604	0.71	positive regulation of macromolecule metabolic process
GO:0080135	0.70	regulation of cellular response to stress
GO:0048584	0.70	positive regulation of response to stimulus
GO:0045732	0.70	positive regulation of protein catabolic process
GO:0030433	0.70	ER-associated ubiquitin-dependent protein catabolic process
GO:1904294	0.69	positive regulation of ERAD pathway
GO:0032270	0.69	positive regulation of cellular protein metabolic process
GO:1903071	0.68	positive regulation of ER-associated ubiquitin-dependent protein catabolic process
GO:0051051	0.68	negative regulation of transport
GO:0048523	0.59	negative regulation of cellular process
GO:0009966	0.57	regulation of signal transduction

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:0044444	0.79	cytoplasmic part
GO:0043226	0.74	organelle
GO:0043229	0.73	intracellular organelle
GO:0043227	0.72	membrane-bounded organelle
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0005737	0.70	cytoplasm
GO:0016020	0.67	membrane
GO:0044446	0.59	intracellular organelle part
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

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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	2np0A	0.268	8.46	0.030	0.454	3.4.24.69	NA
2	0.060	1ofdA	0.250	8.09	0.028	0.413	1.4.7.1	NA
3	0.060	1sliA	0.238	8.08	0.036	0.391	4.2.2.15 3.2.1.18	NA
4	0.060	2vdcA	0.266	6.88	0.035	0.385	1.4.1.13	NA
5	0.060	1ynnJ	0.149	6.24	0.039	0.210	2.7.7.6	58,60,62

	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

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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	2vumA	0.274	7.84	0.042	0.436	0.19	III	complex1.pdb.gz	34,35,36,37,38
2	0.01	1vs82	0.105	4.63	0.109	0.130	0.31	III	complex2.pdb.gz	76,78,95
3	0.01	1l0l9	0.050	3.69	0.055	0.058	0.23	III	complex3.pdb.gz	35,78,79
4	0.01	1pg51	0.156	6.73	0.053	0.229	0.16	III	complex4.pdb.gz	53,54,55,59

	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.