D-I-TASSER Q92990

D-I-TASSER results for Q92990

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

Summary of the Protein

Uniprot ID: Q92990
Protein Name: Glomulin
Gene Name: GLMN

Input Sequence in FASTA format

>Q92990 (594 residues)
MAVEELQSIIKRCQILEEQDFKEEDFGLFQLAGQRCIEEGHTDQLLEIIQNEKNKVIIKN
MGWNLVGPVVRCLLCKDKEDSKRKVYFLIFDLLVKLCNPKELLLGLLELIEEPSGKQISQ
SILLLLQPLQTVIQKLHNKAYSIGLALSTLWNQLSLLPVPYSKEQIQMDDYGLCQCCKAL
IEFTKPFVEEVIDNKENSLENEKLKDELLKFCFKSLKCPLLTAQFFEQSEEGGNDPFRYF
ASEIIGFLSAIGHPFPKMIFNHGRKKRTWNYLEFEEEENKQLADSMASLAYLVFVQGIHI
DQLPMVLSPLYLLQFNMGHIEVFLQRTEESVISKGLELLENSLLRIEDNSLLYQYLEIKS
FLTVPQGLVKVMTLCPIETLRKKSLAMLQLYINKLDSQGKYTLFRCLLNTSNHSGVEAFI
IQNIKNQIDMSLKRTRNNKWFTGPQLISLLDLVLFLPEGAETDLLQNSDRIMASLNLLRY
LVIKDNENDNQTGLWTELGNIENNFLKPLHIGLNMSKAHYEAEIKNSQEAQKSKDLCSIT
VSGEEIPNMPPEMQLKVLHSALFTFDLIESVLARVEELIEIKTKSTSEENIGIK

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	Q92990-D1	1-113	113		MAVEELQSIIKRCQILEEQDFKEEDFGLFQLAGQRCIEEGHTDQLLEIIQNEKNKVIIKNMGWNLVGPVVRCLLCKDKEDSKRKVYFLIFDLLVKLCNPKELLLGLLELIEEP
2	Q92990-D2	114-350	237		SGKQISQSILLLLQPLQTVIQKLHNKAYSIGLALSTLWNQLSLLPVPYSKEQIQMDDYGLCQCCKALIEFTKPFVEEVIDNKENSLENEKLKDELLKFCFKSLKCPLLTAQFFEQSEEGGNDPFRYFASEIIGFLSAIGHPFPKMIFNHGRKKRTWNYLEFEEEENKQLADSMASLAYLVFVQGIHIDQLPMVLSPLYLLQFNMGHIEVFLQRTEESVISKGLELLENSLLRIEDNS
3	Q92990-D3	351-594	244		LLYQYLEIKSFLTVPQGLVKVMTLCPIETLRKKSLAMLQLYINKLDSQGKYTLFRCLLNTSNHSGVEAFIIQNIKNQIDMSLKRTRNNKWFTGPQLISLLDLVLFLPEGAETDLLQNSDRIMASLNLLRYLVIKDNENDNQTGLWTELGNIENNFLKPLHIGLNMSKAHYEAEIKNSQEAQKSKDLCSITVSGEEIPNMPPEMQLKVLHSALFTFDLIESVLARVEELIEIKTKSTSEENIGIK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.85

(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	4f52E	0.81	2.93	0.929	0.880	model1_4f52E.pdb.gz
2	2qj0A	0.60	6.39	0.076	0.852	model1_2qj0A.pdb.gz
3	5t8vA	0.55	6.35	0.080	0.788	model1_5t8vA.pdb.gz
4	5hb4B	0.55	6.74	0.066	0.801	model1_5hb4B.pdb.gz
5	6wg3E	0.54	6.82	0.083	0.803	model1_6wg3E.pdb.gz
6	5nvrA	0.54	6.68	0.084	0.798	model1_5nvrA.pdb.gz
7	5f0oA	0.54	6.63	0.062	0.783	model1_5f0oA.pdb.gz
8	7dl2A	0.54	6.26	0.075	0.754	model1_7dl2A.pdb.gz
9	5frpA	0.53	6.67	0.083	0.774	model1_5frpA.pdb.gz
10	6zz6D	0.53	6.55	0.084	0.766	model1_6zz6D.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:0055105	1.00	ubiquitin-protein transferase inhibitor 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:0048523	1.00	negative regulation of cellular process
GO:0032268	1.00	regulation of cellular protein metabolic process
GO:0009987	0.94	cellular process
GO:0044699	0.91	single-organism process
GO:0044763	0.90	single-organism cellular process
GO:0031325	0.90	positive regulation of cellular metabolic process
GO:0010604	0.90	positive regulation of macromolecule metabolic process
GO:1903050	0.89	regulation of proteolysis involved in cellular protein catabolic process
GO:0051247	0.89	positive regulation of protein metabolic process
GO:0051239	0.89	regulation of multicellular organismal process
GO:0042327	0.89	positive regulation of phosphorylation
GO:0031328	0.89	positive regulation of cellular biosynthetic process
GO:0010557	0.89	positive regulation of macromolecule biosynthetic process
GO:0010468	0.89	regulation of gene expression
GO:0008285	0.89	negative regulation of cell proliferation
GO:0002682	0.89	regulation of immune system process
GO:0050715	0.88	positive regulation of cytokine secretion
GO:0045086	0.88	positive regulation of interleukin-2 biosynthetic process
GO:0042692	0.88	muscle cell differentiation
GO:0042130	0.88	negative regulation of T cell proliferation
GO:0040029	0.88	regulation of gene expression, epigenetic
GO:0032434	0.88	regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0001570	0.88	vasculogenesis

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:0005737	1.00	cytoplasm
GO:0032991	0.55	macromolecular complex
GO:0043234	0.53	protein complex
GO:0000151	0.50	ubiquitin ligase 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	2jgdA	0.323	7.99	0.050	0.542	1.2.4.2	NA
2	0.060	1i8qA	0.328	8.40	0.057	0.569	4.2.2.1	NA
3	0.060	1hn0A	0.382	8.07	0.048	0.641	4.2.2.20	NA
4	0.060	2pziA	0.364	7.62	0.056	0.583	2.7.11.1	NA
5	0.060	1f1sA	0.327	7.88	0.050	0.534	4.2.2.1	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	1jdh0	0.463	6.97	0.079	0.702	0.14	III	complex1.pdb.gz	62,291,292,333,337,341
2	0.01	1bk50	0.456	5.80	0.117	0.628	0.12	III	complex2.pdb.gz	63,64,67,332,336
3	0.01	1q1sC	0.445	6.24	0.077	0.628	0.19	III	complex3.pdb.gz	64,66,67
4	0.01	2c1t0	0.456	5.84	0.114	0.628	0.12	III	complex4.pdb.gz	63,66,67,127,183,184,333,336
5	0.01	2c1m0	0.464	5.82	0.075	0.638	0.15	III	complex5.pdb.gz	30,60,64,70,71,104,150,277
6	0.01	1i7x3	0.467	6.84	0.105	0.702	0.18	III	complex6.pdb.gz	60,63,64,67,291,330,333,334,338
7	0.01	1ejyI	0.447	5.99	0.091	0.625	0.15	III	complex7.pdb.gz	63,67,74,291,334,337
8	0.01	2ot8A	0.394	6.22	0.071	0.557	0.19	III	complex8.pdb.gz	63,67,105
9	0.01	1ejlI	0.447	5.95	0.091	0.623	0.14	III	complex9.pdb.gz	75,116,152,156
10	0.01	2gl7D	0.467	6.83	0.102	0.700	0.17	III	complex10.pdb.gz	127,131,134,181,183

	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.