D-I-TASSER Q12959

D-I-TASSER results for Q12959

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

Summary of the Protein

Uniprot ID: Q12959
Protein Name: Disks large homolog 1
Gene Name: DLG1

Input Sequence in FASTA format

>Q12959 (904 residues)
MPVRKQDTQRALHLLEEYRSKLSQTEDRQLRSSIERVINIFQSNLFQALIDIQEFYEVTL
LDNPKCIDRSKPSEPIQPVNTWEISSLPSSTVTSETLPSSLSPSVEKYRYQDEDTPPQEH
ISPQITNEVIGPELVHVSEKNLSEIENVHGFVSHSHISPIKPTEAVLPSPPTVPVIPVLP
VPAENTVILPTIPQANPPPVLVNTDSLETPTYVNGTDADYEYEEITLERGNSGLGFSIAG
GTDNPHIGDDSSIFITKIITGGAAAQDGRLRVNDCILRVNEVDVRDVTHSKAVEALKEAG
SIVRLYVKRRKPVSEKIMEIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAH
KDGKLQIGDKLLAVNNVCLEEVTHEEAVTALKNTSDFVYLKVAKPTSMYMNDGYAPPDIT
NSSSQPVDNHVSPSSFLGQTPASPARYSPVSKAVLGDDEITREPRKVVLHRGSTGLGFNI
VGGEDGEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVT
IVAQYRPEEYSRFEAKIHDLREQMMNSSISSGSGSLRTSQKRSLYVRALFDYDKTKDSGL
PSQGLNFKFGDILHVINASDDEWWQARQVTPDGESDEVGVIPSKRRVEKKERARLKTVKF
NSKTRDKGEIPDDMGSKGLKHVTSNASDSESSYRGQEEYVLSYEPVNQQEVNYTRPVIIL
GPMKDRINDDLISEFPDKFGSCVPHTTRPKRDYEVDGRDYHFVTSREQMEKDIQEHKFIE
AGQYNNHLYGTSVQSVREVAEKGKHCILDVSGNAIKRLQIAQLYPISIFIKPKSMENIME
MNKRLTEEQARKTFERAMKLEQEFTEHFTAIVQGDTLEDIYNQVKQIIEEQSGSYIWVPA
KEKL

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	Q12959-D1	1-904	904		MPVRKQDTQRALHLLEEYRSKLSQTEDRQLRSSIERVINIFQSNLFQALIDIQEFYEVTLLDNPKCIDRSKPSEPIQPVNTWEISSLPSSTVTSETLPSSLSPSVEKYRYQDEDTPPQEHISPQITNEVIGPELVHVSEKNLSEIENVHGFVSHSHISPIKPTEAVLPSPPTVPVIPVLPVPAENTVILPTIPQANPPPVLVNTDSLETPTYVNGTDADYEYEEITLERGNSGLGFSIAGGTDNPHIGDDSSIFITKIITGGAAAQDGRLRVNDCILRVNEVDVRDVTHSKAVEALKEAGSIVRLYVKRRKPVSEKIMEIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGKLQIGDKLLAVNNVCLEEVTHEEAVTALKNTSDFVYLKVAKPTSMYMNDGYAPPDITNSSSQPVDNHVSPSSFLGQTPASPARYSPVSKAVLGDDEITREPRKVVLHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYRPEEYSRFEAKIHDLREQMMNSSISSGSGSLRTSQKRSLYVRALFDYDKTKDSGLPSQGLNFKFGDILHVINASDDEWWQARQVTPDGESDEVGVIPSKRRVEKKERARLKTVKFNSKTRDKGEIPDDMGSKGLKHVTSNASDSESSYRGQEEYVLSYEPVNQQEVNYTRPVIILGPMKDRINDDLISEFPDKFGSCVPHTTRPKRDYEVDGRDYHFVTSREQMEKDIQEHKFIEAGQYNNHLYGTSVQSVREVAEKGKHCILDVSGNAIKRLQIAQLYPISIFIKPKSMENIMEMNKRLTEEQARKTFERAMKLEQEFTEHFTAIVQGDTLEDIYNQVKQIIEEQSGSYIWVPAKEKL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5565

(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	2xkxA	0.78	0.92	0.736	0.791	model1_2xkxA.pdb.gz
2	5xjcA	0.34	9.21	0.031	0.568	model1_5xjcA.pdb.gz
3	5nrlA	0.34	9.04	0.035	0.550	model1_5nrlA.pdb.gz
4	6uebA	0.34	8.47	0.029	0.512	model1_6uebA.pdb.gz
5	3cmuA	0.34	8.72	0.036	0.524	model1_3cmuA.pdb.gz
6	3qmzA	0.34	8.92	0.040	0.534	model1_3qmzA.pdb.gz
7	4c2mA	0.32	9.26	0.040	0.534	model1_4c2mA.pdb.gz
8	1kjwA	0.32	0.64	0.719	0.323	model1_1kjwA.pdb.gz
9	7b0yA	0.32	9.15	0.049	0.519	model1_7b0yA.pdb.gz
10	3gtgA	0.32	9.07	0.048	0.514	model1_3gtgA.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:0016740	0.69	transferase activity
GO:0016772	0.67	transferase activity, transferring phosphorus-containing groups
GO:0016301	0.66	kinase activity
GO:0005102	0.65	receptor binding
GO:0004385	0.64	guanylate kinase activity
GO:0035254	0.58	glutamate receptor binding
GO:0035255	0.56	ionotropic glutamate receptor 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:0044699	0.94	single-organism process
GO:0009987	0.93	cellular process
GO:0044763	0.89	single-organism cellular process
GO:0016043	0.82	cellular component organization
GO:0051179	0.74	localization
GO:0032502	0.72	developmental process
GO:0008104	0.68	protein localization
GO:0048856	0.67	anatomical structure development
GO:0051641	0.64	cellular localization
GO:0007163	0.64	establishment or maintenance of cell polarity
GO:0065007	0.63	biological regulation
GO:1902578	0.62	single-organism localization
GO:0045197	0.61	establishment or maintenance of epithelial cell apical/basal polarity
GO:0034613	0.60	cellular protein localization
GO:0007267	0.60	cell-cell signaling
GO:1902580	0.59	single-organism cellular localization
GO:0072657	0.58	protein localization to membrane
GO:0050789	0.58	regulation of biological process
GO:0007268	0.55	chemical synaptic transmission
GO:0043113	0.53	receptor clustering
GO:0097120	0.52	receptor localization to synapse
GO:0050794	0.52	regulation of cellular process
GO:0048731	0.52	system development

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:0044464	0.99	cell part
GO:0044424	0.90	intracellular part
GO:0016020	0.80	membrane
GO:0044425	0.77	membrane part
GO:0044459	0.75	plasma membrane part
GO:0043226	0.73	organelle
GO:0043229	0.70	intracellular organelle
GO:0098590	0.67	plasma membrane region
GO:0097458	0.64	neuron part
GO:0032991	0.63	macromolecular complex
GO:0043234	0.60	protein complex
GO:0016323	0.60	basolateral plasma membrane
GO:0044456	0.58	synapse part
GO:0043232	0.58	intracellular non-membrane-bounded organelle
GO:0098797	0.56	plasma membrane protein complex
GO:0099572	0.55	postsynaptic specialization
GO:0034702	0.55	ion channel complex
GO:0014069	0.54	postsynaptic density
GO:0097060	0.53	synaptic membrane
GO:0045211	0.52	postsynaptic membrane
GO:0008328	0.52	ionotropic glutamate receptor 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	3h0gA	0.309	9.34	0.048	0.512	2.7.7.6	264,269
2	0.060	2pffD	0.255	8.33	0.025	0.385	2.3.1.86	NA
3	0.060	3c46B	0.236	8.47	0.042	0.362	2.7.7.6	NA
4	0.060	1ug9A	0.268	8.82	0.024	0.425	3.2.1.70	NA
5	0.060	2e1qA	0.297	8.86	0.042	0.476	1.17.3.2 1.17.1.4	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	0.63	2i0iB	0.088	1.24	1.000	0.090	1.51	III	complex1.pdb.gz	233,234,235,236,237,238,239,256,289
2	0.27	2awuB	0.098	1.32	0.511	0.100	1.41	III	complex2.pdb.gz	232,233,234,235,236,237,259,293
3	0.12	2i0iA	0.088	1.28	1.000	0.090	1.58	III	complex3.pdb.gz	230,231,261,262,263,266
4	0.12	1pdr2	0.105	1.03	0.969	0.106	1.51	III	complex4.pdb.gz	227,228,261,263,266
5	0.12	1pdr1	0.105	1.03	0.969	0.106	1.50	III	complex5.pdb.gz	230,231,300,301

	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.