D-I-TASSER P78352

D-I-TASSER results for P78352

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

Summary of the Protein

Uniprot ID: P78352
Protein Name: Disks large homolog 4
Gene Name: DLG4

Input Sequence in FASTA format

>P78352 (724 residues)
MDCLCIVTTKKYRYQDEDTPPLEHSPAHLPNQANSPPVIVNTDTLEAPGYELQVNGTEGE
MEYEEITLERGNSGLGFSIAGGTDNPHIGDDPSIFITKIIPGGAAAQDGRLRVNDSILFV
NEVDVREVTHSAAVEALKEAGSIVRLYVMRRKPPAEKVMEIKLIKGPKGLGFSIAGGVGN
QHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVY
LKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTAMTPTSPRRYSPVAKD
LLGEEDIPREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDQIL
SVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRFEAKIHDLREQLMNSSLGSGT
ASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDASDEEWWQARRVHSDS
ETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYETVTQMEVHYARPIIIL
GPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIE
AGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLE
INKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPA
RERL

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	P78352-D1	1-154	154		MDCLCIVTTKKYRYQDEDTPPLEHSPAHLPNQANSPPVIVNTDTLEAPGYELQVNGTEGEMEYEEITLERGNSGLGFSIAGGTDNPHIGDDPSIFITKIIPGGAAAQDGRLRVNDSILFVNEVDVREVTHSAAVEALKEAGSIVRLYVMRRKPP
2	P78352-D2	155-294,419-524	246		AEKVMEIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVYLKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTAMTPTSPRRYGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDASDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYE
3	P78352-D3	295-418	124		SPVAKDLLGEEDIPREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRFEAKIHDLREQLMNSSLGS
4	P78352-D4	525-724	200		TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.57

(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	0.68	5.26	0.716	0.844	model1_2xkxA.pdb.gz
2	1kjwA	0.38	2.51	0.921	0.403	model1_1kjwA.pdb.gz
3	6um1A	0.36	8.68	0.036	0.593	model1_6um1A.pdb.gz
4	7bdiB	0.36	8.19	0.052	0.572	model1_7bdiB.pdb.gz
5	4bedB	0.35	8.01	0.038	0.552	model1_4bedB.pdb.gz
6	3cmuA	0.35	8.88	0.037	0.590	model1_3cmuA.pdb.gz
7	5gm6B	0.35	8.17	0.044	0.548	model1_5gm6B.pdb.gz
8	6ysgA	0.34	8.56	0.066	0.569	model1_6ysgA.pdb.gz
9	5m59A	0.34	8.40	0.039	0.550	model1_5m59A.pdb.gz
10	6v85A	0.34	8.83	0.039	0.570	model1_6v85A.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	0.69	catalytic activity
GO:0016740	0.66	transferase activity
GO:0016301	0.63	kinase activity
GO:0005102	0.63	receptor binding
GO:0004385	0.61	guanylate kinase activity
GO:0035254	0.55	glutamate receptor binding
GO:0035255	0.53	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	0.93	single-organism process
GO:0009987	0.92	cellular process
GO:0044763	0.87	single-organism cellular process
GO:0016043	0.81	cellular component organization
GO:0051179	0.73	localization
GO:0032502	0.71	developmental process
GO:0008104	0.67	protein localization
GO:0065007	0.64	biological regulation
GO:0048856	0.64	anatomical structure development
GO:0051641	0.62	cellular localization
GO:0007163	0.62	establishment or maintenance of cell polarity
GO:1902578	0.61	single-organism localization
GO:0035088	0.59	establishment or maintenance of apical/basal cell polarity
GO:0050789	0.58	regulation of biological process
GO:0045197	0.58	establishment or maintenance of epithelial cell apical/basal polarity
GO:0034613	0.58	cellular protein localization
GO:1902580	0.57	single-organism cellular localization
GO:0072657	0.56	protein localization to membrane
GO:0007267	0.55	cell-cell signaling
GO:0050794	0.54	regulation of cellular process
GO:0043113	0.50	receptor clustering

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	0.98	cell part
GO:0044424	0.88	intracellular part
GO:0016020	0.79	membrane
GO:0044425	0.75	membrane part
GO:0044459	0.73	plasma membrane part
GO:0043226	0.71	organelle
GO:0043229	0.68	intracellular organelle
GO:0098590	0.65	plasma membrane region
GO:0097458	0.64	neuron part
GO:0032991	0.62	macromolecular complex
GO:0043234	0.59	protein complex
GO:0044456	0.57	synapse part
GO:0043232	0.56	intracellular non-membrane-bounded organelle
GO:0016323	0.56	basolateral plasma membrane
GO:0098796	0.54	membrane protein complex
GO:0098797	0.53	plasma membrane protein complex
GO:0034702	0.52	ion channel complex
GO:0014069	0.52	postsynaptic density
GO:0097060	0.51	synaptic membrane
GO:0008328	0.50	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	2q1fA	0.287	8.28	0.025	0.461	4.2.2.21	72
2	0.060	1zcjA	0.181	7.10	0.027	0.265	1.1.1.35	NA
3	0.060	1bf2A	0.280	8.85	0.069	0.478	3.2.1.68	NA
4	0.060	2vdcF	0.313	8.55	0.046	0.515	1.4.1.13	NA
5	0.060	1z0hB	0.176	7.23	0.034	0.260	3.4.24.69	135

	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	0.67	1be9A	0.135	2.49	0.817	0.142	1.27	III	complex1.pdb.gz	74,75,76,77,78,79,80,97,130,138
2	0.34	2awuB	0.123	0.96	0.522	0.124	1.64	III	complex2.pdb.gz	73,74,75,76,77,78,100,134
3	0.13	2g2lB	0.123	0.82	0.522	0.124	1.25	III	complex3.pdb.gz	75,76,77,79,138
4	0.10	2i0iA	0.111	0.69	0.877	0.112	1.64	III	complex4.pdb.gz	71,72,102,103,104,107
5	0.10	1pdr1	0.127	1.85	0.813	0.131	1.58	III	complex5.pdb.gz	71,72,141,142
6	0.10	1pdr2	0.127	1.85	0.813	0.131	1.58	III	complex6.pdb.gz	68,69,102,104,107
7	0.05	2x7z0	0.131	1.59	0.465	0.134	1.40	III	complex7.pdb.gz	63,65,66,67,108,110

	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.