D-I-TASSER O95196

D-I-TASSER results for O95196

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

Summary of the Protein

Uniprot ID: O95196
Protein Name: Chondroitin sulfate proteoglycan 5
Gene Name: CSPG5

Input Sequence in FASTA format

>O95196 (566 residues)
MGRAGGGGPGRGPPPLLLFLGAALVLASGAVPAREAGSAVEAEELVKGSPAWEPPANDTR
EEAGPPAAGEDEASWTAPGGELAGPEEVLQESAAVTGTAWLEADSPGLGGVTAEAGSGDA
QALPATLQAPHEVLGQSIMPPAIPEATEASGPPSPTPGDKLSPASELPKESPLEVWLNLG
GSTPDPQGPELTYPFQGTLEPQPASDIIDIDYFEGLDGEGRGADLGSFPGSPGTSENHPD
TEGETPSWSLLDLYDDFTPFDESDFYPTTSFYDDLDEEEEEEEDDKDAVGGGDLEDENEL
LVPTGKPGLGPGTGQPTSRWHAVPPQHTLGSVPGSSIALRPRPGEPGRDLASSENGTECR
SGFVRHNGSCRSVCDLFPSYCHNGGQCYLVENIGAFCRCNTQDYIWHKGMRCESIITDFQ
VMCVAVGSAALVLLLLFMMTVFFAKKLYLLKTENTKLRRTNKFRTPSELHNDNFSLSTIA
EGSHPNVRKLCNTPRTSSPHARALAHYDNVICQDDPSAPHKIQEVLKSCLKEEESFNIQN
SMSPKLEGGKGDQADLDVNCLQNNLT

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	O95196-D1	1-204	204		MGRAGGGGPGRGPPPLLLFLGAALVLASGAVPAREAGSAVEAEELVKGSPAWEPPANDTREEAGPPAAGEDEASWTAPGGELAGPEEVLQESAAVTGTAWLEADSPGLGGVTAEAGSGDAQALPATLQAPHEVLGQSIMPPAIPEATEASGPPSPTPGDKLSPASELPKESPLEVWLNLGGSTPDPQGPELTYPFQGTLEPQPA
2	O95196-D2	205-411	207		SDIIDIDYFEGLDGEGRGADLGSFPGSPGTSENHPDTEGETPSWSLLDLYDDFTPFDESDFYPTTSFYDDLDEEEEEEEDDKDAVGGGDLEDENELLVPTGKPGLGPGTGQPTSRWHAVPPQHTLGSVPGSSIALRPRPGEPGRDLASSENGTECRSGFVRHNGSCRSVCDLFPSYCHNGGQCYLVENIGAFCRCNTQDYIWHKGMR
3	O95196-D3	412-566	155		CESIITDFQVMCVAVGSAALVLLLLFMMTVFFAKKLYLLKTENTKLRRTNKFRTPSELHNDNFSLSTIAEGSHPNVRKLCNTPRTSSPHARALAHYDNVICQDDPSAPHKIQEVLKSCLKEEESFNIQNSMSPKLEGGKGDQADLDVNCLQNNLT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.36

(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	5xjyA	0.39	7.40	0.034	0.601	model1_5xjyA.pdb.gz
2	7lkpA	0.38	6.14	0.048	0.535	model1_7lkpA.pdb.gz
3	1ej6A	0.34	7.88	0.050	0.571	model1_1ej6A.pdb.gz
4	7cpxA	0.34	7.20	0.054	0.526	model1_7cpxA.pdb.gz
5	6wg3E	0.34	7.38	0.044	0.526	model1_6wg3E.pdb.gz
6	4i43B	0.34	8.15	0.040	0.580	model1_4i43B.pdb.gz
7	6l7eA	0.34	7.73	0.043	0.551	model1_6l7eA.pdb.gz
8	6eqoA	0.33	7.02	0.037	0.503	model1_6eqoA.pdb.gz
9	5ganA	0.33	8.34	0.036	0.581	model1_5ganA.pdb.gz
10	6n8eA	0.32	8.02	0.049	0.537	model1_6n8eA.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:0005102	0.91	receptor binding
GO:0008083	0.86	growth factor 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:0044699	0.98	single-organism process
GO:0044763	0.97	single-organism cellular process
GO:0016043	0.97	cellular component organization
GO:0065007	0.75	biological regulation
GO:0050789	0.74	regulation of biological process
GO:0050794	0.73	regulation of cellular process
GO:0032502	0.70	developmental process
GO:0048856	0.69	anatomical structure development
GO:0008152	0.69	metabolic process
GO:1902589	0.67	single-organism organelle organization
GO:0048583	0.67	regulation of response to stimulus
GO:0022411	0.67	cellular component disassembly
GO:0007005	0.67	mitochondrion organization
GO:0098792	0.66	xenophagy
GO:0098779	0.66	mitophagy in response to mitochondrial depolarization
GO:0002230	0.66	positive regulation of defense response to virus by host
GO:0071704	0.65	organic substance metabolic process
GO:0043170	0.51	macromolecule metabolic process

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:0044444	0.97	cytoplasmic part
GO:0016020	0.97	membrane
GO:0098588	0.96	bounding membrane of organelle
GO:0044431	0.96	Golgi apparatus part
GO:0043231	0.95	intracellular membrane-bounded organelle
GO:0030660	0.94	Golgi-associated vesicle membrane
GO:0005794	0.94	Golgi apparatus

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	3b8cB	0.269	7.26	0.034	0.413	3.6.3.6	NA
2	0.060	2qf7A	0.295	8.08	0.063	0.495	6.4.1.1	NA
3	0.060	1mo7A	0.156	5.30	0.025	0.205	3.6.3.9	NA
4	0.060	2vkzG	0.288	7.56	0.034	0.468	2.3.1.38 3.1.2.14	31
5	0.060	2vz9B	0.274	7.62	0.049	0.438	2.3.1.85	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	3tw6C	0.250	7.21	0.040	0.382	0.14	ADP	complex1.pdb.gz	33,35,38,97
2	0.01	2p9i5	0.129	4.36	0.045	0.155	0.17	III	complex2.pdb.gz	82,83,85,118
3	0.01	2vz9B	0.274	7.62	0.049	0.438	0.11	NAP	complex3.pdb.gz	36,85,117,181,183
4	0.01	2qf7B	0.244	8.04	0.026	0.415	0.12	SAP	complex4.pdb.gz	24,34,35,100,172
5	0.01	3tw6A	0.295	7.61	0.083	0.482	0.16	ADP	complex5.pdb.gz	24,25,98
6	0.01	1qlb4	0.122	6.09	0.063	0.173	0.12	III	complex6.pdb.gz	12,129,178
7	0.01	2vkzG	0.288	7.56	0.034	0.468	0.12	FMN	complex7.pdb.gz	97,115,116

	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.