D-I-TASSER O95498

D-I-TASSER results for O95498

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

Summary of the Protein

Uniprot ID: O95498
Protein Name: Vascular non-inflammatory molecule 2
Gene Name: VNN2

Input Sequence in FASTA format

>O95498 (520 residues)
MVTSSFPISVAVFALITLQVGTQDSFIAAVYEHAVILPNKTETPVSQEDALNLMNENIDI
LETAIKQAAEQGARIIVTPEDALYGWKFTRETVFPYLEDIPDPQVNWIPCQDPHRFGHTP
VQARLSCLAKDNSIYVLANLGDKKPCNSRDSTCPPNGYFQYNTNVVYNTEGKLVARYHKY
HLYSEPQFNVPEKPELVTFNTAFGRFGIFTCFDIFFYDPGVTLVKDFHVDTILFPTAWMN
VLPLLTAIEFHSAWAMGMGVNLLVANTHHVSLNMTGSGIYAPNGPKVYHYDMKTELGKLL
LSEVDSHPLSSLAYPTAVNWNAYATTIKPFPVQKNTFRGFISRDGFNFTELFENAGNLTV
CQKELCCHLSYRMLQKEENEVYVLGAFTGLHGRRRREYWQVCTLLKCKTTNLTTCGRPVE
TASTRFEMFSLSGTFGTEYVFPEVLLTEIHLSPGKFEVLKDGRLVNKNGSSGPILTVSLF
GRWYTKDSLYSSCGTSNSAITYLLIFILLMIIALQNIVML

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	O95498-D1	1-311	311		MVTSSFPISVAVFALITLQVGTQDSFIAAVYEHAVILPNKTETPVSQEDALNLMNENIDILETAIKQAAEQGARIIVTPEDALYGWKFTRETVFPYLEDIPDPQVNWIPCQDPHRFGHTPVQARLSCLAKDNSIYVLANLGDKKPCNSRDSTCPPNGYFQYNTNVVYNTEGKLVARYHKYHLYSEPQFNVPEKPELVTFNTAFGRFGIFTCFDIFFYDPGVTLVKDFHVDTILFPTAWMNVLPLLTAIEFHSAWAMGMGVNLLVANTHHVSLNMTGSGIYAPNGPKVYHYDMKTELGKLLLSEVDSHPLSS
2	O95498-D2	312-520	209		LAYPTAVNWNAYATTIKPFPVQKNTFRGFISRDGFNFTELFENAGNLTVCQKELCCHLSYRMLQKEENEVYVLGAFTGLHGRRRREYWQVCTLLKCKTTNLTTCGRPVETASTRFEMFSLSGTFGTEYVFPEVLLTEIHLSPGKFEVLKDGRLVNKNGSSGPILTVSLFGRWYTKDSLYSSCGTSNSAITYLLIFILLMIIALQNIVML

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.82

(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	4cyfA	0.87	1.07	0.674	0.885	model1_4cyfA.pdb.gz
2	2vhhC	0.52	3.02	0.147	0.565	model1_2vhhC.pdb.gz
3	6ftqA	0.50	3.08	0.138	0.552	model1_6ftqA.pdb.gz
4	2plqA	0.49	3.08	0.134	0.533	model1_2plqA.pdb.gz
5	2gglA	0.47	2.89	0.176	0.517	model1_2gglA.pdb.gz
6	2dyvA	0.47	3.16	0.106	0.519	model1_2dyvA.pdb.gz
7	1f89A	0.46	2.56	0.193	0.496	model1_1f89A.pdb.gz
8	4h5uA	0.46	2.70	0.160	0.496	model1_4h5uA.pdb.gz
9	2w1vA	0.46	2.53	0.198	0.488	model1_2w1vA.pdb.gz
10	1emsA1	0.45	2.84	0.169	0.494	model1_1emsA1.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:0016810	1.00	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0016811	0.66	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
GO:0017159	0.62	pantetheine hydrolase 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:0071704	0.99	organic substance metabolic process
GO:0044699	0.99	single-organism process
GO:0044237	0.99	cellular metabolic process
GO:0044763	0.98	single-organism cellular process
GO:0044281	0.98	small molecule metabolic process
GO:0006082	0.97	organic acid metabolic process
GO:0007417	0.96	central nervous system development
GO:0006768	0.96	biotin metabolic process
GO:0006732	0.73	coenzyme metabolic process
GO:0015939	0.72	pantothenate 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	1.00	cell part
GO:0044424	0.90	intracellular part
GO:0043226	0.83	organelle
GO:0043227	0.81	membrane-bounded organelle
GO:0044421	0.79	extracellular region part
GO:0044444	0.72	cytoplasmic part
GO:0070062	0.71	extracellular exosome
GO:0005737	0.53	cytoplasm
GO:0043229	0.51	intracellular organelle
GO:0044422	0.50	organelle part

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	0.080	2w1vA	0.459	2.53	0.198	0.488	3.5.1.3	NA
2	0.075	1f89A	0.464	2.56	0.193	0.496	3.5.-.-	125
3	0.067	2vhhC	0.516	3.02	0.147	0.565	3.5.1.6	74
4	0.067	2dyvA	0.470	3.16	0.106	0.519	3.5.1.49	NA
5	0.067	2uxyA	0.485	3.15	0.116	0.533	3.5.1.4	72

	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	0.02	1uf5B	0.476	2.85	0.187	0.519	0.32	CDT	complex1.pdb.gz	80,211,212,214,215
2	0.02	3hkx0	0.448	3.11	0.187	0.492	0.11	III	complex2.pdb.gz	124,125,127
3	0.01	3ogvA	0.397	6.66	0.035	0.589	0.12	UUU	complex3.pdb.gz	203,204,206
4	0.01	2pweA	0.404	6.74	0.075	0.608	0.12	SUC	complex4.pdb.gz	71,74,262
5	0.01	3dlaC	0.456	3.72	0.082	0.513	0.18	NXX	complex5.pdb.gz	61,64,65,135
6	0.01	1jqnA	0.421	7.40	0.053	0.677	0.14	DCO	complex6.pdb.gz	74,204,206,231,232
7	0.01	3ogsA	0.394	6.69	0.040	0.585	0.10	UUU	complex7.pdb.gz	9,252,278
8	0.01	3ogrA	0.399	6.67	0.035	0.590	0.17	GAL	complex8.pdb.gz	73,75,76,204,233,280
9	0.01	1uh2A	0.394	6.71	0.056	0.594	0.12	GLC	complex9.pdb.gz	73,134,136,169
10	0.01	2wmgA	0.415	6.47	0.061	0.617	0.14	UUU	complex10.pdb.gz	65,68,69,71

	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.