D-I-TASSER O95025

D-I-TASSER results for O95025

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

Summary of the Protein

Uniprot ID: O95025
Protein Name: Semaphorin-3D
Gene Name: SEMA3D

Input Sequence in FASTA format

>O95025 (777 residues)
MNANKDERLKARSQDFHLFPALMMLSMTMLFLPVTGTLKQNIPRLKLTYKDLLLSNSCIP
FLGSSEGLDFQTLLLDEERGRLLLGAKDHIFLLSLVDLNKNFKKIYWPAAKERVELCKLA
GKDANTECANFIRVLQPYNKTHIYVCGTGAFHPICGYIDLGVYKEDIIFKLDTHNLESGR
LKCPFDPQQPFASVMTDEYLYSGTASDFLGKDTAFTRSLGPTHDHHYIRTDISEHYWLNG
AKFIGTFFIPDTYNPDDDKIYFFFRESSQEGSTSDKTILSRVGRVCKNDVGGQRSLINKW
TTFLKARLICSIPGSDGADTYFDELQDIYLLPTRDERNPVVYGVFTTTSSIFKGSAVCVY
SMADIRAVFNGPYAHKESADHRWVQYDGRIPYPRPGTCPSKTYDPLIKSTRDFPDDVISF
IKRHSVMYKSVYPVAGGPTFKRINVDYRLTQIVVDHVIAEDGQYDVMFLGTDIGTVLKVV
SISKEKWNMEEVVLEELQIFKHSSIILNMELSLKQQQLYIGSRDGLVQLSLHRCDTYGKA
CADCCLARDPYCAWDGNACSRYAPTSKRRARRQDVKYGDPITQCWDIEDSISHETADEKV
IFGIEFNSTFLECIPKSQQATIKWYIQRSGDEHREELKPDERIIKTEYGLLIRSLQKKDS
GMYYCKAQEHTFIHTIVKLTLNVIENEQMENTQRAEHEEGKVKDLLAESRLRYKDYIQIL
SSPNFSLDQYCEQMWHREKRRQRNKGGPKWKHMQEMKKKRNRRHHRDLDELPRAVAT

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	O95025-D1	1-179,446-586	320		MNANKDERLKARSQDFHLFPALMMLSMTMLFLPVTGTLKQNIPRLKLTYKDLLLSNSCIPFLGSSEGLDFQTLLLDEERGRLLLGAKDHIFLLSLVDLNKNFKKIYWPAAKERVELCKLAGKDANTECANFIRVLQPYNKTHIYVCGTGAFHPICGYIDLGVYKEDIIFKLDTHNLESGDYRLTQIVVDHVIAEDGQYDVMFLGTDIGTVLKVVSISKEKWNMEEVVLEELQIFKHSSIILNMELSLKQQQLYIGSRDGLVQLSLHRCDTYGKACADCCLARDPYCAWDGNACSRYAPTSKRRARRQDVKYGDPITQCWD
2	O95025-D2	180-241	62		RLKCPFDPQQPFASVMTDEYLYSGTASDFLGKDTAFTRSLGPTHDHHYIRTDISEHYWLNGA
3	O95025-D3	242-445	204		KFIGTFFIPDTYNPDDDKIYFFFRESSQEGSTSDKTILSRVGRVCKNDVGGQRSLINKWTTFLKARLICSIPGSDGADTYFDELQDIYLLPTRDERNPVVYGVFTTTSSIFKGSAVCVYSMADIRAVFNGPYAHKESADHRWVQYDGRIPYPRPGTCPSKTYDPLIKSTRDFPDDVISFIKRHSVMYKSVYPVAGGPTFKRINV
4	O95025-D4	587-777	191		IEDSISHETADEKVIFGIEFNSTFLECIPKSQQATIKWYIQRSGDEHREELKPDERIIKTEYGLLIRSLQKKDSGMYYCKAQEHTFIHTIVKLTLNVIENEQMENTQRAEHEEGKVKDLLAESRLRYKDYIQILSSPNFSLDQYCEQMWHREKRRQRNKGGPKWKHMQEMKKKRNRRHHRDLDELPRAVAT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.75

(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	1olzA	0.68	3.39	0.320	0.740	model1_1olzA.pdb.gz
2	7m0rC	0.67	3.36	0.520	0.728	model1_7m0rC.pdb.gz
3	6qp7A	0.66	3.92	0.290	0.741	model1_6qp7A.pdb.gz
4	3nvqA	0.62	3.95	0.238	0.703	model1_3nvqA.pdb.gz
5	3afcA	0.61	3.00	0.326	0.661	model1_3afcA.pdb.gz
6	1q47B	0.59	2.36	0.568	0.625	model1_1q47B.pdb.gz
7	6qp9A	0.59	2.96	0.327	0.634	model1_6qp9A.pdb.gz
8	6fkkA	0.59	3.25	0.315	0.642	model1_6fkkA.pdb.gz
9	5l56A	0.55	4.88	0.126	0.640	model1_5l56A.pdb.gz
10	5l5kA	0.55	4.88	0.125	0.636	model1_5l5kA.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	0.97	receptor binding
GO:0045499	0.95	chemorepellent activity
GO:0030215	0.95	semaphorin receptor binding
GO:0038191	0.74	neuropilin 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	0.99	single-organism process
GO:0044763	0.98	single-organism cellular process
GO:0065007	0.97	biological regulation
GO:0050789	0.97	regulation of biological process
GO:0006928	0.97	movement of cell or subcellular component
GO:0050794	0.96	regulation of cellular process
GO:0032879	0.95	regulation of localization
GO:0007165	0.95	signal transduction
GO:0071526	0.94	semaphorin-plexin signaling pathway
GO:0050770	0.94	regulation of axonogenesis
GO:0048583	0.94	regulation of response to stimulus
GO:0030334	0.94	regulation of cell migration
GO:0016477	0.94	cell migration
GO:0048841	0.93	regulation of axon extension involved in axon guidance
GO:0048523	0.93	negative regulation of cellular process
GO:0048522	0.93	positive regulation of cellular process
GO:0001755	0.93	neural crest cell migration
GO:0048843	0.91	negative regulation of axon extension involved in axon guidance
GO:0030335	0.91	positive regulation of cell migration
GO:0006935	0.72	chemotaxis
GO:0050919	0.71	negative chemotaxis

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	0.81	cell part
GO:0044421	0.78	extracellular region part
GO:0005615	0.77	extracellular space

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	1euuA	0.358	5.78	0.033	0.454	3.2.1.18	106
2	0.060	1s0kA	0.352	6.93	0.068	0.495	3.2.1.18	NA
3	0.060	2madH	0.333	4.22	0.086	0.385	1.4.99.3	86,147
4	0.060	3c75J	0.335	4.34	0.071	0.389	1.4.99.3	NA
5	0.060	2vsmA	0.309	5.54	0.090	0.393	3.2.1.18	131

	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	0.07	1q470	0.582	2.39	0.567	0.613	0.12	III	complex1.pdb.gz	146,147,148,153,154,155
2	0.01	2d0vD	0.386	4.84	0.089	0.458	0.14	PQQ	complex2.pdb.gz	146,189,241
3	0.01	1h4iA	0.386	4.83	0.097	0.458	0.15	PQQ	complex3.pdb.gz	134,326,470
4	0.01	1flgA	0.382	4.68	0.076	0.451	0.17	PQQ	complex4.pdb.gz	326,327,470,471
5	0.01	2d0vA	0.386	4.84	0.089	0.458	0.15	PQQ	complex5.pdb.gz	84,85,86
6	0.01	1lrwA	0.386	4.87	0.088	0.458	0.14	PQQ	complex6.pdb.gz	86,88,156,157,158,159
7	0.01	2vc2A	0.399	4.48	0.088	0.469	0.35	180	complex7.pdb.gz	90,132,133
8	0.01	1flgB	0.382	4.72	0.074	0.452	0.15	PQQ	complex8.pdb.gz	86,146,147,148,172,521

	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.