D-I-TASSER Q13214

D-I-TASSER results for Q13214

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

Summary of the Protein

Uniprot ID: Q13214
Protein Name: Semaphorin-3B
Gene Name: SEMA3B

Input Sequence in FASTA format

>Q13214 (749 residues)
MGRAGAAAVIPGLALLWAVGLGSAAPSPPRLRLSFQELQAWHGLQTFSLERTCCYQALLV
DEERGRLFVGAENHVASLNLDNISKRAKKLAWPAPVEWREECNWAGKDIGTECMNFVKLL
HAYNRTHLLACGTGAFHPTCAFVEVGHRAEEPVLRLDPGRIEDGKGKSPYDPRHRAASVL
VGEELYSGVAADLMGRDFTIFRSLGQRPSLRTEPHDSRWLNEPKFVKVFWIPESENPDDD
KIYFFFRETAVEAAPALGRLSVSRVGQICRNDVGGQRSLVNKWTTFLKARLVCSVPGVEG
DTHFDQLQDVFLLSSRDHRTPLLYAVFSTSSSIFQGSAVCVYSMNDVRRAFLGPFAHKEG
PMHQWVSYQGRVPYPRPGMCPSKTFGTFSSTKDFPDDVIQFARNHPLMYNSVLPTGGRPL
FLQVGANYTFTQIAADRVAAADGHYDVLFIGTDVGTVLKVISVPKGSRPSAEGLLLEELH
VFEDSAAVTSMQISSKRHQLYVASRSAVAQIALHRCAAHGRVCTECCLARDPYCAWDGVA
CTRFQPSAKRRFRRQDVRNGDPSTLCSGDSSRPALLEHKVFGVEGSSAFLECEPRSLQAR
VEWTFQRAGVTAHTQVLAEERTERTARGLLLRRLRRRDSGVYLCAAVEQGFTQPLRRLSL
HVLSATQAERLARAEEAAPAAPPGPKLWYRDFLQLVEPGGGGSANSLRMCRPQPALQSLP
LESRRKGRNRRTHAPEPRAERGPRSATHW

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	Q13214-D1	1-31,512-749	269		MGRAGAAAVIPGLALLWAVGLGSAAPSPPRLALHRCAAHGRVCTECCLARDPYCAWDGVACTRFQPSAKRRFRRQDVRNGDPSTLCSGDSSRPALLEHKVFGVEGSSAFLECEPRSLQARVEWTFQRAGVTAHTQVLAEERTERTARGLLLRRLRRRDSGVYLCAAVEQGFTQPLRRLSLHVLSATQAERLARAEEAAPAAPPGPKLWYRDFLQLVEPGGGGSANSLRMCRPQPALQSLPLESRRKGRNRRTHAPEPRAERGPRSATHW
2	Q13214-D2	32-215,488-511	208		RLSFQELQAWHGLQTFSLERTCCYQALLVDEERGRLFVGAENHVASLNLDNISKRAKKLAWPAPVEWREECNWAGKDIGTECMNFVKLLHAYNRTHLLACGTGAFHPTCAFVEVGHRAEEPVLRLDPGRIEDGKGKSPYDPRHRAASVLVGEELYSGVAADLMGRDFTIFRSLGQRPSLRTEPHVTSMQISSKRHQLYVASRSAVAQI
3	Q13214-D3	216-487	272		DSRWLNEPKFVKVFWIPESENPDDDKIYFFFRETAVEAAPALGRLSVSRVGQICRNDVGGQRSLVNKWTTFLKARLVCSVPGVEGDTHFDQLQDVFLLSSRDHRTPLLYAVFSTSSSIFQGSAVCVYSMNDVRRAFLGPFAHKEGPMHQWVSYQGRVPYPRPGMCPSKTFGTFSSTKDFPDDVIQFARNHPLMYNSVLPTGGRPLFLQVGANYTFTQIAADRVAAADGHYDVLFIGTDVGTVLKVISVPKGSRPSAEGLLLEELHVFEDSAA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.56

(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	0.55	6.47	0.247	0.748	model1_1olzA.pdb.gz
2	7m0rC	0.52	6.10	0.420	0.673	model1_7m0rC.pdb.gz
3	6qp7A	0.52	6.50	0.175	0.716	model1_6qp7A.pdb.gz
4	6fkkA	0.49	5.49	0.244	0.610	model1_6fkkA.pdb.gz
5	3afcA	0.49	5.72	0.271	0.618	model1_3afcA.pdb.gz
6	1q47B	0.49	4.96	0.463	0.575	model1_1q47B.pdb.gz
7	6qp9A	0.49	5.64	0.283	0.610	model1_6qp9A.pdb.gz
8	3nvqA	0.48	6.73	0.215	0.662	model1_3nvqA.pdb.gz
9	5l56A	0.45	7.30	0.109	0.634	model1_5l56A.pdb.gz
10	5l5kA	0.45	7.36	0.100	0.635	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:0005008	0.99	hepatocyte growth factor-activated receptor activity
GO:0005102	0.95	receptor binding
GO:0045499	0.94	chemorepellent activity
GO:0030215	0.94	semaphorin receptor binding
GO:0038191	0.72	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:0048585	1.00	negative regulation of response to stimulus
GO:0048523	1.00	negative regulation of cellular process
GO:1901299	0.99	negative regulation of hydrogen peroxide-mediated programmed cell death
GO:0044699	0.99	single-organism process
GO:0044763	0.97	single-organism cellular process
GO:0006928	0.96	movement of cell or subcellular component
GO:0071526	0.94	semaphorin-plexin signaling pathway
GO:0050770	0.94	regulation of axonogenesis
GO:0030334	0.94	regulation of cell migration
GO:0040011	0.93	locomotion
GO:0048841	0.92	regulation of axon extension involved in axon guidance
GO:0001755	0.92	neural crest cell migration
GO:0048522	0.91	positive regulation of cellular process
GO:0048843	0.90	negative regulation of axon extension involved in axon guidance
GO:0030335	0.90	positive regulation of cell migration
GO:0006935	0.70	chemotaxis
GO:0050919	0.69	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:0009925	0.99	basal plasma membrane
GO:0005615	0.75	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	2d5lA	0.322	6.58	0.043	0.435	3.4.14.-	NA
2	0.060	2pffD	0.344	8.42	0.026	0.555	2.3.1.86	180
3	0.060	2pdaA	0.331	8.52	0.023	0.542	1.2.7.1	NA
4	0.060	1bxrA	0.312	8.81	0.059	0.523	6.3.5.5	NA
5	0.060	1sliA	0.309	6.78	0.041	0.429	4.2.2.15 3.2.1.18	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	1w6s0	0.347	6.36	0.059	0.465	0.15	III	complex1.pdb.gz	76,92,479,481
2	0.01	2d0vD	0.347	6.35	0.065	0.465	0.10	PQQ	complex2.pdb.gz	70,116,167,496,497
3	0.01	4aahA	0.346	6.42	0.050	0.469	0.13	PQQ	complex3.pdb.gz	117,120,189,190
4	0.01	1lrwA	0.349	6.35	0.059	0.474	0.17	PQQ	complex4.pdb.gz	56,117,189,190
5	0.01	1h4iA	0.346	6.31	0.052	0.469	0.15	PQQ	complex5.pdb.gz	56,57,131,168,188
6	0.01	1ms1A	0.372	6.30	0.070	0.493	0.20	UUU	complex6.pdb.gz	68,131,133
7	0.01	3i7kA	0.356	6.85	0.052	0.495	0.22	III	complex7.pdb.gz	10,35,132,178,189
8	0.01	1n1vA	0.373	6.39	0.062	0.503	0.10	DAN	complex8.pdb.gz	67,121,132
9	0.01	2ah2A	0.370	6.12	0.067	0.485	0.15	FSI	complex9.pdb.gz	58,59,70
10	0.01	1yiqA	0.345	6.66	0.046	0.473	0.20	PQQ	complex10.pdb.gz	58,70,120,132

	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.