D-I-TASSER Q13275

D-I-TASSER results for Q13275

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

Summary of the Protein

Uniprot ID: Q13275
Protein Name: Semaphorin-3F
Gene Name: SEMA3F

Input Sequence in FASTA format

>Q13275 (785 residues)
MLVAGLLLWASLLTGAWPSFPTQDHLPATPRVRLSFKELKATGTAHFFNFLLNTTDYRIL
LKDEDHDRMYVGSKDYVLSLDLHDINREPLIIHWAASPQRIEECVLSGKDVNGECGNFVR
LIQPWNRTHLYVCGTGAYNPMCTYVNRGRRAQATPWTQTQAVRGRGSRATDGALRPMPTA
PRQDYIFYLEPERLESGKGKCPYDPKLDTASALINEELYAGVYIDFMGTDAAIFRTLGKQ
TAMRTDQYNSRWLNDPSFIHAELIPDSAERNDDKLYFFFRERSAEAPQSPAVYARIGRIC
LNDDGGHCCLVNKWSTFLKARLVCSVPGEDGIETHFDELQDVFVQQTQDVRNPVIYAVFT
SSGSVFRGSAVCVYSMADIRMVFNGPFAHKEGPNYQWMPFSGKMPYPRPGTCPGGTFTPS
MKSTKDYPDEVINFMRSHPLMYQAVYPLQRRPLVVRTGAPYRLTTIAVDQVDAADGRYEV
LFLGTDRGTVQKVIVLPKDDQELEELMLEEVEVFKDPAPVKTMTISSKRQQLYVASAVGV
THLSLHRCQAYGAACADCCLARDPYCAWDGQACSRYTASSKRRSRRQDVRHGNPIRQCRG
FNSNANKNAVESVQYGVAGSAAFLECQPRSPQATVKWLFQRDPGDRRREIRAEDRFLRTE
QGLLLRALQLSDRGLYSCTATENNFKHVVTRVQLHVLGRDAVHAALFPPLSMSAPPPPGA
GPPTPPYQELAQLLAQPEVGLIHQYCQGYWRHVPPSPREAPGAPRSPEPQDQKKPRNRRH
HPPDT

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	Q13275-D1	1-785	785		MLVAGLLLWASLLTGAWPSFPTQDHLPATPRVRLSFKELKATGTAHFFNFLLNTTDYRILLKDEDHDRMYVGSKDYVLSLDLHDINREPLIIHWAASPQRIEECVLSGKDVNGECGNFVRLIQPWNRTHLYVCGTGAYNPMCTYVNRGRRAQATPWTQTQAVRGRGSRATDGALRPMPTAPRQDYIFYLEPERLESGKGKCPYDPKLDTASALINEELYAGVYIDFMGTDAAIFRTLGKQTAMRTDQYNSRWLNDPSFIHAELIPDSAERNDDKLYFFFRERSAEAPQSPAVYARIGRICLNDDGGHCCLVNKWSTFLKARLVCSVPGEDGIETHFDELQDVFVQQTQDVRNPVIYAVFTSSGSVFRGSAVCVYSMADIRMVFNGPFAHKEGPNYQWMPFSGKMPYPRPGTCPGGTFTPSMKSTKDYPDEVINFMRSHPLMYQAVYPLQRRPLVVRTGAPYRLTTIAVDQVDAADGRYEVLFLGTDRGTVQKVIVLPKDDQELEELMLEEVEVFKDPAPVKTMTISSKRQQLYVASAVGVTHLSLHRCQAYGAACADCCLARDPYCAWDGQACSRYTASSKRRSRRQDVRHGNPIRQCRGFNSNANKNAVESVQYGVAGSAAFLECQPRSPQATVKWLFQRDPGDRRREIRAEDRFLRTEQGLLLRALQLSDRGLYSCTATENNFKHVVTRVQLHVLGRDAVHAALFPPLSMSAPPPPGAGPPTPPYQELAQLLAQPEVGLIHQYCQGYWRHVPPSPREAPGAPRSPEPQDQKKPRNRRHHPPDT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5809

(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	0.74	1.92	0.330	0.772	model1_1olzA.pdb.gz
2	6qp7A	0.70	2.98	0.304	0.750	model1_6qp7A.pdb.gz
3	3nvqA	0.66	3.24	0.273	0.730	model1_3nvqA.pdb.gz
4	3afcA	0.62	2.53	0.320	0.657	model1_3afcA.pdb.gz
5	5l5gA	0.60	4.43	0.136	0.694	model1_5l5gA.pdb.gz
6	1q47B	0.60	2.33	0.538	0.628	model1_1q47B.pdb.gz
7	5l5kA	0.59	4.63	0.107	0.696	model1_5l5kA.pdb.gz
8	6fkkA	0.59	2.64	0.328	0.633	model1_6fkkA.pdb.gz
9	6qp9A	0.59	2.56	0.311	0.627	model1_6qp9A.pdb.gz
10	5l56A	0.58	5.17	0.129	0.685	model1_5l56A.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	0.96	receptor binding
GO:0045499	0.94	chemorepellent activity
GO:0030215	0.94	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	0.96	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0006928	0.96	movement of cell or subcellular component
GO:0050794	0.95	regulation of cellular process
GO:0032879	0.94	regulation of localization
GO:0007165	0.94	signal transduction
GO:0071526	0.93	semaphorin-plexin signaling pathway
GO:0050770	0.93	regulation of axonogenesis
GO:0040011	0.93	locomotion
GO:0030334	0.93	regulation of cell migration
GO:0048583	0.92	regulation of response to stimulus
GO:0048522	0.92	positive regulation of cellular process
GO:0048519	0.92	negative regulation of biological process
GO:0001755	0.92	neural crest cell migration
GO:0048841	0.91	regulation of axon extension involved in axon guidance
GO:0048523	0.91	negative regulation of cellular process
GO:0048843	0.89	negative regulation of axon extension involved in axon guidance
GO:0030335	0.89	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:0044421	0.79	extracellular region part
GO:0005615	0.77	extracellular space
GO:0044464	0.76	cell 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	0.060	1s0kA	0.371	5.64	0.047	0.473	3.2.1.18	210
2	0.060	3gvjA	0.366	5.81	0.049	0.466	3.2.1.129	117
3	0.060	1cruB	0.326	4.61	0.090	0.383	1.1.5.2	NA
4	0.060	1sliA	0.358	5.93	0.072	0.462	4.2.2.15 3.2.1.18	NA
5	0.060	1g72A	0.373	4.80	0.069	0.443	1.1.99.8	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	1shy1	0.494	3.85	0.136	0.555	0.19	III	complex1.pdb.gz	131,133,134,135,146
2	0.01	1flg0	0.374	4.92	0.093	0.448	0.39	III	complex2.pdb.gz	44,45,46,48,50,54,56,57,511,512,513,514,543,549
3	0.01	1h4j0	0.380	5.11	0.077	0.457	0.21	III	complex3.pdb.gz	45,46,50,489,491,510,511,512,513,514
4	0.01	2vdoA	0.367	5.01	0.077	0.446	0.38	III	complex4.pdb.gz	72,76,77,94,118
5	0.01	1h4iA	0.379	5.08	0.077	0.456	0.18	PQQ	complex5.pdb.gz	59,119,121,197,258
6	0.01	2eieA	0.388	4.40	0.054	0.454	0.17	AZI	complex6.pdb.gz	75,188,189
7	0.01	3ijeA	0.421	5.30	0.050	0.513	0.39	UUU	complex7.pdb.gz	72,118,120,133

	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.