D-I-TASSER Q9Y5Q0

D-I-TASSER results for Q9Y5Q0

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

Summary of the Protein

Uniprot ID: Q9Y5Q0
Protein Name: Fatty acid desaturase 3
Gene Name: FADS3

Input Sequence in FASTA format

>Q9Y5Q0 (445 residues)
MGGVGEPGPREGPAQPGAPLPTFCWEQIRAHDQPGDKWLVIERRVYDISRWAQRHPGGSR
LIGHHGAEDATDAFRAFHQDLNFVRKFLQPLLIGELAPEEPSQDGPLNAQLVEDFRALHQ
AAEDMKLFDASPTFFAFLLGHILAMEVLAWLLIYLLGPGWVPSALAAFILAISQAQSWCL
QHDLGHASIFKKSWWNHVAQKFVMGQLKGFSAHWWNFRHFQHHAKPNIFHKDPDVTVAPV
FLLGESSVEYGKKKRRYLPYNQQHLYFFLIGPPLLTLVNFEVENLAYMLVCMQWADLLWA
ASFYARFFLSYLPFYGVPGVLLFFVAVRVLESHWFVWITQMNHIPKEIGHEKHRDWVSSQ
LAATCNVEPSLFTNWFSGHLNFQIEHHLFPRMPRHNYSRVAPLVKSLCAKHGLSYEVKPF
LTALVDIVRSLKKSGDIWLDAYLHQ

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	Q9Y5Q0-D1	1-100	100		MGGVGEPGPREGPAQPGAPLPTFCWEQIRAHDQPGDKWLVIERRVYDISRWAQRHPGGSRLIGHHGAEDATDAFRAFHQDLNFVRKFLQPLLIGELAPEE
2	Q9Y5Q0-D2	101-445	345		PSQDGPLNAQLVEDFRALHQAAEDMKLFDASPTFFAFLLGHILAMEVLAWLLIYLLGPGWVPSALAAFILAISQAQSWCLQHDLGHASIFKKSWWNHVAQKFVMGQLKGFSAHWWNFRHFQHHAKPNIFHKDPDVTVAPVFLLGESSVEYGKKKRRYLPYNQQHLYFFLIGPPLLTLVNFEVENLAYMLVCMQWADLLWAASFYARFFLSYLPFYGVPGVLLFFVAVRVLESHWFVWITQMNHIPKEIGHEKHRDWVSSQLAATCNVEPSLFTNWFSGHLNFQIEHHLFPRMPRHNYSRVAPLVKSLCAKHGLSYEVKPFLTALVDIVRSLKKSGDIWLDAYLHQ

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.72

(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	4bedA	0.41	7.06	0.074	0.665	model1_4bedA.pdb.gz
2	4m5dA	0.40	6.84	0.054	0.647	model1_4m5dA.pdb.gz
3	7m8iA	0.40	7.39	0.075	0.670	model1_7m8iA.pdb.gz
4	6tg9A	0.39	7.49	0.053	0.670	model1_6tg9A.pdb.gz
5	1gkuB	0.38	6.98	0.027	0.616	model1_1gkuB.pdb.gz
6	4ddtA	0.38	7.06	0.044	0.616	model1_4ddtA.pdb.gz
7	6fa5A	0.38	6.75	0.044	0.596	model1_6fa5A.pdb.gz
8	2c6fA	0.38	6.88	0.048	0.600	model1_2c6fA.pdb.gz
9	6rc9A1	0.38	7.05	0.041	0.620	model1_6rc9A1.pdb.gz
10	5xdrA	0.38	7.05	0.038	0.620	model1_5xdrA.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:0003824	0.98	catalytic activity
GO:0016491	0.96	oxidoreductase activity
GO:0016705	0.71	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0016717	0.58	oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water

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:0008152	0.98	metabolic process
GO:0044699	0.96	single-organism process
GO:0009987	0.96	cellular process
GO:0044237	0.95	cellular metabolic process
GO:0071704	0.94	organic substance metabolic process
GO:0044710	0.94	single-organism metabolic process
GO:0044763	0.91	single-organism cellular process
GO:0044238	0.89	primary metabolic process
GO:0044281	0.86	small molecule metabolic process
GO:0006629	0.86	lipid metabolic process
GO:0044255	0.85	cellular lipid metabolic process
GO:0043436	0.83	oxoacid metabolic process
GO:0044249	0.82	cellular biosynthetic process
GO:1901576	0.77	organic substance biosynthetic process
GO:0044711	0.77	single-organism biosynthetic process
GO:0019752	0.77	carboxylic acid metabolic process
GO:0008610	0.76	lipid biosynthetic process
GO:0006631	0.76	fatty acid metabolic process
GO:0046394	0.69	carboxylic acid biosynthetic process
GO:0006633	0.68	fatty acid biosynthetic process
GO:0033559	0.62	unsaturated fatty acid metabolic process
GO:0006636	0.61	unsaturated fatty acid biosynthetic 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	0.94	cell part
GO:0044424	0.90	intracellular part
GO:0044444	0.83	cytoplasmic part
GO:0016020	0.65	membrane
GO:0043226	0.56	organelle
GO:0043229	0.55	intracellular organelle
GO:0043227	0.54	membrane-bounded organelle
GO:0043231	0.53	intracellular membrane-bounded organelle

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	1t3tA	0.369	7.16	0.061	0.605	6.3.5.3	NA
2	0.060	1kwmA	0.346	6.67	0.070	0.539	3.4.17.2	NA
3	0.060	1r1jA	0.346	6.82	0.067	0.553	3.4.24.11	NA
4	0.060	3dwbA	0.349	7.12	0.036	0.573	3.4.24.71	NA
5	0.060	1nsaA	0.345	6.61	0.073	0.539	3.4.17.2	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	0.05	3l3nA	0.370	7.13	0.052	0.593	0.20	LSW	complex1.pdb.gz	213,339,340
2	0.04	1r4lA	0.368	7.35	0.041	0.607	0.20	XX5	complex2.pdb.gz	212,215,219,222,380
3	0.04	1j36A	0.367	6.91	0.052	0.580	0.17	LPR	complex3.pdb.gz	215,218,219,379
4	0.03	1o86A	0.362	7.02	0.057	0.582	0.11	LPR	complex4.pdb.gz	175,211,333
5	0.01	2c6nA	0.338	7.07	0.033	0.546	0.13	LPR	complex5.pdb.gz	146,184,395
6	0.01	1b25A	0.362	7.41	0.045	0.616	0.10	PTT	complex6.pdb.gz	177,276,378,379,380
7	0.01	3nxqB	0.378	7.00	0.060	0.600	0.10	RX4	complex7.pdb.gz	186,187,215,216,219,223
8	0.01	2c6nB	0.336	7.11	0.039	0.548	0.14	LPR	complex8.pdb.gz	181,205,212
9	0.01	2x90A	0.363	6.86	0.051	0.566	0.14	EAL	complex9.pdb.gz	174,210,324
10	0.01	2yajA	0.365	6.68	0.051	0.573	0.15	4HP	complex10.pdb.gz	182,209,210,331

	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.