D-I-TASSER P54577

D-I-TASSER results for P54577

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

Summary of the Protein

Uniprot ID: P54577
Protein Name: Tyrosine--tRNA ligase, cytoplasmic
Gene Name: YARS1

Input Sequence in FASTA format

>P54577 (528 residues)
MGDAPSPEEKLHLITRNLQEVLGEEKLKEILKERELKIYWGTATTGKPHVAYFVPMSKIA
DFLKAGCEVTILFADLHAYLDNMKAPWELLELRVSYYENVIKAMLESIGVPLEKLKFIKG
TDYQLSKEYTLDVYRLSSVVTQHDSKKAGAEVVKQVEHPLLSGLLYPGLQALDEEYLKVD
AQFGGIDQRKIFTFAEKYLPALGYSKRVHLMNPMVPGLTGSKMSSSEEESKIDLLDRKED
VKKKLKKAFCEPGNVENNGVLSFIKHVLFPLKSEFVILRDEKWGGNKTYTAYVDLEKDFA
AEVVHPGDLKNSVEVALNKLLDPIREKFNTPALKKLASAAYPDPSKQKPMAKGPAKNSEP
EEVIPSRLDIRVGKIITVEKHPDADSLYVEKIDVGEAEPRTVVSGLVQFVPKEELQDRLV
VVLCNLKPQKMRGVESQGMLLCASIEGINRQVEPLDPPAGSAPGEHVFVKGYEKGQPDEE
LKPKKKVFEKLQADFKISEECIAQWKQTNFMTKLGSISCKSLKGGNIS

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	P54577-D1	1-360	360		MGDAPSPEEKLHLITRNLQEVLGEEKLKEILKERELKIYWGTATTGKPHVAYFVPMSKIADFLKAGCEVTILFADLHAYLDNMKAPWELLELRVSYYENVIKAMLESIGVPLEKLKFIKGTDYQLSKEYTLDVYRLSSVVTQHDSKKAGAEVVKQVEHPLLSGLLYPGLQALDEEYLKVDAQFGGIDQRKIFTFAEKYLPALGYSKRVHLMNPMVPGLTGSKMSSSEEESKIDLLDRKEDVKKKLKKAFCEPGNVENNGVLSFIKHVLFPLKSEFVILRDEKWGGNKTYTAYVDLEKDFAAEVVHPGDLKNSVEVALNKLLDPIREKFNTPALKKLASAAYPDPSKQKPMAKGPAKNSEP
2	P54577-D2	361-528	168		EEVIPSRLDIRVGKIITVEKHPDADSLYVEKIDVGEAEPRTVVSGLVQFVPKEELQDRLVVVLCNLKPQKMRGVESQGMLLCASIEGINRQVEPLDPPAGSAPGEHVFVKGYEKGQPDEELKPKKKVFEKLQADFKISEECIAQWKQTNFMTKLGSISCKSLKGGNIS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.57

(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	3vgjA	0.62	1.97	0.304	0.646	model1_3vgjA.pdb.gz
2	2cycA	0.61	1.71	0.288	0.638	model1_2cycA.pdb.gz
3	2dlcX	0.60	1.41	0.573	0.621	model1_2dlcX.pdb.gz
4	1n3lA	0.60	1.80	0.997	0.629	model1_1n3lA.pdb.gz
5	2cyaA	0.59	2.04	0.308	0.616	model1_2cyaA.pdb.gz
6	2cybA	0.58	1.69	0.381	0.602	model1_2cybA.pdb.gz
7	3p0hA	0.57	3.87	0.180	0.653	model1_3p0hA.pdb.gz
8	1zh6A	0.56	1.73	0.366	0.580	model1_1zh6A.pdb.gz
9	2j5bA	0.55	2.25	0.244	0.585	model1_2j5bA.pdb.gz
10	3a04A	0.52	2.69	0.166	0.568	model1_3a04A.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	0.76	catalytic activity
GO:0004812	0.69	aminoacyl-tRNA ligase activity
GO:1901363	0.63	heterocyclic compound binding
GO:0097159	0.63	organic cyclic compound binding
GO:0004832	0.61	valine-tRNA ligase activity
GO:0004831	0.50	tyrosine-tRNA ligase 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:1901564	1.00	organonitrogen compound metabolic process
GO:0044763	1.00	single-organism cellular process
GO:0044281	1.00	small molecule metabolic process
GO:0006139	1.00	nucleobase-containing compound metabolic process
GO:0043039	0.99	tRNA aminoacylation
GO:0006418	0.97	tRNA aminoacylation for protein translation
GO:0006438	0.57	valyl-tRNA aminoacylation

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:0044444	1.00	cytoplasmic part
GO:0005829	0.75	cytosol

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	0.320	1yi8A	0.479	2.78	0.170	0.526	6.1.1.2	222
2	0.309	3jxeB	0.501	3.20	0.153	0.561	6.1.1.2	222
3	0.287	2cycB	0.613	1.73	0.288	0.638	6.1.1.1	49,74,170,188,190,222
4	0.270	2yy5B	0.480	3.05	0.190	0.530	6.1.1.2	222
5	0.260	1q11A	0.603	1.52	1.000	0.623	6.1.1.1	40,42,46,49,51,55,74,84,153,166,185,187,214

	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	0.86	1q11A	0.603	1.52	1.000	0.623	1.62	TYE	complex1.pdb.gz	39,41,72,74,77,152,166,170,173,182,188
2	0.70	2dlcX	0.604	1.41	0.573	0.621	1.73	YMP	complex2.pdb.gz	39,40,41,42,43,49,51,52,72,74,77,152,166,170,173,182,184,185,187,188,212,213,214,215
3	0.55	3qe4B	0.561	1.45	0.361	0.578	1.10	4CF	complex3.pdb.gz	41,42,43,74,77,166,170,188
4	0.50	3n2yB	0.556	1.55	0.355	0.576	0.99	TEF	complex4.pdb.gz	72,74,166,170,173,174,188
5	0.45	1n3l0	0.602	1.80	0.997	0.629	1.68	III	complex5.pdb.gz	125,130,134,135,137,138,139,140,141,142,145,159,160,161,162,164,165
6	0.30	2hgzA	0.559	1.54	0.367	0.578	1.06	PBF	complex6.pdb.gz	39,40,41,43,72,74,77,166,170,173,174,177,188
7	0.18	2quiA	0.523	2.89	0.173	0.574	0.94	LTN	complex7.pdb.gz	39,40,41,42,43,72,74,77,170,184,188,192
8	0.17	1yiaB	0.480	2.65	0.182	0.521	0.97	HRP	complex8.pdb.gz	39,40,41,77,170,173,188
9	0.14	1vbnB	0.468	3.70	0.162	0.545	0.95	YSA	complex9.pdb.gz	41,51,52,54,55,72,166,170,173,184,185,187,188,213,214,215
10	0.06	1yidB	0.479	2.65	0.182	0.521	1.02	ATP	complex10.pdb.gz	41,42,43,51,52,214,215,223,224,226

	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.