D-I-TASSER Q9Y2Z4

D-I-TASSER results for Q9Y2Z4

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

Summary of the Protein

Uniprot ID: Q9Y2Z4
Protein Name: Tyrosine--tRNA ligase, mitochondrial
Gene Name: YARS2

Input Sequence in FASTA format

>Q9Y2Z4 (477 residues)
MAAPILRSFSWGRWSGTLNLSVLLPLGLRKAHSGAQGLLAAQKARGLFKDFFPETGTKIE
LPELFDRGTASFPQTIYCGFDPTADSLHVGHLLALLGLFHLQRAGHNVIALVGGATARLG
DPSGRTKEREALETERVRANARALRLGLEALAANHQQLFTDGRSWGSFTVLDNSAWYQKQ
HLVDFLAAVGGHFRMGTLLSRQSVQLRLKSPEGMSLAEFFYQVLQAYDFYYLFQRYGCRV
QLGGSDQLGNIMSGYEFINKLTGEDVFGITVPLITSTTGAKLGKSAGNAVWLNRDKTSPF
ELYQFFVRQPDDSVERYLKLFTFLPLPEIDHIMQLHVKEPERRGPQKRLAAEVTKLVHGR
EGLDSAKRCTQALYHSSIDALEVMSDQELKELFKEAPFSEFFLDPGTSVLDTCRKANAIP
DGPRGYRMITEGGVSINHQQVTNPESVLIVGQHILKNGLSLLKIGKRNFYIIKWLQL

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	Q9Y2Z4-D1	1-273	273		MAAPILRSFSWGRWSGTLNLSVLLPLGLRKAHSGAQGLLAAQKARGLFKDFFPETGTKIELPELFDRGTASFPQTIYCGFDPTADSLHVGHLLALLGLFHLQRAGHNVIALVGGATARLGDPSGRTKEREALETERVRANARALRLGLEALAANHQQLFTDGRSWGSFTVLDNSAWYQKQHLVDFLAAVGGHFRMGTLLSRQSVQLRLKSPEGMSLAEFFYQVLQAYDFYYLFQRYGCRVQLGGSDQLGNIMSGYEFINKLTGEDVFGITVPL
2	Q9Y2Z4-D2	274-359	86		ITSTTGAKLGKSAGNAVWLNRDKTSPFELYQFFVRQPDDSVERYLKLFTFLPLPEIDHIMQLHVKEPERRGPQKRLAAEVTKLVHG
3	Q9Y2Z4-D3	360-477	118		REGLDSAKRCTQALYHSSIDALEVMSDQELKELFKEAPFSEFFLDPGTSVLDTCRKANAIPDGPRGYRMITEGGVSINHQQVTNPESVLIVGQHILKNGLSLLKIGKRNFYIIKWLQL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.85

(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	6otjA	0.80	2.77	0.337	0.878	model1_6otjA.pdb.gz
2	2janA	0.75	3.27	0.336	0.851	model1_2janA.pdb.gz
3	1h3eA	0.67	4.20	0.224	0.813	model1_1h3eA.pdb.gz
4	6n0wA	0.67	3.25	0.329	0.750	model1_6n0wA.pdb.gz
5	2pidB	0.66	1.32	0.994	0.679	model1_2pidB.pdb.gz
6	1y42X	0.64	2.78	0.361	0.700	model1_1y42X.pdb.gz
7	1wq3A	0.64	2.05	0.402	0.673	model1_1wq3A.pdb.gz
8	5ihxA	0.64	2.76	0.381	0.696	model1_5ihxA.pdb.gz
9	1tycA	0.63	1.93	0.448	0.665	model1_1tycA.pdb.gz
10	1jilA	0.63	2.34	0.410	0.675	model1_1jilA.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:0004812	0.99	aminoacyl-tRNA ligase activity
GO:0004831	0.98	tyrosine-tRNA ligase activity
GO:1901363	0.58	heterocyclic compound binding
GO:0097159	0.58	organic cyclic compound 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:0043039	1.00	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	0.99	cytosol
GO:0043226	0.82	organelle
GO:0043229	0.81	intracellular organelle
GO:0043227	0.80	membrane-bounded organelle
GO:0043231	0.79	intracellular membrane-bounded organelle
GO:0005739	0.76	mitochondrion

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	0.471	2ts1A	0.632	1.94	0.448	0.665	6.1.1.1	78,80,83,88,90,120,124,221,245,247,249,272
2	0.429	2yxnA	0.638	2.04	0.402	0.673	6.1.1.1	80,111,120,204,224,229,243,245,247,249,253
3	0.368	2cyaA	0.521	3.61	0.143	0.610	6.1.1.1	281,284
4	0.355	2j5bA	0.500	3.87	0.143	0.595	6.1.1.1	281,284
5	0.347	1yi8A	0.475	3.18	0.152	0.543	6.1.1.2	281,284

	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	0.91	2pidA	0.636	1.72	0.997	0.665	1.88	YSA	complex1.pdb.gz	77,79,80,81,90,91,111,116,121,221,225,228,241,243,244,246,247,272,273,274
2	0.78	1tyaE	0.633	1.93	0.451	0.665	1.53	TYR	complex2.pdb.gz	77,79,81,111,116,121,173,221,225,228,247
3	0.14	3p0hB	0.518	3.87	0.103	0.616	1.28	FSE	complex3.pdb.gz	77,78,79,111,113,225,228,243,244,246,247
4	0.14	3a05A	0.527	3.98	0.131	0.631	0.92	TRP	complex4.pdb.gz	78,79,116,173,225,228
5	0.11	1h3eA	0.674	4.20	0.224	0.813	1.13	ATP	complex5.pdb.gz	79,80,81,88,90,91,93,94,129,243,244,247,272,273,274,282
6	0.08	2ts10	0.632	1.94	0.448	0.665	1.44	III	complex6.pdb.gz	115,118,119,128,129,174,177,180,181,182,183,185,186,187,190,191,193,194,195,196,198,199,208,214,215,216,217,219,220
7	0.07	1jil0	0.630	2.34	0.410	0.675	1.17	III	complex7.pdb.gz	49,50,52,53,55,126,197,200,202,248,252,256,273,276,277,312,333,336,337

	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.