D-I-TASSER P0DPI2

D-I-TASSER results for P0DPI2

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

Summary of the Protein

Uniprot ID: P0DPI2
Protein Name: Glutamine amidotransferase-like class 1 domain-containing protein 3A, mitochondrial
Gene Name: GATD3A

Input Sequence in FASTA format

>P0DPI2 (268 residues)
MAAVRVLVASRLAAASAFTSLSPGGRTPSQRAALHLSVPRPAARVALVLSGCGVYDGTEI
HEASAILVHLSRGGAEVQIFAPDVPQMHVIDHTKGQPSEGESRNVLTESARIARGKITDL
ANLSAANHDAAIFPGGFGAAKNLSTFAVDGKDCKVNKEVERVLKEFHQAGKPIGLCCIAP
VLAAKVLRGVEVTVGHEQEEGGKWPYAGTAEAIKALGAKHCVKEVVEAHVDQKNKVVTTP
AFMCETALHYIHDGIGAMVRKVLELTGK

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	P0DPI2-D1	1-268	268		MAAVRVLVASRLAAASAFTSLSPGGRTPSQRAALHLSVPRPAARVALVLSGCGVYDGTEIHEASAILVHLSRGGAEVQIFAPDVPQMHVIDHTKGQPSEGESRNVLTESARIARGKITDLANLSAANHDAAIFPGGFGAAKNLSTFAVDGKDCKVNKEVERVLKEFHQAGKPIGLCCIAPVLAAKVLRGVEVTVGHEQEEGGKWPYAGTAEAIKALGAKHCVKEVVEAHVDQKNKVVTTPAFMCETALHYIHDGIGAMVRKVLELTGK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7493

(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	3l3bB	0.76	1.13	0.343	0.784	model1_3l3bB.pdb.gz
2	1oy1A	0.76	1.30	0.474	0.787	model1_1oy1A.pdb.gz
3	5xr2A	0.67	3.09	0.151	0.791	model1_5xr2A.pdb.gz
4	4i2nA	0.67	3.10	0.145	0.791	model1_4i2nA.pdb.gz
5	1n57A	0.66	3.18	0.149	0.780	model1_1n57A.pdb.gz
6	1u9cA	0.61	2.92	0.181	0.698	model1_1u9cA.pdb.gz
7	3n7tA	0.61	3.16	0.158	0.720	model1_3n7tA.pdb.gz
8	3miiA	0.61	2.95	0.144	0.698	model1_3miiA.pdb.gz
9	4p5pA	0.60	2.95	0.153	0.694	model1_4p5pA.pdb.gz
10	2vrnA	0.58	2.95	0.141	0.653	model1_2vrnA.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	1.00	catalytic activity
GO:0016836	0.91	hydro-lyase activity
GO:0019172	0.84	glyoxalase III activity
GO:0097159	0.58	organic cyclic compound binding
GO:1901363	0.57	heterocyclic compound binding
GO:0043167	0.52	ion binding
GO:0043169	0.51	cation binding
GO:0003676	0.51	nucleic acid 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:0071704	1.00	organic substance metabolic process
GO:0044763	1.00	single-organism cellular process
GO:0044710	1.00	single-organism metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0044281	0.88	small molecule metabolic process
GO:0061727	0.86	methylglyoxal catabolic process to lactate
GO:0019243	0.75	methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione
GO:0065007	0.73	biological regulation
GO:0050789	0.73	regulation of biological process
GO:0050794	0.72	regulation of cellular process
GO:0044238	0.68	primary metabolic process
GO:0019222	0.66	regulation of metabolic process
GO:0080090	0.65	regulation of primary metabolic process
GO:0031323	0.65	regulation of cellular metabolic process
GO:1901576	0.61	organic substance biosynthetic process
GO:0044249	0.61	cellular biosynthetic process
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:2000112	0.58	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.58	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.58	regulation of gene expression
GO:1903506	0.57	regulation of nucleic acid-templated transcription
GO:0043170	0.55	macromolecule metabolic process
GO:0044711	0.54	single-organism biosynthetic process
GO:0044260	0.54	cellular macromolecule metabolic process
GO:0006629	0.52	lipid metabolic process
GO:0008299	0.51	isoprenoid biosynthetic process
GO:0006807	0.51	nitrogen compound metabolic process
GO:0048518	0.50	positive regulation of biological process
GO:0034641	0.50	cellular nitrogen compound metabolic 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:0044444	1.00	cytoplasmic part
GO:0043226	0.99	organelle
GO:0005739	0.98	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	0.066	1i7qB	0.458	3.91	0.136	0.586	4.1.3.27	NA
2	0.066	1i7sB	0.456	3.85	0.138	0.582	4.1.3.27	54,176
3	0.066	1qdlB	0.462	4.10	0.085	0.590	4.1.3.27	NA
4	0.060	2jfdA	0.366	5.65	0.069	0.586	2.3.1.85	NA
5	0.060	1enpA	0.484	4.47	0.139	0.657	1.3.1.9	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	0.04	1vcoA	0.519	4.57	0.114	0.716	0.45	GLN	complex1.pdb.gz	135,136,137,177,178,181
2	0.03	2ab00	0.557	2.60	0.200	0.623	0.86	III	complex2.pdb.gz	59,60,61,64,65,67,68,71,72,195,196,240,242,256
3	0.03	2qioA	0.489	4.34	0.117	0.653	0.42	NAD	complex3.pdb.gz	61,62,134,241
4	0.03	3k31A	0.492	4.48	0.113	0.668	0.50	NAD	complex4.pdb.gz	135,182,242,243
5	0.03	1rw70	0.610	2.97	0.157	0.702	0.68	III	complex5.pdb.gz	189,191,219,220,221,228,229,230,231,262
6	0.01	2ad5A	0.515	5.15	0.084	0.746	0.65	CTP	complex6.pdb.gz	162,163,164,167

	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.