D-I-TASSER Q9BZG2

D-I-TASSER results for Q9BZG2

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

Summary of the Protein

Uniprot ID: Q9BZG2
Protein Name: Testicular acid phosphatase
Gene Name: ACP4

Input Sequence in FASTA format

>Q9BZG2 (426 residues)
MAGLGFWGHPAGPLLLLLLLVLPPRALPEGPLVFVALVFRHGDRAPLASYPMDPHKEVAS
TLWPRGLGQLTTEGVRQQLELGRFLRSRYEAFLSPEYRREEVYIRSTDFDRTLESAQANL
AGLFPEAAPGSPEARWRPIPVHTVPVAEDKLLRFPMRSCPRYHELLREATEAAEYQEALE
GWTGFLSRLENFTGLSLVGEPLRRAWKVLDTLMCQQAHGLPLPAWASPDVLRTLAQISAL
DIGAHVGPPRAAEKAQLTGGILLNAILANFSRVQRLGLPLKMVMYSAHDSTLLALQGALG
LYDGHTPPYAACLGFEFRKHLGNPAKDGGNVTVSLFYRNDSAHLPLPLSLPGCPAPCPLG
RFYQLTAPARPPAHGVSCHGPYEAAIPPAPVVPLLAGAVAVLVALSLGLGLLAWRPGCLR
ALGGPV

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	Q9BZG2-D1	1-426	426		MAGLGFWGHPAGPLLLLLLLVLPPRALPEGPLVFVALVFRHGDRAPLASYPMDPHKEVASTLWPRGLGQLTTEGVRQQLELGRFLRSRYEAFLSPEYRREEVYIRSTDFDRTLESAQANLAGLFPEAAPGSPEARWRPIPVHTVPVAEDKLLRFPMRSCPRYHELLREATEAAEYQEALEGWTGFLSRLENFTGLSLVGEPLRRAWKVLDTLMCQQAHGLPLPAWASPDVLRTLAQISALDIGAHVGPPRAAEKAQLTGGILLNAILANFSRVQRLGLPLKMVMYSAHDSTLLALQGALGLYDGHTPPYAACLGFEFRKHLGNPAKDGGNVTVSLFYRNDSAHLPLPLSLPGCPAPCPLGRFYQLTAPARPPAHGVSCHGPYEAAIPPAPVVPLLAGAVAVLVALSLGLGLLAWRPGCLRALGGPV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6788

(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	1nd6B	0.77	1.41	0.441	0.798	model1_1nd6B.pdb.gz
2	4jobA	0.70	2.81	0.288	0.775	model1_4jobA.pdb.gz
3	3it3A	0.70	2.48	0.281	0.758	model1_3it3A.pdb.gz
4	5cdhA	0.68	2.18	0.280	0.737	model1_5cdhA.pdb.gz
5	1dkpA	0.67	3.30	0.252	0.772	model1_1dkpA.pdb.gz
6	4aroA	0.67	3.39	0.210	0.768	model1_4aroA.pdb.gz
7	1nt4A	0.67	3.03	0.189	0.756	model1_1nt4A.pdb.gz
8	1ihpA	0.65	4.16	0.154	0.782	model1_1ihpA.pdb.gz
9	3zhcA2	0.49	2.69	0.287	0.535	model1_3zhcA2.pdb.gz
10	4h5uA	0.28	6.36	0.046	0.430	model1_4h5uA.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:0016791	1.00	phosphatase activity
GO:0003993	0.90	acid phosphatase activity
GO:0008253	0.82	5'-nucleotidase activity
GO:0052642	0.81	lysophosphatidic acid phosphatase activity
GO:0042131	0.71	thiamine phosphate phosphatase activity
GO:0043167	0.64	ion binding
GO:0043169	0.63	cation binding
GO:0033265	0.59	choline 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:0009987	0.99	cellular process
GO:0008152	0.99	metabolic process
GO:0044237	0.98	cellular metabolic process
GO:0006796	0.97	phosphate-containing compound metabolic process
GO:0016311	0.96	dephosphorylation
GO:0044699	0.93	single-organism process
GO:0071704	0.87	organic substance metabolic process
GO:0044763	0.85	single-organism cellular process
GO:0044710	0.84	single-organism metabolic process
GO:0044238	0.83	primary metabolic process
GO:0065007	0.82	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0050794	0.81	regulation of cellular process
GO:1901135	0.80	carbohydrate derivative metabolic process
GO:0044281	0.80	small molecule metabolic process
GO:0006807	0.78	nitrogen compound metabolic process
GO:1901564	0.77	organonitrogen compound metabolic process
GO:0048522	0.76	positive regulation of cellular process
GO:0034641	0.75	cellular nitrogen compound metabolic process
GO:0006790	0.75	sulfur compound metabolic process
GO:0010646	0.74	regulation of cell communication
GO:0006139	0.74	nucleobase-containing compound metabolic process
GO:0055086	0.73	nucleobase-containing small molecule metabolic process
GO:0051239	0.73	regulation of multicellular organismal process
GO:0009966	0.73	regulation of signal transduction
GO:0060168	0.72	positive regulation of adenosine receptor signaling pathway
GO:0051930	0.72	regulation of sensory perception of pain
GO:0046085	0.72	adenosine metabolic process
GO:0006772	0.72	thiamine 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:0044464	0.98	cell part
GO:0044424	0.77	intracellular part
GO:0044421	0.77	extracellular region part
GO:0016020	0.74	membrane
GO:0044422	0.67	organelle part
GO:0043227	0.65	membrane-bounded organelle
GO:0005886	0.65	plasma membrane
GO:0044444	0.63	cytoplasmic part
GO:0031090	0.62	organelle membrane
GO:0043231	0.60	intracellular membrane-bounded organelle
GO:0005615	0.58	extracellular space
GO:0012506	0.56	vesicle membrane

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	0.464	1rptA	0.767	1.49	0.428	0.796	3.1.3.2	69,105,111,141,143
2	0.271	1dkpA	0.674	3.30	0.252	0.772	3.1.3.2 3.1.3.26	44,67,111,118,288
3	0.217	1skaA	0.638	4.42	0.167	0.784	3.1.3.8	44,111,289
4	0.190	1nd6B	0.772	1.41	0.441	0.798	3.1.3.2	40,41,44
5	0.189	1rpaA	0.768	1.46	0.428	0.796	3.1.3.2	40,41,44

	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	0.50	2hpaA	0.769	1.43	0.442	0.796	1.47	PT3	complex1.pdb.gz	40,41,44,47,111,288,289
2	0.46	1cviD	0.768	1.52	0.438	0.798	0.92	GLY	complex2.pdb.gz	40,41,44,111
3	0.08	2hpa0	0.769	1.43	0.442	0.796	1.48	III	complex3.pdb.gz	65,72,75,79,97,98,99,108,110,114,117,118,129,130,131,134,136,138,139,140,142,143

	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.