D-I-TASSER A0A1B0GVQ0

D-I-TASSER results for A0A1B0GVQ0

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

Summary of the Protein

Uniprot ID: A0A1B0GVQ0
Protein Name: Small regulatory polypeptide of amino acid response
Gene Name: SPAAR

Input Sequence in FASTA format

>A0A1B0GVQ0 (90 residues)
MGAKAPRGPKVAQWAMETAVIGVVVVLFVVTVAITCVLCCFSCDSRAQDPQGGPGRSFTV
ATFRQEASLFTGPVRHAQPVPSAQDFWTFM

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	A0A1B0GVQ0-D1	1-90	90		MGAKAPRGPKVAQWAMETAVIGVVVVLFVVTVAITCVLCCFSCDSRAQDPQGGPGRSFTVATFRQEASLFTGPVRHAQPVPSAQDFWTFM

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5971

(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	6rlbA	0.67	2.93	0.058	0.944	model1_6rlbA.pdb.gz
2	4tqlA	0.66	3.45	0.011	0.922	model1_4tqlA.pdb.gz
3	4uosA	0.65	2.89	0.012	0.844	model1_4uosA.pdb.gz
4	5mawD	0.65	3.22	0.089	0.967	model1_5mawD.pdb.gz
5	3feyA	0.64	3.36	0.000	0.911	model1_3feyA.pdb.gz
6	4d8mA	0.64	3.46	0.056	0.956	model1_4d8mA.pdb.gz
7	5xa5A	0.64	3.63	0.011	0.967	model1_5xa5A.pdb.gz
8	1w99A1	0.55	3.40	0.034	0.822	model1_1w99A1.pdb.gz
9	3ljbA	0.55	3.67	0.044	0.822	model1_3ljbA.pdb.gz
10	3c98B	0.55	3.61	0.060	0.822	model1_3c98B.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

./A0A1B0GVQ0-D1/GOsearchresult_final_MF.svg

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0019904	0.09	protein domain specific binding
GO:0044822	0.08	poly(A) RNA binding
GO:0000339	0.08	RNA cap binding
GO:0060228	0.07	phosphatidylcholine-sterol O-acyltransferase activator activity
GO:0042803	0.07	protein homodimerization activity
GO:0031210	0.07	phosphatidylcholine binding
GO:0017127	0.07	cholesterol transporter activity
GO:0016209	0.07	antioxidant activity
GO:0015485	0.07	cholesterol binding
GO:0005507	0.07	copper ion 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]

./A0A1B0GVQ0-D1/GOsearchresult_final_BP.svg

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0051726	0.09	regulation of cell cycle
GO:0042994	0.09	cytoplasmic sequestering of transcription factor
GO:0032886	0.09	regulation of microtubule-based process
GO:0030953	0.09	astral microtubule organization
GO:0030097	0.09	hemopoiesis
GO:0022027	0.09	interkinetic nuclear migration
GO:0021987	0.09	cerebral cortex development
GO:0001666	0.09	response to hypoxia
GO:1900363	0.08	regulation of mRNA polyadenylation
GO:0098789	0.08	pre-mRNA cleavage required for polyadenylation
GO:0045292	0.08	mRNA cis splicing, via spliceosome
GO:0042795	0.08	snRNA transcription from RNA polymerase II promoter
GO:0031442	0.08	positive regulation of mRNA 3'-end processing
GO:0031047	0.08	gene silencing by RNA
GO:0030307	0.08	positive regulation of cell growth
GO:0008543	0.08	fibroblast growth factor receptor signaling pathway
GO:0008334	0.08	histone mRNA metabolic process
GO:0006446	0.08	regulation of translational initiation
GO:0006406	0.08	mRNA export from nucleus
GO:0006370	0.08	7-methylguanosine mRNA capping
GO:0006369	0.08	termination of RNA polymerase II transcription
GO:0006368	0.08	transcription elongation from RNA polymerase II promoter
GO:0000184	0.08	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0070328	0.07	triglyceride homeostasis
GO:0051006	0.07	positive regulation of lipoprotein lipase activity
GO:0046470	0.07	phosphatidylcholine metabolic process
GO:0045723	0.07	positive regulation of fatty acid biosynthetic process
GO:0044240	0.07	multicellular organism lipid catabolic process
GO:0043691	0.07	reverse cholesterol transport
GO:0042744	0.07	hydrogen peroxide catabolic process
GO:0042632	0.07	cholesterol homeostasis
GO:0042158	0.07	lipoprotein biosynthetic process
GO:0035634	0.07	response to stilbenoid
GO:0034445	0.07	negative regulation of plasma lipoprotein particle oxidation
GO:0034380	0.07	high-density lipoprotein particle assembly
GO:0034378	0.07	chylomicron assembly
GO:0034375	0.07	high-density lipoprotein particle remodeling
GO:0034372	0.07	very-low-density lipoprotein particle remodeling
GO:0034371	0.07	chylomicron remodeling
GO:0033700	0.07	phospholipid efflux
GO:0033344	0.07	cholesterol efflux
GO:0031102	0.07	neuron projection regeneration
GO:0030300	0.07	regulation of intestinal cholesterol absorption
GO:0019430	0.07	removal of superoxide radicals
GO:0010898	0.07	positive regulation of triglyceride catabolic process
GO:0010873	0.07	positive regulation of cholesterol esterification
GO:0007159	0.07	leukocyte cell-cell adhesion
GO:0006982	0.07	response to lipid hydroperoxide
GO:0006695	0.07	cholesterol biosynthetic process
GO:0002227	0.07	innate immune response in mucosa
GO:0001523	0.07	retinoid 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]

./A0A1B0GVQ0-D1/GOsearchresult_final_CC.svg

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	0.92	intracellular part
GO:0043229	0.85	intracellular organelle
GO:0044444	0.77	cytoplasmic part
GO:0044446	0.69	intracellular organelle part
GO:0043231	0.69	intracellular membrane-bounded organelle
GO:0005829	0.62	cytosol
GO:0005737	0.62	cytoplasm

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	0.155	3e7kH	0.460	2.81	0.107	0.589	2.7.11.1	11
2	0.060	3g61A	0.576	3.28	0.100	0.867	3.6.3.44	34
3	0.060	2rgrA	0.619	3.02	0.050	0.833	5.99.1.3	NA
4	0.060	3e08A	0.521	3.63	0.035	0.800	1.13.11.11	NA
5	0.060	1sesA	0.439	3.74	0.033	0.722	6.1.1.11	45,47

	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:

Click to view	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	3q7gA	0.596	3.80	0.057	0.922	0.65	SCR	complex1.pdb.gz	21,25,28,71
	2	0.01	3qmkA	0.592	3.71	0.047	0.944	0.41	UUU	complex2.pdb.gz	21,25,69,73

	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.