D-I-TASSER A6NHS1

D-I-TASSER results for A6NHS1

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Summary of the Protein

Uniprot ID: A6NHS1
Protein Name: Putative uncharacterized protein ENSP00000347057
Gene Name: YJU2

Input Sequence in FASTA format

>A6NHS1 (94 residues)
MVLLAGTRPQGGEARCMIPPPPSPLLGAQVEEDRTEFKEFQDFSSLPDTRSVASDDSLYP
FQDEEEHGVEGVESVPEEGILEAWGSCGRWCGVG

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	A6NHS1-D1	1-94	94		MVLLAGTRPQGGEARCMIPPPPSPLLGAQVEEDRTEFKEFQDFSSLPDTRSVASDDSLYPFQDEEEHGVEGVESVPEEGILEAWGSCGRWCGVG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5516

(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	3mk7A	0.50	3.82	0.037	0.830	model1_3mk7A.pdb.gz
2	6xkwn	0.49	3.99	0.037	0.840	model1_6xkwn.pdb.gz
3	5doqA2	0.49	3.74	0.091	0.787	model1_5doqA2.pdb.gz
4	2lqgA	0.49	4.15	0.098	0.830	model1_2lqgA.pdb.gz
5	6bhpA	0.48	3.67	0.075	0.766	model1_6bhpA.pdb.gz
6	7k18A2	0.48	3.77	0.062	0.766	model1_7k18A2.pdb.gz
7	5mqiA	0.48	4.10	0.095	0.755	model1_5mqiA.pdb.gz
8	4g32A	0.47	3.46	0.074	0.734	model1_4g32A.pdb.gz
9	2idgC	0.47	3.67	0.068	0.755	model1_2idgC.pdb.gz
10	3ayfA	0.47	4.10	0.037	0.798	model1_3ayfA.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:0051120	0.07	hepoxilin A3 synthase activity
GO:0051015	0.07	actin filament binding
GO:0047977	0.07	hepoxilin-epoxide hydrolase activity
GO:0030274	0.07	LIM domain binding
GO:0017166	0.07	vinculin binding
GO:0016165	0.07	linoleate 13S-lipoxygenase activity
GO:0005506	0.07	iron ion binding
GO:0005487	0.07	nucleocytoplasmic transporter activity
GO:0005200	0.07	structural constituent of cytoskeleton
GO:0005178	0.07	integrin binding
GO:0004052	0.07	arachidonate 12-lipoxygenase 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:2001306	0.07	lipoxin B4 biosynthetic process
GO:2001303	0.07	lipoxin A4 biosynthetic process
GO:1901751	0.07	leukotriene A4 metabolic process
GO:1900034	0.07	regulation of cellular response to heat
GO:0090331	0.07	negative regulation of platelet aggregation
GO:0075733	0.07	intracellular transport of virus
GO:0071396	0.07	cellular response to lipid
GO:0061436	0.07	establishment of skin barrier
GO:0051901	0.07	positive regulation of mitochondrial depolarization
GO:0051122	0.07	hepoxilin biosynthetic process
GO:0048661	0.07	positive regulation of smooth muscle cell proliferation
GO:0045909	0.07	positive regulation of vasodilation
GO:0045785	0.07	positive regulation of cell adhesion
GO:0045766	0.07	positive regulation of angiogenesis
GO:0045603	0.07	positive regulation of endothelial cell differentiation
GO:0043651	0.07	linoleic acid metabolic process
GO:0043280	0.07	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0042554	0.07	superoxide anion generation
GO:0031408	0.07	oxylipin biosynthetic process
GO:0031047	0.07	gene silencing by RNA
GO:0030866	0.07	cortical actin cytoskeleton organization
GO:0030307	0.07	positive regulation of cell growth
GO:0019395	0.07	fatty acid oxidation
GO:0019372	0.07	lipoxygenase pathway
GO:0019369	0.07	arachidonic acid metabolic process
GO:0019083	0.07	viral transcription
GO:0016925	0.07	protein sumoylation
GO:0015031	0.07	protein transport
GO:0010827	0.07	regulation of glucose transport
GO:0010656	0.07	negative regulation of muscle cell apoptotic process
GO:0010628	0.07	positive regulation of gene expression
GO:0010595	0.07	positive regulation of endothelial cell migration
GO:0007568	0.07	aging
GO:0007077	0.07	mitotic nuclear envelope disassembly
GO:0007062	0.07	sister chromatid cohesion
GO:0007044	0.07	cell-substrate junction assembly
GO:0007016	0.07	cytoskeletal anchoring at plasma membrane
GO:0006409	0.07	tRNA export from nucleus
GO:0006406	0.07	mRNA export from nucleus

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	0.65	cell part
GO:0016020	0.59	membrane
GO:0044425	0.53	membrane part

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	0.060	1m56A	0.460	3.98	0.049	0.830	1.9.3.1	NA
2	0.060	3crlB	0.443	4.21	0.089	0.798	2.7.11.2	81
3	0.060	2cvtA	0.446	4.33	0.047	0.851	1.17.4.1	NA
4	0.060	1occA	0.444	4.33	0.073	0.808	1.9.3.1	NA
5	0.060	2owoA	0.451	4.35	0.025	0.840	6.5.1.2	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	0.01	1p271	0.471	3.81	0.105	0.787	0.28	III	complex1.pdb.gz	78,82,85,86,89,90,93,94
2	0.01	1q16C	0.467	4.08	0.048	0.755	0.22	HEM	complex2.pdb.gz	40,44,81,84,85,88,89
3	0.01	1cc1L	0.469	4.17	0.024	0.840	0.36	FCO	complex3.pdb.gz	59,83,87,88,92
4	0.01	1m57A	0.463	3.95	0.049	0.830	0.20	PEH	complex4.pdb.gz	66,72,77,80,84
5	0.01	1y4zC	0.448	3.99	0.012	0.766	0.35	AGA	complex5.pdb.gz	70,71,84
6	0.01	2j0s0	0.462	4.13	0.104	0.798	0.18	III	complex6.pdb.gz	60,71,87
7	0.01	1m56A	0.460	3.98	0.049	0.830	0.12	HEA	complex7.pdb.gz	55,58,80,83,84,87
8	0.01	2gsmA	0.448	4.34	0.061	0.819	0.30	CA	complex8.pdb.gz	86,88,89,90
9	0.01	3fyeA	0.457	4.20	0.048	0.819	0.39	DMU	complex9.pdb.gz	78,79,82
10	0.01	3ehbA	0.431	4.65	0.037	0.830	0.13	UUU	complex10.pdb.gz	63,69,71,72,77,80,81,84,85

	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.