D-I-TASSER A6NJ88

D-I-TASSER results for A6NJ88

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

Summary of the Protein

Uniprot ID: A6NJ88
Protein Name: Putative SAGE1-like protein
Gene Name: SAGE2P

Input Sequence in FASTA format

>A6NJ88 (616 residues)
MYSQEDHIFQLCSTDLCASYVPVINQSVLVTHIVNYEDYLQIQASPLQTSQPTPPEELHT
VGYVFTNDGQQTRSDEVNQVATGHQSKQKRSRESKRHSSSKRRKSMSRWLNKQEDAAVTH
IVCEEKINNDQPAPDNVLSTAPPWLRDMAAAGISSTSTRDLYATVTHNVCDERMENDQLQ
LNNVLLTFPPERVNMAVADFSAMSPRDLYATINHNVYEVRMENNQPQFNNVLSTVKPGHI
NMAAAGIPAMSAKDAVVNLNVHGEKINKGQPAPDNFLSSVTPGLINVSGDGATVTHNAYE
EKMENGQQAADNILSAVPPGLINTSEAGIPAMSTNDLYATITHDVSEKKIKNSQPATDNF
LCTVTPGLINLAEAGILATSTRDLYDTATHNVHEEKMKNKHLITPCQQFHWDLLICQELL
NFFIWIPDATVIHNIQEEEMENGQMPPDGFLSNSAPLELINMTEDCMPLNALDSFSYDFT
SLSREELLYKHDSNEFAVGTKNYSVSAGDPPVTAMSSVETPQISPAMAKKINQDIKCQLM
KEVQRFGQNYKRIFILLEELQGSMKVKRQFVEFTIREAVRFKKVALIQQLEKVLKEIDSH
CHLRKVKHMRKKIIVI

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	A6NJ88-D1	1-249	249		MYSQEDHIFQLCSTDLCASYVPVINQSVLVTHIVNYEDYLQIQASPLQTSQPTPPEELHTVGYVFTNDGQQTRSDEVNQVATGHQSKQKRSRESKRHSSSKRRKSMSRWLNKQEDAAVTHIVCEEKINNDQPAPDNVLSTAPPWLRDMAAAGISSTSTRDLYATVTHNVCDERMENDQLQLNNVLLTFPPERVNMAVADFSAMSPRDLYATINHNVYEVRMENNQPQFNNVLSTVKPGHINMAAAGIPA
2	A6NJ88-D2	250-380	131		MSAKDAVVNLNVHGEKINKGQPAPDNFLSSVTPGLINVSGDGATVTHNAYEEKMENGQQAADNILSAVPPGLINTSEAGIPAMSTNDLYATITHDVSEKKIKNSQPATDNFLCTVTPGLINLAEAGILATS
3	A6NJ88-D3	381-519	139		TRDLYDTATHNVHEEKMKNKHLITPCQQFHWDLLICQELLNFFIWIPDATVIHNIQEEEMENGQMPPDGFLSNSAPLELINMTEDCMPLNALDSFSYDFTSLSREELLYKHDSNEFAVGTKNYSVSAGDPPVTAMSSVE
4	A6NJ88-D4	520-616	97		TPQISPAMAKKINQDIKCQLMKEVQRFGQNYKRIFILLEELQGSMKVKRQFVEFTIREAVRFKKVALIQQLEKVLKEIDSHCHLRKVKHMRKKIIVI

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.43

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	4f91B	0.42	7.65	0.046	0.667	model1_4f91B.pdb.gz
2	4bgdA	0.42	7.54	0.049	0.666	model1_4bgdA.pdb.gz
3	5m59A	0.42	8.10	0.046	0.693	model1_5m59A.pdb.gz
4	6g7eB	0.40	7.91	0.060	0.662	model1_6g7eB.pdb.gz
5	6vr4A	0.39	8.33	0.048	0.657	model1_6vr4A.pdb.gz
6	6sytA	0.39	7.45	0.035	0.596	model1_6sytA.pdb.gz
7	7dxjA	0.39	8.32	0.043	0.657	model1_7dxjA.pdb.gz
8	5yz0A	0.39	8.15	0.057	0.648	model1_5yz0A.pdb.gz
9	6eqoA	0.38	7.85	0.046	0.627	model1_6eqoA.pdb.gz
10	6z2wE	0.38	7.85	0.055	0.625	model1_6z2wE.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:0005198	0.58	structural molecule activity
GO:0005201	0.54	extracellular matrix structural constituent
GO:0097367	0.53	carbohydrate derivative binding
GO:0003676	0.53	nucleic acid binding
GO:0035639	0.52	purine ribonucleoside triphosphate binding
GO:0032559	0.52	adenyl ribonucleotide binding
GO:0032550	0.52	purine ribonucleoside 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	0.98	cellular process
GO:0065007	0.66	biological regulation
GO:0032501	0.64	multicellular organismal process
GO:0044763	0.62	single-organism cellular process
GO:0065008	0.60	regulation of biological quality
GO:0044707	0.59	single-multicellular organism process
GO:0048731	0.58	system development
GO:0044767	0.58	single-organism developmental process
GO:0009653	0.58	anatomical structure morphogenesis
GO:0046331	0.55	lateral inhibition
GO:0044719	0.55	regulation of imaginal disc-derived wing size
GO:0040005	0.55	chitin-based cuticle attachment to epithelium
GO:0008362	0.55	chitin-based embryonic cuticle biosynthetic process
GO:0007475	0.55	apposition of dorsal and ventral imaginal disc-derived wing surfaces
GO:0007424	0.55	open tracheal system development
GO:0044260	0.53	cellular macromolecule metabolic process
GO:0044238	0.53	primary 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:0044424	1.00	intracellular part
GO:0043226	0.89	organelle
GO:0043229	0.88	intracellular organelle
GO:0043227	0.72	membrane-bounded organelle
GO:0005634	0.71	nucleus
GO:0044446	0.60	intracellular organelle part
GO:0044428	0.57	nuclear 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

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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	1z1wA	0.331	7.97	0.043	0.542	3.4.11.-	NA
2	0.060	3ebgA	0.346	7.91	0.051	0.568	3.4.11.-	NA
3	0.060	2ecfA	0.347	7.92	0.037	0.563	3.4.14.5	NA
4	0.060	1xc6A	0.327	8.45	0.039	0.568	3.2.1.23	NA
5	0.060	2gbcA	0.343	8.28	0.055	0.583	3.4.14.5 3.4.15.5	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

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Template proteins with similar binding site:

No Binding sites was predicted

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

	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.