D-I-TASSER Q6NSW5

D-I-TASSER results for Q6NSW5

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

Summary of the Protein

Uniprot ID: Q6NSW5
Protein Name: Putative DENN domain-containing protein 10 B
Gene Name: DENND10P1

Input Sequence in FASTA format

>Q6NSW5 (357 residues)
MAAAELADTQLMLGVGLIEKDTNGEVLWVWCYPSTTATLRNLLLRKCCLTDENKLLHPFV
FGQYRRTWFYITIIEVPDSSILKKVTHFSIVLTAKDFNPEKYAAFTRILCRMYLKHGSPV
KMMESYIAVLTKGICQSEENGSFLSKDFDARKAYPAGSIKDIVSQFGMETVILHTALMLK
KRIVVYHPKIEAVQEFTRTLPALVWHRQDWTILHSYVHLNADELEALQMCTGYVAGFVDL
EVSNRPDLYDVFVNLAESEITIAPLAKEAMAMGKLHKEMGQLIVQSAEDPEKSESQVIQD
IALKTREIFTNLAPFSEVSADGEKRVLNLEALKQKRFPPATENFLYHLAAAEQMLKI

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	Q6NSW5-D1	1-148	148		MAAAELADTQLMLGVGLIEKDTNGEVLWVWCYPSTTATLRNLLLRKCCLTDENKLLHPFVFGQYRRTWFYITIIEVPDSSILKKVTHFSIVLTAKDFNPEKYAAFTRILCRMYLKHGSPVKMMESYIAVLTKGICQSEENGSFLSKDF
2	Q6NSW5-D2	149-272	124		DARKAYPAGSIKDIVSQFGMETVILHTALMLKKRIVVYHPKIEAVQEFTRTLPALVWHRQDWTILHSYVHLNADELEALQMCTGYVAGFVDLEVSNRPDLYDVFVNLAESEITIAPLAKEAMAM
3	Q6NSW5-D3	273-357	85		GKLHKEMGQLIVQSAEDPEKSESQVIQDIALKTREIFTNLAPFSEVSADGEKRVLNLEALKQKRFPPATENFLYHLAAAEQMLKI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.77

(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	6ekkA	0.68	4.85	0.093	0.924	model1_6ekkA.pdb.gz
2	3tw8A	0.66	4.67	0.102	0.882	model1_3tw8A.pdb.gz
3	6lt0C	0.46	5.00	0.099	0.639	model1_6lt0C.pdb.gz
4	6nzdI	0.44	4.82	0.097	0.585	model1_6nzdI.pdb.gz
5	5v9xA	0.42	7.09	0.051	0.731	model1_5v9xA.pdb.gz
6	6um1A	0.41	6.43	0.034	0.681	model1_6um1A.pdb.gz
7	4c2mB	0.41	6.96	0.058	0.723	model1_4c2mB.pdb.gz
8	6v4uA	0.41	4.93	0.071	0.560	model1_6v4uA.pdb.gz
9	6ed1A	0.41	7.22	0.031	0.717	model1_6ed1A.pdb.gz
10	2z86C	0.41	6.15	0.034	0.641	model1_2z86C.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:0005088	0.80	Ras guanyl-nucleotide exchange factor activity
GO:0017112	0.68	Rab guanyl-nucleotide exchange factor activity
GO:1901363	0.65	heterocyclic compound binding
GO:0097159	0.65	organic cyclic compound binding
GO:0003824	0.64	catalytic activity
GO:0001882	0.61	nucleoside 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:0051179	0.84	localization
GO:0006810	0.80	transport
GO:0016192	0.79	vesicle-mediated transport
GO:0044351	0.67	macropinocytosis
GO:0009987	0.67	cellular process
GO:0065007	0.61	biological regulation
GO:0044699	0.56	single-organism process
GO:0050789	0.55	regulation of biological process
GO:0008152	0.51	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:0043229	0.99	intracellular organelle
GO:0043232	0.90	intracellular non-membrane-bounded organelle
GO:0005811	0.89	lipid particle
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0043234	0.70	protein complex
GO:0000428	0.68	DNA-directed RNA polymerase complex
GO:0044444	0.66	cytoplasmic part
GO:0044446	0.64	intracellular organelle part
GO:0005634	0.57	nucleus
GO:0044428	0.55	nuclear part
GO:0055029	0.51	nuclear DNA-directed RNA polymerase complex

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	1ojnA	0.378	6.77	0.034	0.633	4.2.2.1	NA
2	0.060	1itzB	0.328	7.12	0.051	0.571	2.2.1.1	NA
3	0.060	3e7xA	0.371	6.50	0.056	0.611	6.1.1.13	NA
4	0.060	1hn0A	0.379	6.98	0.048	0.655	4.2.2.20	NA
5	0.060	1ultA	0.379	6.16	0.065	0.594	6.2.1.3	28

	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	2z86C	0.405	6.15	0.034	0.641	0.16	UGA	complex1.pdb.gz	165,167,168,170
2	0.01	2z86A	0.403	6.18	0.034	0.641	0.12	UGA	complex2.pdb.gz	194,199,200
3	0.01	3ks0A	0.136	4.69	0.075	0.182	0.30	HEM	complex3.pdb.gz	236,245,246,247
4	0.01	2x2iA	0.447	6.86	0.048	0.770	0.31	QPS	complex4.pdb.gz	236,239,241,242,243,250,251
5	0.01	2oaq2	0.324	7.19	0.057	0.574	0.26	PO4	complex5.pdb.gz	233,234,235,236
6	0.01	1fcbA	0.379	6.71	0.065	0.630	0.13	HEM	complex6.pdb.gz	167,170,171,175
7	0.01	2vu9A	0.320	6.63	0.044	0.529	0.27	UUU	complex7.pdb.gz	236,244,245
8	0.01	1lcoA	0.378	6.77	0.071	0.633	0.17	HEM	complex8.pdb.gz	158,159,170,173,174,176
9	0.01	1ry2A	0.379	6.08	0.048	0.594	0.18	AMP	complex9.pdb.gz	234,252,253,254,255
10	0.01	1rwcA	0.387	6.67	0.063	0.644	0.12	UUU	complex10.pdb.gz	161,162,251

	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.