D-I-TASSER E9PJI5

D-I-TASSER results for E9PJI5

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

Summary of the Protein

Uniprot ID: E9PJI5
Protein Name: Nuclear pore complex-interacting protein family member A7
Gene Name: NPIPA7

Input Sequence in FASTA format

>E9PJI5 (369 residues)
MFCCLGYEWLSGGCTTWHSAWVINTLADHRHRGTDFGGSPWLLIITVFLRSYKFAISLCT
SYLCVSFLKTIFPSQNGHDGSTDVQQRARRSNRRRQEGIKIVLEDIFTLWRQVETKVRAK
IRKMKVTTKVNRHDKINGKRKTAKEHLRKLSMKEREHREEERQVSEAEENGKLDMKEIHT
YMEMFQRAQALRRRAEDYYRCKITPSARKPLCNRVRMAAVEHRHSSGLPYWPYLTAETLK
NRMGHQPPPPTQQHSIIDNSLSLKTPSECVLYPLPPSADDNLKTPPECLLTPLPPSALPS
ADDNLKTPAECLLYPLPPSADDNLKTPPECLLTPLPPSAPPSADDNLKTPPECVCSLPFH
PQRMIISRN

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 DeepPotential. 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	E9PJI5-D1	1-369	369		MFCCLGYEWLSGGCTTWHSAWVINTLADHRHRGTDFGGSPWLLIITVFLRSYKFAISLCTSYLCVSFLKTIFPSQNGHDGSTDVQQRARRSNRRRQEGIKIVLEDIFTLWRQVETKVRAKIRKMKVTTKVNRHDKINGKRKTAKEHLRKLSMKEREHREEERQVSEAEENGKLDMKEIHTYMEMFQRAQALRRRAEDYYRCKITPSARKPLCNRVRMAAVEHRHSSGLPYWPYLTAETLKNRMGHQPPPPTQQHSIIDNSLSLKTPSECVLYPLPPSADDNLKTPPECLLTPLPPSALPSADDNLKTPAECLLYPLPPSADDNLKTPPECLLTPLPPSAPPSADDNLKTPPECVCSLPFHPQRMIISRN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4092

(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 DeepPotential, 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	3ebgA	0.46	6.40	0.032	0.726	model1_3ebgA.pdb.gz
2	2dqmA	0.45	6.33	0.031	0.699	model1_2dqmA.pdb.gz
3	6h02A	0.44	6.68	0.042	0.721	model1_6h02A.pdb.gz
4	6oiuA	0.44	6.35	0.061	0.705	model1_6oiuA.pdb.gz
5	4f5cA	0.44	6.54	0.036	0.715	model1_4f5cA.pdb.gz
6	4kx7A	0.44	6.56	0.044	0.724	model1_4kx7A.pdb.gz
7	6yejA	0.44	6.43	0.057	0.680	model1_6yejA.pdb.gz
8	1z5hA	0.44	6.39	0.036	0.691	model1_1z5hA.pdb.gz
9	2gtqA	0.44	6.44	0.034	0.694	model1_2gtqA.pdb.gz
10	2xdtA	0.44	6.65	0.051	0.729	model1_2xdtA.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:0046872	0.59	metal ion binding
GO:0046914	0.58	transition metal 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]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	0.87	cellular process
GO:0065007	0.72	biological regulation
GO:0044699	0.72	single-organism process
GO:0044763	0.65	single-organism cellular process
GO:0008152	0.65	metabolic process
GO:0071704	0.63	organic substance metabolic process
GO:0044238	0.63	primary metabolic process
GO:0050789	0.61	regulation of biological process
GO:0043170	0.60	macromolecule metabolic process
GO:0050794	0.58	regulation of cellular process
GO:0019538	0.57	protein metabolic process
GO:0044237	0.55	cellular 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	0.74	organelle
GO:0016020	0.74	membrane
GO:0044444	0.73	cytoplasmic part
GO:0044422	0.70	organelle part
GO:0044446	0.69	intracellular organelle part
GO:0005886	0.68	plasma membrane
GO:0043227	0.66	membrane-bounded organelle
GO:0005737	0.66	cytoplasm
GO:0043229	0.65	intracellular organelle
GO:0044425	0.62	membrane part
GO:0043231	0.56	intracellular membrane-bounded organelle
GO:0016021	0.56	integral component of 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	0.060	1sj2A	0.378	7.15	0.037	0.658	1.11.1.6 1.11.1.7	NA
2	0.060	1c7sA	0.374	7.29	0.066	0.672	3.2.1.52	NA
3	0.060	2jg0A	0.373	6.47	0.038	0.607	3.2.1.28	NA
4	0.060	1jqnA	0.372	7.04	0.034	0.648	4.1.1.31	NA
5	0.060	2c4mC	0.394	6.91	0.038	0.667	2.4.1.1	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	2zxgA	0.449	6.29	0.037	0.694	0.14	S23	complex1.pdb.gz	194,195,196,219,227,228
2	0.01	3ebhA	0.448	6.22	0.030	0.686	0.14	BES	complex2.pdb.gz	203,204,205,218,219,222,226
3	0.01	1ce8G	0.398	7.21	0.054	0.705	0.12	IMP	complex3.pdb.gz	219,220,227,235
4	0.01	3b34A	0.445	6.16	0.038	0.683	0.10	PHE	complex4.pdb.gz	196,197,219
5	0.01	1ce8A	0.399	7.35	0.037	0.715	0.16	IMP	complex5.pdb.gz	196,198,220,232
6	0.01	2ww0F	0.381	6.55	0.056	0.615	0.12	SWA	complex6.pdb.gz	20,22,38,282

	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.