D-I-TASSER Q9P0N9-D1

D-I-TASSER results for Q9P0N9-D1

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

Input Sequence in FASTA format

>Q9P0N9 (69 residues)
MTEDSQRNFRSVYYEKVGFRGVEEKKSLEILLKDDRLDTEKLCTFSQRFPLPSMYRALVW
KVLLGILPP

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MTEDSQRNFRSVYYEKVGFRGVEEKKSLEILLKDDRLDTEKLCTFSQRFPLPSMYRALVWKVLLGILPP
Prediction	CCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCC
Confidence	987553116999987757774037899999985576789999999997199557899999999768999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MTEDSQRNFRSVYYEKVGFRGVEEKKSLEILLKDDRLDTEKLCTFSQRFPLPSMYRALVWKVLLGILPP
Prediction	846676541243215413154264453144116743252740240035151344234301310143348
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60

                   |                   |                   |

SS
Seq

CCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCC
MTEDSQRNFRSVYYEKVGFRGVEEKKSLEILLKDDRLDTEKLCTFSQRFPLPSMYRALVWKVLLGILPP

7c6oA2

0.07

0.06

2.38

1.00

DEthreader

------------DATAGVMADWMYEQLTQRYLDNRMTLHGMAERLLEAWQPAPETLDGLRQVLLETEG-

3qwlA

1.00

0.71

19.88

1.13

SPARKS-K

--------------------GVEEKKSLEILLKDDRLDTEKLCTFSQRFPLPSMYRALVWKVLLGILPP

3qwlA

1.00

0.71

19.88

1.04

MUSTER

--------------------GVEEKKSLEILLKDDRLDTEKLCTFSQRFPLPSMYRALVWKVLLGILPP

3qwlA

1.00

0.71

19.88

1.40

HHsearch

--------------------GVEEKKSLEILLKDDRLDTEKLCTFSQRFPLPSMYRALVWKVLLGILPP

4k7dA

0.11

0.10

3.67

1.00

DEthreader

---PTYHSFFPITPVLVVICLDCFHLYCVTRLNDRQFVYSLPLIELHHFILGEEQYNRYQQY--GAEEL

2qfzA

0.30

0.20

6.14

0.99

SPARKS-K

----------------------SRLDKFKQLLAGPNTDLEELRRLSWS-GIPKPVRPMTWKLLSGYLPA

6iuyA

0.09

3.35

0.71

MapAlign

VRAEGPQLISQMVSRILGIDCVPGAEMCGTLKNIVAVGAQGLSEMRKFCTFFESGVADLIASSYGGRNR

3qwlA

1.00

0.71

19.88

0.75

CEthreader

--------------------GVEEKKSLEILLKDDRLDTEKLCTFSQRFPLPSMYRALVWKVLLGILPP

2qfzA

0.30

0.20

6.14

0.88

MUSTER

----------------------SRLDKFKQLLAGPNTDLEELRRLSWS-GIPKPVRPMTWKLLSGYLPA

2qfzA1

0.30

0.20

6.14

1.36

HHsearch

----------------------SRLDKFKQLLAGPNTDLEELRRLS-WSGIPKPVRPMTWKLLSGYLPA

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5735

(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	3qwlA	0.68	0.62	1.000	0.710	model1_3qwlA.pdb.gz
2	2g77A	0.64	1.88	0.245	0.739	model1_2g77A.pdb.gz
3	2qfzA1	0.61	0.95	0.304	0.667	model1_2qfzA1.pdb.gz
4	3qyeA	0.49	3.43	0.049	0.826	model1_3qyeA.pdb.gz
5	4p17A2	0.47	2.70	0.161	0.696	model1_4p17A2.pdb.gz
6	3ismC	0.46	3.68	0.075	0.783	model1_3ismC.pdb.gz
7	2qq8A2	0.45	2.71	0.106	0.623	model1_2qq8A2.pdb.gz
8	1p8kZ	0.43	3.19	0.034	0.710	model1_1p8kZ.pdb.gz
9	1b1xA2	0.38	3.64	0.047	0.667	model1_1b1xA2.pdb.gz
10	3o1lA2	0.38	3.35	0.068	0.667	model1_3o1lA2.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:0005096	1.00	GTPase activator activity
GO:0019899	0.87	enzyme binding
GO:0017137	0.86	Rab GTPase 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:0043087	1.00	regulation of GTPase activity
GO:0050794	0.95	regulation of cellular process
GO:0090630	0.93	activation of GTPase activity
GO:0048583	0.85	regulation of response to stimulus
GO:0048523	0.84	negative regulation of cellular process
GO:0032006	0.84	regulation of TOR signaling
GO:0050896	0.83	response to stimulus
GO:0032007	0.83	negative regulation of TOR signaling
GO:0070848	0.82	response to growth factor
GO:0048518	0.59	positive regulation of biological process
GO:0048522	0.56	positive regulation of cellular process
GO:0080090	0.55	regulation of primary metabolic process
GO:0060255	0.55	regulation of macromolecule metabolic process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0032270	0.54	positive regulation of cellular protein metabolic process
GO:0031401	0.53	positive regulation of protein modification process
GO:0031398	0.52	positive regulation of protein ubiquitination

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	1.00	cell part
GO:0044424	0.94	intracellular part
GO:0044444	0.90	cytoplasmic part
GO:0043227	0.87	membrane-bounded organelle
GO:0031410	0.83	cytoplasmic vesicle
GO:0044446	0.69	intracellular organelle part
GO:0044430	0.57	cytoskeletal part
GO:0044463	0.56	cell projection part
GO:0005815	0.56	microtubule organizing center
GO:0036064	0.55	ciliary basal body

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	1ho8A	0.500	2.93	0.043	0.739	3.6.3.14	NA
2	0.060	1ub2A	0.507	2.87	0.031	0.812	1.11.1.7	NA
3	0.060	1dc1B	0.538	2.87	0.079	0.870	3.1.21.4	4,51
4	0.060	1d8dA	0.525	3.12	0.121	0.812	2.5.1.58	26
5	0.060	1clcA	0.522	3.05	0.062	0.812	3.2.1.4	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	2wm91	0.537	2.92	0.116	0.739	0.13	III	complex1.pdb.gz	40,44,47,48,49
2	0.01	1t330	0.562	2.37	0.060	0.710	0.12	III	complex2.pdb.gz	10,11,15,17,18,41,51,52,53,65
3	0.01	3c23A	0.523	3.37	0.029	0.870	0.16	3AT	complex3.pdb.gz	22,23,24,26
4	0.01	3c21A	0.540	3.20	0.059	0.841	0.19	2BA	complex4.pdb.gz	12,15,19,20,21

	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.