D-I-TASSER Q3MIR4-D2

D-I-TASSER results for Q3MIR4-D2

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

Input Sequence in FASTA format

>Q3MIR4 (116 residues)
YQNNRRYGVSRDDAQLSGLPSALRHPVNECAPYQRSAAGLPIAPCGAIANSLSGIAWWTD
YHVKFRNPPLVNGSLALAFQGTAPPPNWRRPVYELSPDPNNTGFINQDFVVWMRTA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| YQNNRRYGVSRDDAQLSGLPSALRHPVNECAPYQRSAAGLPIAPCGAIANSLSGIAWWTDYHVKFRNPPLVNGSLALAFQGTAPPPNWRRPVYELSPDPNNTGFINQDFVVWMRTA
Prediction	CCCHHHHHHCCCHHHHCCCCCCCCCCCCCCCCCSSCCCCCSSSCCCHCHHHHCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCSCC
Confidence	97524656429988972686555677788875156699977643650032322520114664445688777765231324776897535667788888899987443445213049
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| YQNNRRYGVSRDDAQLSGLPSALRHPVNECAPYQRSAAGLPIAPCGAIANSLSGIAWWTDYHVKFRNPPLVNGSLALAFQGTAPPPNWRRPVYELSPDPNNTGFINQDFVVWMRTA
Prediction	74333210502236204454463754454042144376531100011103233413142545341544545456344415521313414442352455552523421301331358
	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                  80                 100

                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHCCCHHHHCCCCCCCCCCCCCCCCCSSCCCCCSSSCCCHCHHHHCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCSCC
YQNNRRYGVSRDDAQLSGLPSALRHPVNECAPYQRSAAGLPIAPCGAIANSLSGIAWWTDYHVKFRNPPLVNGSLALAFQGTAPPPNWRRPVYELSPDPNNTGFINQDFVVWMRTA

6k7gC

0.48

0.47

13.53

1.17

DEthreader

YQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRNE-DKPIPCG-AIASMFND--IAWTDKNVKFRNPPGGDNLEERFKGTTKPVNWLKPVYMLDSDPDNNGFINEDFIVWMRTA

6k7gC

0.64

0.63

17.97

3.50

SPARKS-K

YQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRN-EDKPIAPCGAIANSMKGIAWWTDKNVKFRNPPG-GDNLEERFKGTTKPVNWLKPVYMLDSDPDNNGFINEDFIVWMRTA

6k7gC

0.62

0.57

16.28

1.45

MapAlign

------YVKSRDDSQLNGDSSALLNPSKECEPYRRN-EDKPIAPCGAIANKKKGIAWWTDKNVKFRNPPGG-DNLEERFKGTTKPVNWLKPVYMLDSDPDNNGFINEDFIVWMRT-

6k7gC

0.64

0.63

17.97

1.72

CEthreader

YQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRN-EDKPIAPCGAIANSMKGIAWWTDKNVKFRNPP-GGDNLEERFKGTTKPVNWLKPVYMLDSDPDNNGFINEDFIVWMRTA

6k7gC

0.64

0.63

17.97

1.15

MUSTER

YQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRN-EDKPIAPCGAIANSMFGIAWWTDKNVKFRNPPG-GDNLEERFKGTTKPVNWLKPVYMLDSDPDNNGFINEDFIVWMRTA

6k7gC

0.64

0.63

17.97

4.92

HHsearch

YQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRN-EDKPIAPCGAIANSMKGIAWWTDKNVKFRNPPGG-DNLEERFKGTTKPVNWLKPVYMLDSDPDNNGFINEDFIVWMRTA

6rohC

0.30

9.14

1.56

FFAS-3D

YQNHRRYVQSFDTKQILGEPIKKDDLDTSCSPIR-SREDKIIYPCGLIANSMFNDTFSQNKHISWSIDRHRFKTTKYNASDIVPPPNWMKKYPDGYTENLPDIHTWEEFQVWMRTA

6k7gC

0.43

12.64

1.62

EigenThreader

YQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRNEDKPIAPCGAIANSMFKKGIAWWTDKNVKFRNPPGGDNLEERFKGTTKPVNWLKPVYMLDSDPDNNGFINEDFIVWMRTA

1e2uA

0.13

0.04

1.50

0.53

CNFpred

-----------------------------------------ANLQDLLIFVLRGIAIYGEKLKELGQPDRNDDFVLQGLF------------------------------------

7bspC

0.49

0.47

13.52

1.17

DEthreader

YQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRNED-KPIPCG-AIMSMFND--IAW-WTDKKFRN-PPGGNLEERFKGTTKPVNWLKPVYMLDSDPDNNGFINEDFIVWMRTA

(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	0.7554

(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	6k7gC	0.94	1.29	0.632	0.983	model1_6k7gC.pdb.gz
2	6rohC	0.73	2.24	0.384	0.853	model1_6rohC.pdb.gz
3	6lcpB	0.72	2.60	0.314	0.879	model1_6lcpB.pdb.gz
4	7ky5B	0.69	2.94	0.298	0.879	model1_7ky5B.pdb.gz
5	1eg3A	0.46	4.84	0.083	0.871	model1_1eg3A.pdb.gz
6	2yvkA	0.45	4.50	0.075	0.767	model1_2yvkA.pdb.gz
7	3ldtA	0.45	4.24	0.054	0.759	model1_3ldtA.pdb.gz
8	1w2wA1	0.43	4.26	0.034	0.741	model1_1w2wA1.pdb.gz
9	2a0uA1	0.43	4.81	0.094	0.793	model1_2a0uA1.pdb.gz
10	1t9kC1	0.40	4.68	0.067	0.741	model1_1t9kC1.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:0003824	0.53	catalytic 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:0065007	0.88	biological regulation
GO:0044699	0.74	single-organism process
GO:0009987	0.74	cellular process
GO:0050789	0.72	regulation of biological process
GO:0044763	0.66	single-organism cellular process
GO:0051234	0.64	establishment of localization
GO:0006810	0.63	transport
GO:0048518	0.60	positive regulation of biological process
GO:0032879	0.58	regulation of localization
GO:0051049	0.57	regulation of transport
GO:0044765	0.55	single-organism transport
GO:0065008	0.54	regulation of biological quality
GO:0016043	0.53	cellular component organization
GO:0097035	0.52	regulation of membrane lipid distribution
GO:0071702	0.51	organic substance transport

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:0044444	0.96	cytoplasmic part
GO:0043226	0.85	organelle
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0016020	0.80	membrane
GO:0005737	0.64	cytoplasm
GO:0005783	0.59	endoplasmic reticulum

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	1ub2A	0.433	4.38	0.049	0.750	1.11.1.7	NA
2	0.060	3a8tA	0.421	4.92	0.035	0.793	2.5.1.27	106
3	0.060	1r76A	0.417	4.81	0.028	0.750	4.2.2.2	NA
4	0.060	2cseA	0.418	4.42	0.037	0.733	2.7.7.50	NA
5	0.060	1t9kD	0.416	4.67	0.043	0.741	5.3.1.23	7,51

	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	0.05	3acyA	0.439	4.63	0.046	0.819	0.15	702	complex1.pdb.gz	13,17,45,46,49,52,54
2	0.01	2uxpA	0.435	4.04	0.041	0.690	0.30	CLM	complex2.pdb.gz	15,64,66,109
3	0.01	3p9eh	0.437	4.58	0.040	0.776	0.11	UUU	complex3.pdb.gz	7,8,9,46,47,48,49
4	0.01	1azs1	0.254	5.31	0.011	0.483	0.30	III	complex4.pdb.gz	11,105,108,109,111
5	0.01	2uxhB	0.428	4.31	0.020	0.724	0.16	QUE	complex5.pdb.gz	19,49,63
6	0.01	2uxi0	0.426	4.41	0.050	0.733	0.13	III	complex6.pdb.gz	50,51,53,66,67,79,83,84,86,87
7	0.01	3p9dE	0.426	4.52	0.028	0.759	0.14	UUU	complex7.pdb.gz	13,16,49
8	0.01	3ae0A	0.441	4.64	0.046	0.819	0.10	GGS	complex8.pdb.gz	10,19,47
9	0.01	3ae0B	0.434	4.86	0.045	0.828	0.11	GGS	complex9.pdb.gz	9,15,19,47,83
10	0.01	3nriA	0.368	4.57	0.033	0.664	0.10	DH7	complex10.pdb.gz	17,48,52

	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.