D-I-TASSER Q8IZL2-D3

D-I-TASSER results for Q8IZL2-D3

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

Input Sequence in FASTA format

>Q8IZL2 (83 residues)
MSQTLNGQTMGPLRGLNLRPNQLSTQILPNLNQSGTGLNQSRTGINQPPSLTADFIDSLL
KTEPGNDDWMKDINLDEILGNNS

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MSQTLNGQTMGPLRGLNLRPNQLSTQILPNLNQSGTGLNQSRTGINQPPSLTADFIDSLLKTEPGNDDWMKDINLDEILGNNS
Prediction	CCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHCCHHHHHCCCC
Confidence	98676874246755677770031021157889888775777777788987662489998733899704665334888853589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MSQTLNGQTMGPLRGLNLRPNQLSTQILPNLNQSGTGLNQSRTGINQPPSLTADFIDSLLKTEPGNDDWMKDINLDEILGNNS
Prediction	86544646434425535344541444324434552443444544345445244510331164653444115414144235758
	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 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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHCCHHHHHCCCC
MSQTLNGQTMGPLRGLNLRPNQLSTQILPNLNQSGTGLNQSRTGINQPPSLTADFIDSLLKTEPGNDDWMKDINLDEILGNNS

1vt4I3

0.10

3.60

0.77

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

6fpcA

0.10

3.60

0.48

EigenThreader

AITGVVPLTWDDVPGYSEKGKGHNSLNLEIHETLHAVDRLVLNEVSGTPTEYFAEAASLYLYSDATRSDLKDSMPLTYEFMAK

7a24z2

0.19

0.18

5.83

0.36

FFAS-3D

-SKWSGPPKDKPKYTTDEAVQHVRDLYRESIVKYRVQDSGKKSPDSSEPDIQTELRDKLLALDPLNDVHVAKVNQDEILG---

6sriq4

0.14

0.13

4.53

1.00

SPARKS-K

--KTWVLEPENPARCATSRRIAIGNNVSVNIEVDPRHPKMLPECYFLGADHAVNPLRTKLNNNMHL--WDPEINLKDLLEIDF

4oqrA

0.19

0.07

2.33

0.46

CNFpred

----------------------------------------------------DDLLGSLITDTDLTDEELTNIALILLVAGHE

3rkoN

0.06

0.05

2.12

0.83

DEthreader

GMIVG-LGFLSASKIAIGVRLFAGRVLAIIAFAIIGNMALSQ--TNIKLLSSISHLGYLLVALIALQSM--VG----------

7btxL

0.07

2.95

0.84

MapAlign

VSSFKESLNVLTCYFQRDSHRNLQEWIFSDLLCGYRVLHNFLNSSLSLGAEFWLTTLRYYTHSTNTGRPLTLTLSWNPLFGHI

5yfpB

0.16

5.23

0.54

MUSTER

ILQNNTNQDKSQGCVELSKINQLFQIISDTGKDSEGLKSTVEPNKVNTISGTSYLNLNCQPSSQGLTDSPTIIEMWLLILKND

6v1vA

0.31

0.13

4.00

0.65

HHsearch

------------------------------------------DYFNGIYGFAKDIMGMIFKTDTG------NLTLDEILKNQN

4mhcA

0.11

3.93

0.61

CEthreader

LIVATLFDIYILTISFNDRTHEFNTGLKVNVTGFNVSNIISYERTGQIFFTGATDGVNVWELQYNKICLTKSNLEETISQLEV

(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	0.5578

(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	2vlcA	0.48	3.74	0.085	0.855	model1_2vlcA.pdb.gz
2	3l83A	0.47	3.90	0.000	0.819	model1_3l83A.pdb.gz
3	3gqjA	0.47	3.61	0.162	0.771	model1_3gqjA.pdb.gz
4	6e60A	0.47	4.19	0.114	0.916	model1_6e60A.pdb.gz
5	2fcrA	0.47	3.85	0.026	0.795	model1_2fcrA.pdb.gz
6	1yobA	0.47	3.94	0.064	0.807	model1_1yobA.pdb.gz
7	1bu5A	0.43	4.00	0.070	0.747	model1_1bu5A.pdb.gz
8	1ofvA	0.43	4.10	0.026	0.795	model1_1ofvA.pdb.gz
9	3esxB	0.42	4.48	0.051	0.819	model1_3esxB.pdb.gz
10	3kaqA	0.42	3.99	0.082	0.747	model1_3kaqA.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:0003713	1.00	transcription coactivator 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:0045944	1.00	positive regulation of transcription from RNA polymerase II promoter
GO:0007221	0.82	positive regulation of transcription of Notch receptor target
GO:0009987	0.50	cellular 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:0005634	1.00	nucleus

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	1u7zC	0.443	3.98	0.038	0.819	4.1.1.36 6.3.2.5	NA
2	0.060	1aupA	0.454	4.21	0.077	0.855	1.4.1.2	57
3	0.060	2h2wA	0.438	4.54	0.038	0.855	2.3.1.46	23
4	0.060	2o7qA	0.395	4.84	0.013	0.831	4.2.1.10 1.1.1.25	NA
5	0.060	1eveA	0.328	4.74	0.013	0.675	3.1.1.7	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	1n83A	0.439	4.00	0.060	0.819	0.20	CLR	complex1.pdb.gz	53,61,64,69,73
2	0.01	1tx90	0.344	3.71	0.053	0.602	0.14	III	complex2.pdb.gz	12,16,17,18,20,44,47
3	0.01	3k6pA	0.455	4.14	0.060	0.807	0.16	5FB	complex3.pdb.gz	38,55,73
4	0.01	1vq00	0.459	3.59	0.065	0.783	0.15	III	complex4.pdb.gz	36,38,45,46,47,49
5	0.01	1yobA	0.467	3.94	0.064	0.807	0.26	FMN	complex5.pdb.gz	7,8,9,30,31,33,35,55,56
6	0.01	1xb70	0.298	4.64	0.015	0.626	0.18	III	complex6.pdb.gz	34,35,56,59,63
7	0.01	3phiB	0.425	4.25	0.053	0.819	0.15	NDP	complex7.pdb.gz	53,54,57,59
8	0.01	1u7wA	0.351	4.90	0.026	0.759	0.30	CTP	complex8.pdb.gz	52,57,58,59,76,79
9	0.01	2fcrA	0.468	3.85	0.026	0.795	0.21	FMN	complex9.pdb.gz	4,5,6,7,8,9,38
10	0.01	2o7sA	0.430	3.94	0.026	0.819	0.11	DHK	complex10.pdb.gz	75,76,79

	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.