D-I-TASSER Q9ULI2-D3

D-I-TASSER results for Q9ULI2-D3

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

Input Sequence in FASTA format

>Q9ULI2 (98 residues)
VKESHGRDVRVIVVGGRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNI
LGMDVCGIDLLMKDDGSFCVCEANANVGFIAFDKACNL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| VKESHGRDVRVIVVGGRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMKDDGSFCVCEANANVGFIAFDKACNL
Prediction	CCCCCCCSSSSSSSCCSSSSSSSSSCCCCCSSSSCCCCCSSSSSCCCHHHHHHHHHHHHHHCCCSSSSSSSSCCCCCSSSSSSCCCHHHHHHHHHHCC
Confidence	99899923999998999999999967999415412679779994599999999999999979968999999859998799985797337899987597
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| VKESHGRDVRVIVVGGRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMKDDGSFCVCEANANVGFIAFDKACNL
Prediction	57557442000000443010002131574423432446441452614740250033005214031000000237724010000033412420362377
	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

CCCCCCCSSSSSSSCCSSSSSSSSSCCCCCSSSSCCCCCSSSSSCCCHHHHHHHHHHHHHHCCCSSSSSSSSCCCCCSSSSSSCCCHHHHHHHHHHCC
VKESHGRDVRVIVVGGRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMKDDGSFCVCEANANVGFIAFDKACNL

4iwxA

0.26

7.87

1.33

DEthreader

YIKEAQCDIRCLVVGDEVVAAIERRAKEDFRSNL-HRGGAASVASITPQEREIAIKAARTMALDVAGVDILRA-NRGPLVMEVNASPGLEGIEKTTGI

4iwxA3

0.32

0.31

9.23

2.36

SPARKS-K

--EAQGCDIRCLVVGDEVVAAIERRAKEGDFRSNLHRGGAASVASITPQEREIAIKAARTMALDVAGVDILRANR-GPLVMEVNASPGLEGIEKTTGI

4iwxA

0.30

0.29

8.67

0.76

MapAlign

---KEACDIRCLVVGDEVVAAIERRAKEGDFRSNLHRGGAASVASITPQEREIAIKAARTMALDVAGVDILRAN-RGPLVMEVNASPGLEGIEKTTGI

4iwxA

0.32

9.53

0.62

CEthreader

IKEAQGCDIRCLVVGDEVVAAIERRAKEGDFRSNLHRGGAASVASITPQEREIAIKAARTMALDVAGVDILRA-NRGPLVMEVNASPGLEGIEKTTGI

4iwxA3

0.33

0.32

9.51

2.00

MUSTER

--EAQGCDIRCLVVGDEVVAAIERRAKEGDFRSNLHRGGAASVASITPQEREIAIKAARTMALDVAGVDILRANRG-PLVMEVNASPGLEGIEKTTGI

4iwxA3

0.32

0.31

9.23

1.47

HHsearch

--EAQGCDIRCLVVGDEVVAAIERRAKEGDFRSNLHRGGAASVASITPQEREIAIKAARTMALDVAGVDILRAN-RGPLVMEVNASPGLEGIEKTTGI

4iwxA3

0.33

0.32

9.51

1.64

FFAS-3D

--EAQGCDIRCLVVGDEVVAAIERRAKEGDFRSNLHRGGAASVASITPQEREIAIKAARTMALDVAGVDILRANRG-PLVMEVNASPGLEGIEKTTGI

3vpbB

0.21

6.79

0.78

EigenThreader

GNIQYKGRDIRIAIGEELLGCYARNIPPNEWRANVALGGTPSNIEVDEKLKETVVKAVSIVHGEFVSIDILEHPNKGYVVNELNDVPEFKGFMVATNI

3vpbA

0.26

7.89

1.46

CNFpred

YIQYKGRDIRCIAIGEELLGCYARNIPPNEWRANVALGGTPSNIEVDEKLKETVVKAVSIVHGEFVSIDILEHPNKGYVVNELNDVPEFKGFMVATNI

4iwxA3

0.29

0.28

8.40

1.33

DEthreader

--EAQGCDIRCLVVGDEVVAAIERRAKEDFRSNL-HRGGAASVASITPQEREIAIKAARTMALDVAGVDILRA-NRGPLVMEVNASPGLEGIEKTTGI

(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	0.8544

(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	4iwxA	0.94	1.01	0.309	0.990	model1_4iwxA.pdb.gz
2	3vpbB	0.89	1.42	0.255	1.000	model1_3vpbB.pdb.gz
3	5k2mA	0.85	1.44	0.277	0.959	model1_5k2mA.pdb.gz
4	3ln6A	0.79	2.21	0.274	0.969	model1_3ln6A.pdb.gz
5	1ehiA	0.79	2.25	0.188	0.980	model1_1ehiA.pdb.gz
6	6vzqA2	0.79	2.46	0.184	1.000	model1_6vzqA2.pdb.gz
7	3lwbA	0.78	2.43	0.168	0.969	model1_3lwbA.pdb.gz
8	6gj4F	0.77	2.47	0.167	0.980	model1_6gj4F.pdb.gz
9	1gsaA	0.77	1.82	0.242	0.929	model1_1gsaA.pdb.gz
10	1iowA	0.77	2.35	0.177	0.980	model1_1iowA.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	1.00	catalytic activity
GO:0016879	0.88	ligase activity, forming carbon-nitrogen bonds
GO:0072590	0.80	N-acetyl-L-aspartate-L-glutamate ligase activity
GO:0072591	0.56	citrate-L-glutamate ligase 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:0009987	1.00	cellular process
GO:0071704	0.99	organic substance metabolic process
GO:0044763	0.99	single-organism cellular process
GO:0044237	0.98	cellular metabolic process
GO:0044238	0.97	primary metabolic process
GO:0044281	0.92	small molecule metabolic process
GO:1901576	0.91	organic substance biosynthetic process
GO:0044711	0.88	single-organism biosynthetic process
GO:0044283	0.86	small molecule biosynthetic process
GO:0044723	0.81	single-organism carbohydrate metabolic process
GO:0019751	0.80	polyol metabolic process
GO:0019637	0.80	organophosphate metabolic process
GO:0006796	0.80	phosphate-containing compound metabolic process
GO:0090407	0.79	organophosphate biosynthetic process
GO:0006020	0.79	inositol metabolic process
GO:0032958	0.77	inositol phosphate biosynthetic process
GO:0043170	0.57	macromolecule metabolic process
GO:0006807	0.57	nitrogen compound metabolic process
GO:0050896	0.56	response to stimulus
GO:0044260	0.56	cellular macromolecule metabolic process
GO:0065007	0.54	biological regulation
GO:0034641	0.54	cellular nitrogen compound metabolic process
GO:0019538	0.54	protein metabolic process
GO:0006950	0.54	response to stress
GO:1901564	0.53	organonitrogen compound metabolic process
GO:0007154	0.53	cell communication
GO:0006464	0.53	cellular protein modification process
GO:0050789	0.52	regulation of biological process
GO:0044249	0.52	cellular biosynthetic process
GO:0009605	0.52	response to external stimulus
GO:0050794	0.51	regulation of cellular process
GO:0043687	0.51	post-translational protein modification
GO:0033554	0.51	cellular response to stress
GO:0031668	0.51	cellular response to extracellular stimulus

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:0005737	0.95	cytoplasm

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	2z04B	0.702	2.27	0.091	0.898	4.1.1.21	NA
2	0.060	2dlnA	0.768	2.35	0.177	0.980	6.3.2.4	16,50
3	0.060	2ys6A	0.676	2.85	0.118	0.949	6.3.4.13	NA
4	0.060	2x0sA	0.607	3.57	0.055	0.898	2.7.9.1	NA
5	0.060	1bxrA	0.740	2.39	0.110	0.929	6.3.5.5	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	0.13	1gsaA	0.774	1.82	0.242	0.929	0.56	GTT	complex1.pdb.gz	10,24,35,36,86,88,89
2	0.13	3t9eA	0.737	2.49	0.267	0.918	0.45	UUU	complex2.pdb.gz	10,24,41,69,82,84,87,91
3	0.03	1jdbE	0.741	2.37	0.110	0.929	0.44	GLN	complex3.pdb.gz	22,46,53,54,68

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.