D-I-TASSER Q86WT6-D2

D-I-TASSER results for Q86WT6-D2

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

Input Sequence in FASTA format

>Q86WT6 (63 residues)
LLKGHPQCPEHGENLKLFSKPDGKLICFQCKDARLSVGQSKEFLQISDAVHFFTEELAIQ
QGQ

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| LLKGHPQCPEHGENLKLFSKPDGKLICFQCKDARLSVGQSKEFLQISDAVHFFTEELAIQQGQ
Prediction	CCCCCCCCCCCCCCSSSSSCCCCSSSSSSSCCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHCC
Confidence	998876522229752689737994999995221112256855043178999999999986169
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| LLKGHPQCPEHGENLKLFSKPDGKLICFQCKDARLSVGQSKEFLQISDAVHFFTEELAIQQGQ
Prediction	746647405737550411146744100020343435464345224145014313541444578
	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

                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCSSSSSCCCCSSSSSSSCCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHCC
LLKGHPQCPEHGENLKLFSKPDGKLICFQCKDARLSVGQSKEFLQISDAVHFFTEELAIQQGQ

3f2gB

0.08

3.13

1.17

DEthreader

TARVSSHCATGAPVPMAVSLVHVHFFASPTAE-DWASKQGLAIVSVHEAFGLGQEFNRHLLQT

5va4A

0.25

0.22

6.89

2.04

SPARKS-K

-----DHCAHHGEKLVLFCQQDGNVICWLCERSQEHR--GHQTFLVEEVAQKYREKLQVALEM

3f2gB

0.08

3.10

1.00

MapAlign

---VSSHCAATGAPVMAVSLVHVHFFASVTAEDWAQGLEGLAIVSVHEAFGLGQEFNRHLLQT

5va4A

0.25

0.22

6.89

0.89

CEthreader

-----DHCAHHGEKLVLFCQQDGNVICWLCERSQEH--RGHQTFLVEEVAQKYREKLQVALEM

5va4A

0.27

0.24

7.32

1.64

MUSTER

-----DHCAHHGEKLVLFCQQDGNVICWLCERSQEHRGHQ--TFLVEEVAQKYREKLQVALEM

5va4A

0.25

0.22

6.89

1.46

HHsearch

-----DHCAHHGEKLVLFCQQDGNVICWLCERSQEH--RGHQTFLVEEVAQKYREKLQVALEM

2csvA

0.23

0.21

6.46

0.79

FFAS-3D

---EARKCPVHGKTMELFCQTDQTCICYLCMFQ---EHKNHSTVTVEEAKAEKETESGPSSG-

2csvA

0.19

0.17

5.65

0.80

EigenThreader

RDFEARKCPVHGKTMELFCQTDQTCICYLCMFQEH---KNHSTVTVEEAKAEKE-TESGPSSG

5va4A

0.25

0.22

6.89

1.53

CNFpred

-----DHCAHHGEKLVLFCQQDGNVICWLCERSQEHR--GHQTFLVEEVAQKYREKLQVALEM

2csvA

0.23

0.19

5.97

1.00

DEthreader

-RDFERKCPVHGKTMELFCQTDQTCICYLCMFQEHKN---HSTVTVEEAKAEKETE-------

(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	0.6871

(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	6h3aA	0.71	1.91	0.233	0.921	model1_6h3aA.pdb.gz
2	2csvA	0.70	1.65	0.203	0.809	model1_2csvA.pdb.gz
3	4tn3A	0.69	1.70	0.255	0.873	model1_4tn3A.pdb.gz
4	3f2gB	0.68	2.83	0.095	1.000	model1_3f2gB.pdb.gz
5	5va4A	0.67	1.60	0.259	0.857	model1_5va4A.pdb.gz
6	6qajA	0.64	2.26	0.233	0.936	model1_6qajA.pdb.gz
7	5c17A	0.62	2.53	0.133	0.952	model1_5c17A.pdb.gz
8	2x49A	0.60	2.63	0.033	0.841	model1_2x49A.pdb.gz
9	2junA	0.60	2.73	0.070	0.857	model1_2junA.pdb.gz
10	2difA	0.59	1.74	0.240	0.698	model1_2difA.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:0004842	1.00	ubiquitin-protein transferase 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:0008152	0.94	metabolic process
GO:0044260	0.93	cellular macromolecule metabolic process
GO:0044238	0.93	primary metabolic process
GO:0006464	0.92	cellular protein modification process
GO:0016567	0.91	protein ubiquitination
GO:0000209	0.90	protein polyubiquitination
GO:0065007	0.67	biological regulation
GO:0050789	0.66	regulation of biological process
GO:0050794	0.63	regulation of cellular process
GO:0048518	0.58	positive regulation of biological process
GO:0010468	0.56	regulation of gene expression
GO:0080090	0.55	regulation of primary metabolic process
GO:0048583	0.55	regulation of response to stimulus
GO:0048522	0.55	positive regulation of cellular process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0031325	0.54	positive regulation of cellular metabolic process
GO:0010604	0.54	positive regulation of macromolecule metabolic process
GO:0009966	0.54	regulation of signal transduction
GO:0065009	0.53	regulation of molecular function
GO:0050776	0.53	regulation of immune response
GO:0048584	0.53	positive regulation of response to stimulus
GO:0043900	0.53	regulation of multi-organism process
GO:0032270	0.53	positive regulation of cellular protein metabolic process
GO:0045089	0.52	positive regulation of innate immune response
GO:0044093	0.52	positive regulation of molecular function
GO:0032101	0.52	regulation of response to external stimulus
GO:0009967	0.52	positive regulation of signal transduction
GO:0002831	0.52	regulation of response to biotic stimulus
GO:0001934	0.52	positive regulation of protein phosphorylation

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	0.97	organelle
GO:0043229	0.96	intracellular organelle
GO:0043227	0.86	membrane-bounded organelle
GO:0043231	0.85	intracellular membrane-bounded organelle
GO:0005737	0.84	cytoplasm
GO:0005634	0.83	nucleus
GO:0044422	0.79	organelle part
GO:0044446	0.78	intracellular organelle part
GO:0044428	0.74	nuclear part
GO:0016607	0.72	nuclear speck
GO:0044444	0.62	cytoplasmic part
GO:0016020	0.57	membrane
GO:0005886	0.52	plasma 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	1wnlA	0.543	3.33	0.033	0.873	6.3.4.15	NA
2	0.060	1bibA	0.412	3.45	0.058	0.667	6.3.4.15	24
3	0.060	1pl6A	0.495	3.57	0.036	0.889	1.1.1.14	47
4	0.060	2w41B	0.543	3.08	0.048	0.952	2.7.1.30	NA
5	0.060	2z1mA	0.515	2.89	0.077	0.794	4.2.1.47	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	3efsA	0.561	3.12	0.083	0.841	0.15	ATP	complex1.pdb.gz	20,23,24,25
2	0.01	2djzB	0.544	3.44	0.033	0.873	0.13	BT5	complex2.pdb.gz	9,17,18
3	0.01	2w41A	0.547	3.28	0.065	0.968	0.25	ADP	complex3.pdb.gz	23,35,36
4	0.01	2dxu0	0.546	3.41	0.033	0.873	0.23	III	complex4.pdb.gz	23,24,25,26,27,28,29,32,37
5	0.01	2dveB	0.545	3.41	0.033	0.873	0.15	BT5	complex5.pdb.gz	8,9,10,11,12,13,16,17,26,27
6	0.01	3efrB	0.556	3.28	0.066	0.857	0.11	BTN	complex6.pdb.gz	33,34,42,43,44
7	0.01	1w7j3	0.426	3.96	0.052	0.714	0.13	III	complex7.pdb.gz	29,30,33,34,35,36,37,38
8	0.01	1w7iA	0.547	3.58	0.016	0.921	0.13	ADP	complex8.pdb.gz	38,40,41
9	0.01	1wnlA	0.543	3.33	0.033	0.873	0.10	ADP	complex9.pdb.gz	17,19,20
10	0.01	1w7i0	0.547	3.58	0.016	0.921	0.26	III	complex10.pdb.gz	29,30,32,33,34,35,37,38

	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.