D-I-TASSER Q86WU2-D3

D-I-TASSER results for Q86WU2-D3

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

Input Sequence in FASTA format

>Q86WU2 (115 residues)
ATVAATCAFPSVQAAVDSTVHILQAAVPVARIEFLDEVMMDACNRYSKLNCLVAPTLFLE
FHGSQQALEEQLQRTEEIVQQNGASDFSWAKEAEERSRLWTARHNAWYAALATRP

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| ATVAATCAFPSVQAAVDSTVHILQAAVPVARIEFLDEVMMDACNRYSKLNCLVAPTLFLEFHGSQQALEEQLQRTEEIVQQNGASDFSWAKEAEERSRLWTARHNAWYAALATRP
Prediction	CCSSSSSSCCCHHHHHHHHHHHHHHCCCCHHHHHCHHHHHHHHHHHHCCCCCCCCSSSSSSCCCHHHHHHHHHHHHHHHHHHCCCSSSSSCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence	9279999759999999999999991997134454139999999998198999744799996499999999999999999990994699959999999999999999999985599
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| ATVAATCAFPSVQAAVDSTVHILQAAVPVARIEFLDEVMMDACNRYSKLNCLVAPTLFLEFHGSQQALEEQLQRTEEIVQQNGASDFSWAKEAEERSRLWTARHNAWYAALATRP
Prediction	4321010304304400500240174413121243114300400252373714230100011213573045105302500572614514216366216402512430130044348
	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

CCSSSSSSCCCHHHHHHHHHHHHHHCCCCHHHHHCHHHHHHHHHHHHCCCCCCCCSSSSSSCCCHHHHHHHHHHHHHHHHHHCCCSSSSSCCHHHHHHHHHHHHHHHHHHHHCCC
ATVAATCAFPSVQAAVDSTVHILQAAVPVARIEFLDEVMMDACNRYSKLNCLVAPTLFLEFHGSQQALEEQLQRTEEIVQQNGASDFSWAKEAEERSRLWTARHNAWYAALATRP

6lpnA2

0.19

6.17

1.50

DEthreader

AVNVAFLGCPGFAEVLQTFSTCKGMLGILSAFEFMDAVCMQLVGRHLHLASQESFYVLIETSGNAGHDAEKLGHFLEHALGSGVTDGTMATDQRKVKMLWALRERITEALSRDGY

3pm9A2

0.17

0.16

5.17

1.46

SPARKS-K

AVETAFVGLQSPDDALKLLGIAQGEAGNLTSFELIAETPLDFSVRHANNRDPYPWYVLIELSSPRDDARAALESILERGFEDGVVDAAIANSVQQQQAFWKLREEISPA------

6lpnA

0.20

0.19

6.14

0.97

MapAlign

AVNVAFLGCPGFAEVLQTFSTCKGMLGILSAFEFMDAVCMQLVGRHLHLASQESFYVLIETSGSAGHDAEKLGHFLEHALGL-VTDGTMATDQRKVKMLWALRERITEALSRD--

6lpnA2

0.19

6.17

0.72

CEthreader

AVNVAFLGCPGFAEVLQTFSTCKGMGEILSAFEFMDAVCMQLVGRHLHLASPSPFYVLIETSGSAGHDAEKLGHFLEHALGGLVTDGTMATDQRKVKMLWALRERITEALSRDGY

3pm9A2

0.17

0.16

5.17

1.48

MUSTER

AVETAFVGLQSPDDALKLLGIAQGEAGNLTSFELIAETPLDFSVRHANNRDPYPWYVLIELSSPRDDARAALESILERGFEDGIVDAAIANSVQQQQAFWKLREEISPA------

6lpnA2

0.19

6.17

2.04

HHsearch

AVNVAFLGCPGFAEVLQTFSTCKGLGEILSAFEFMDAVCMQLVGRHLHLASPSPFYVLIETSGSNAHDAEKLGHFEHALGSGLVTDGTMATDQRKVKMLWALRERITEALSRDGY

3pm9A2

0.17

0.16

5.17

1.57

FFAS-3D

AVETAFVGLQSPDDALKLLGIAQGEAGNLTSFELIAETPLDFSVRHANNRDPYPWYVLIELSSPRDDARAALESILERGFEDGVVDAAIANSVQQQQAFWKLREEISPA------

3pm9A2

0.16

0.15

4.93

0.72

EigenThreader

AVETAFVGLQSPDDALKLLGIAQGEAAGNLTFELIAETPLDFSVRHANNRDPYPWYVLIELSSRD-DARAALESILERGFEDIVVDAAIANSVQQQQAFWKLREEISPA------

3pm9A

0.16

5.22

0.95

CNFpred

AVETAFVGLQSPDDALKLLGIAQGEAGNLTSFELIAETPLDFSVRHANNR-RYPWYVLIELSSPRDDARAALESILERGFEDGVVDAAIANSVQQQQAFWKLREEISPAQKPEGG

6lpnA

0.19

6.17

1.50

DEthreader

AVNVAFLGCPGFAEVLQTFSTCKGMLGILSAFEFMDAVCMQLVGRHLHLASQESFYVLIETSGNAGHDAEKLGHFLEHALGSGVTDGTMATDQRKVKMLWALRERITEALSRDGY

(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	0.9008

(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	6lpnA2	0.94	1.08	0.191	1.000	model1_6lpnA2.pdb.gz
2	3pm9A	0.91	1.26	0.158	0.991	model1_3pm9A.pdb.gz
3	1f0xA2	0.77	2.12	0.157	0.939	model1_1f0xA2.pdb.gz
4	1diqA	0.74	2.83	0.088	0.957	model1_1diqA.pdb.gz
5	1ahvA2	0.72	3.26	0.088	0.957	model1_1ahvA2.pdb.gz
6	2exrA	0.61	3.73	0.081	0.904	model1_2exrA.pdb.gz
7	2bvgA	0.54	3.83	0.098	0.861	model1_2bvgA.pdb.gz
8	3d2dA	0.53	3.29	0.062	0.765	model1_3d2dA.pdb.gz
9	3vteA	0.53	3.42	0.054	0.748	model1_3vteA.pdb.gz
10	1no5B	0.48	3.91	0.030	0.748	model1_1no5B.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	0.88	catalytic activity
GO:0016491	0.85	oxidoreductase activity
GO:0016614	0.81	oxidoreductase activity, acting on CH-OH group of donors
GO:0004457	0.73	lactate dehydrogenase activity
GO:0016616	0.56	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

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:0044237	1.00	cellular metabolic process
GO:0044710	0.96	single-organism metabolic process
GO:0071704	0.94	organic substance metabolic process
GO:0044281	0.94	small molecule metabolic process
GO:0044763	0.93	single-organism cellular process
GO:0044238	0.74	primary metabolic process
GO:0006807	0.68	nitrogen compound metabolic process
GO:0034641	0.67	cellular nitrogen compound metabolic process
GO:1901564	0.66	organonitrogen compound metabolic process
GO:1901360	0.66	organic cyclic compound metabolic process
GO:0006725	0.66	cellular aromatic compound metabolic process
GO:0006139	0.65	nucleobase-containing compound metabolic process
GO:1901135	0.64	carbohydrate derivative metabolic process
GO:0055086	0.64	nucleobase-containing small molecule metabolic process
GO:0019637	0.64	organophosphate metabolic process
GO:0006796	0.64	phosphate-containing compound metabolic process
GO:1901576	0.63	organic substance biosynthetic process
GO:0046034	0.63	ATP metabolic process
GO:0044249	0.62	cellular biosynthetic process
GO:1901566	0.61	organonitrogen compound biosynthetic process
GO:0044711	0.61	single-organism biosynthetic process
GO:0044271	0.61	cellular nitrogen compound biosynthetic process
GO:0006754	0.60	ATP biosynthetic 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:0044444	1.00	cytoplasmic part
GO:0043226	0.89	organelle
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0005739	0.86	mitochondrion
GO:0044446	0.59	intracellular organelle part
GO:0044429	0.55	mitochondrial part

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	0.081	2ko1A	0.558	2.26	0.072	0.678	2.7.6.5	NA
2	0.070	1v3zA	0.507	2.44	0.047	0.635	3.6.1.7	NA
3	0.067	1fvqA	0.474	2.36	0.071	0.609	3.6.3.4	NA
4	0.067	1w2iA	0.507	2.44	0.047	0.635	3.6.1.7	NA
5	0.066	1fwpA	0.487	2.16	0.015	0.591	2.7.13.3	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.04	3pm9A	0.911	1.26	0.158	0.991	0.10	FAD	complex1.pdb.gz	52,53,54,56,82
	2	0.01	3qnrC	0.633	3.36	0.083	0.896	0.18	HEM	complex2.pdb.gz	26,27,75,78,79,82

	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.