D-I-TASSER Q8WWB5-D2

D-I-TASSER results for Q8WWB5-D2

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

Input Sequence in FASTA format

>Q8WWB5 (115 residues)
APEPQLCLQTRILKPKEKILFINLCQWTRIPAPQSTTHPVPLTVGKPEDTTEISDAYTVI
DVAYNPDVLHAAEKDQVKKNQLIQMAMKCIEEKFQFTLSHSYHITKFRIKGSIQR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| APEPQLCLQTRILKPKEKILFINLCQWTRIPAPQSTTHPVPLTVGKPEDTTEISDAYTVIDVAYNPDVLHAAEKDQVKKNQLIQMAMKCIEEKFQFTLSHSYHITKFRIKGSIQR
Prediction	CCCCCSSSSSSSSCCCCSSSSSSSCCCCCCCCCCCCCCCCSSSSCCCSSCCCCCCCSSSSSSSSCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCSSCCCCCCCCCCSCCCCCC
Confidence	9999889998885599838999965887789999998740288437554268899549999997689999986299999999999999999985962147622136520578899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| APEPQLCLQTRILKPKEKILFINLCQWTRIPAPQSTTHPVPLTVGKPEDTTEISDAYTVIDVAYNPDVLHAAEKDQVKKNQLIQMAMKCIEEKFQFTLSHSYHITKFRIKGSIQR
Prediction	8453310010233678631000000217515517555332313214345377575401000000014005304736501410031004103752615125615114343435368
	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

CCCCCSSSSSSSSCCCCSSSSSSSCCCCCCCCCCCCCCCCSSSSCCCSSCCCCCCCSSSSSSSSCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCSSCCCCCCCCCCSCCCCCC
APEPQLCLQTRILKPKEKILFINLCQWTRIPAPQSTTHPVPLTVGKPEDTTEISDAYTVIDVAYNPDVLHAAEKDQVKKNQLIQMAMKCIEEKFQFTLSHSYHITKFRIKGSIQR

4chhA

0.18

5.93

1.33

DEthreader

EPIADFVIKTKLLSQDGRKVFINVCHSPLVPKPEVDVWEIPIITSCYRMDHDKGQECYVWDCCINSDCSRWICDDIQLREILVEWCLESCEIRDSVVLCRDIAFPKMKKKGAELP

4psfA

0.26

0.24

7.52

3.91

SPARKS-K

PGQPGFCIKTNS---SEGKVFINICHSPSIPPPADVTERIPMSLGEPHAELDAKGQCTAYDVAVNSDFYRRMQNSDFLRELVITIAREGLEDKYNLQLNPEWRMMNRPFMGS---

4chhA

0.16

5.18

1.76

MapAlign

EPIADFVIKTKLLNGDGRKVFINVCHSPLVPKPIQNEWEIPIITSCYRMDHDKGQECYVWDCCINSDCSRWICDDIQLREILVEWCLESCEIRDSVVLCRRIAFPMKKKG-----

4chhA

0.18

5.93

2.03

CEthreader

EPIADFVIKTKLLSQDGRKVFINVCHSPLVPKPEVDFWEIPIITSCYRMDHDKKQECYVWDCCINSDCSRWICDDIQLREILVEWCLESCEIRDSVVLCRRIAFPKMKKKGAELP

4psfA

0.27

0.25

7.75

2.46

MUSTER

PGQPGFCIKTNS----EGKVFINICHSPSIPPPADVTFRIPMSLGEPHAELDAKGGCTAYDVAVNSDFYRRMQNSDFLRELVITIAREGLEDKYNLQLNPEWRMMKRPFMGS---

4chhA

0.18

5.93

5.51

HHsearch

EPIADFVIKTKLLSQDGRKVFINVCHSPLVPKPEVDFNEIPIITSCYRMDHDKKQECYVWDCCINSDCSRWICDDIQLREILVEWCLESCEIRDSVVLCRDIAFPKMKKKGELPA

4psfA

0.27

0.25

7.76

2.07

FFAS-3D

PGQPGFCIKTN---SSEGKVFINICHSPSIPPPADVTFRIPMSLGEPHAELDAGQGCTAYDVAVNSDFYRRMQNSDFLRELVITIAREGLEDKYNLQLNPEWRMMKRPFMGS---

4chhA

0.15

4.99

1.20

EigenThreader

EPIADFVIKTKANGPEKRKVFINVCHSPLVPKPEVDFNEIPIITSCYRMDDKKGQECYVWDCCINSDCSRWICDDIQLREILVEWCLESCEIRDSVVRDRIAFPKMKKKGAELPA

4psfA

0.27

0.25

7.75

1.71

CNFpred

PGQPGFCIKTNSS---EGKVFINICHSPSIPPPADVT-RIPMSLGEPHAELDAGQGCTAYDVAVNSDFYRRMQNSDFLRELVITIAREGLEDKYNLQLNPEWRMMKRPFMGS---

4psfA

0.22

0.21

6.57

1.33

DEthreader

PGQPGFCIKTNS-S-E-GKVFINICHSPSI-PPPADVFRIPMSLGEPHAELDKGQGCTAYDVAVNSDFYRRMQNSDFLRELVITIAREGLEDKYNLQLNPEWRMMKRPFM-GS--

(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	0.9039

(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	4chhA	0.95	1.00	0.183	1.000	model1_4chhA.pdb.gz
2	4psfA	0.87	1.41	0.248	0.948	model1_4psfA.pdb.gz
3	2c1fA	0.56	3.43	0.050	0.800	model1_2c1fA.pdb.gz
4	1ks5A	0.55	3.54	0.069	0.765	model1_1ks5A.pdb.gz
5	1xndA	0.55	3.62	0.041	0.783	model1_1xndA.pdb.gz
6	1ynaA	0.54	3.24	0.061	0.756	model1_1ynaA.pdb.gz
7	1xnkA	0.54	3.58	0.042	0.774	model1_1xnkA.pdb.gz
8	2jenA	0.54	3.73	0.078	0.791	model1_2jenA.pdb.gz
9	3wp4A	0.54	3.65	0.060	0.800	model1_3wp4A.pdb.gz
10	1f5jA	0.54	3.49	0.010	0.791	model1_1f5jA.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:0019899	1.00	enzyme binding
GO:0017160	0.77	Ral GTPase binding
GO:1901363	0.60	heterocyclic compound binding
GO:0097159	0.60	organic cyclic compound binding

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	0.98	cellular process
GO:0034622	0.94	cellular macromolecular complex assembly
GO:0044699	0.90	single-organism process
GO:0050794	0.89	regulation of cellular process
GO:0044763	0.88	single-organism cellular process
GO:0048583	0.86	regulation of response to stimulus
GO:0000492	0.84	box C/D snoRNP assembly
GO:0048522	0.83	positive regulation of cellular process
GO:1902531	0.82	regulation of intracellular signal transduction
GO:1902533	0.81	positive regulation of intracellular signal transduction
GO:0080090	0.78	regulation of primary metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0031323	0.78	regulation of cellular metabolic process
GO:0045893	0.77	positive regulation of transcription, DNA-templated
GO:0045184	0.77	establishment of protein localization
GO:0033036	0.77	macromolecule localization
GO:0072594	0.76	establishment of protein localization to organelle
GO:0051338	0.76	regulation of transferase activity
GO:0043086	0.76	negative regulation of catalytic activity
GO:0033043	0.76	regulation of organelle organization
GO:0032270	0.76	positive regulation of cellular protein metabolic process
GO:0032006	0.76	regulation of TOR signaling
GO:0031400	0.76	negative regulation of protein modification process
GO:0030162	0.76	regulation of proteolysis
GO:0006325	0.76	chromatin organization
GO:2001268	0.75	negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway
GO:2000619	0.75	negative regulation of histone H4-K16 acetylation
GO:2000617	0.75	positive regulation of histone H3-K9 acetylation
GO:1904263	0.75	positive regulation of TORC1 signaling
GO:1902661	0.75	positive regulation of glucose mediated signaling pathway
GO:1901838	0.75	positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter
GO:1900113	0.75	negative regulation of histone H3-K9 trimethylation
GO:1900110	0.75	negative regulation of histone H3-K9 dimethylation
GO:0090240	0.75	positive regulation of histone H4 acetylation
GO:0071902	0.75	positive regulation of protein serine/threonine kinase activity
GO:0071169	0.75	establishment of protein localization to chromatin
GO:0051569	0.75	regulation of histone H3-K4 methylation
GO:0048254	0.75	snoRNA localization
GO:0031334	0.75	positive regulation of protein complex assembly
GO:0006338	0.75	chromatin remodeling
GO:0030855	0.70	epithelial cell differentiation

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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0005737	0.87	cytoplasm
GO:0032991	0.80	macromolecular complex
GO:0044446	0.79	intracellular organelle part
GO:0043234	0.78	protein complex
GO:0043226	0.74	organelle
GO:0043229	0.73	intracellular organelle
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0005634	0.69	nucleus
GO:0097255	0.67	R2TP complex
GO:0030529	0.67	intracellular ribonucleoprotein complex
GO:0044428	0.63	nuclear part
GO:0070761	0.56	pre-snoRNP complex
GO:0043232	0.56	intracellular non-membrane-bounded organelle
GO:0005730	0.55	nucleolus

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	1m4wA	0.528	3.48	0.069	0.783	3.2.1.8	NA
2	0.060	1ye9M	0.256	5.09	0.021	0.444	1.11.1.6	NA
3	0.060	1olrA	0.497	3.68	0.030	0.739	3.2.1.4	NA
4	0.060	1iphA	0.467	4.76	0.010	0.887	1.11.1.6	6
5	0.060	3b7mA	0.535	3.51	0.051	0.756	3.2.1.4	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	0.01	2dcyE	0.519	3.73	0.019	0.800	0.46	TAR	complex1.pdb.gz	30,45,63

	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.