D-I-TASSER Q8NHU6-D4

D-I-TASSER results for Q8NHU6-D4

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

Input Sequence in FASTA format

>Q8NHU6 (116 residues)
VKVTNICSDGTLYCQVPCKGLNKLSDLLRKIEDYFHCKHMTSECFVSLPFCGKICLFHCK
GKWLRVEITNVHSSRALDVQFLDSGTVTSVKVSELREIPPRFLQEMIAIPPQAIKC

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| VKVTNICSDGTLYCQVPCKGLNKLSDLLRKIEDYFHCKHMTSECFVSLPFCGKICLFHCKGKWLRVEITNVHSSRALDVQFLDSGTVTSVKVSELREIPPRFLQEMIAIPPQAIKC
Prediction	CSSSSSSCCCSSSSSSCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCSSSSSSCCCSSSSSSSSSSCCCCSSSSSSSSCCCCSSSSHHHHSCCCHHHHHHHHCCCCCCCCC
Confidence	79999977997999967872899999999999999624688522346765570999960991899999998389939999961897289717880027998966552188121349
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| VKVTNICSDGTLYCQVPCKGLNKLSDLLRKIEDYFHCKHMTSECFVSLPFCGKICLFHCKGKWLRVEITNVHSSRALDVQFLDSGTVTSVKVSELREIPPRFLQEMIAIPPQAIKC
Prediction	04001023453010113474263045015304620644743664334423303000022644010020362477730301000113454042740350356026413503320368
	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

CSSSSSSCCCSSSSSSCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCSSSSSSCCCSSSSSSSSSSCCCCSSSSSSSSCCCCSSSSHHHHSCCCHHHHHHHHCCCCCCCCC
VKVTNICSDGTLYCQVPCKGLNKLSDLLRKIEDYFHCKHMTSECFVSLPFCGKICLFHCKGKWLRVEITNVHSSRALDVQFLDSGTVTSVKVSELREIPPRFLQEMIAIPPQAIKC

3bdlA2

0.24

0.23

7.24

1.33

DEthreader

VFVTEITDDLHFYVQDVE-TGTQLEKLMENMRNDIASH-PPVEGSY-APRRGEFCIAKFDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFS--TRVLPAQATEY

5ygbA

0.23

0.22

7.02

2.14

SPARKS-K

VYVSAVASPTKFWVQLIGPQSKKLASMVQEMTSYYSSAENRAKHVLTAPYVGQIVAAVFKEKWYRAEIVDIMPEQVIDLYFVDYGDSEYISPADICELRTDFLT----LRFQAVEC

5vqgA

0.23

0.22

7.02

1.21

MapAlign

VYVSAVSSPSRFWVQFVGPQVAQLDDLVAHMTEYYSKKENREAHTLRHVSVGQVVAAVFDGRWYRARVHDIRSQQVADVFYLDYGDSEYVATHELCEL---RADLL-RLRFQAMEC

5vqgA

0.23

0.22

7.02

0.79

CEthreader

VYVSAVSSPSRFWVQFVGPQVAQLDDLVAHMTEYYSKKENREAHTLRHVSVGQVVAAVFDGRWYRARVHDIRPNQVADVFYLDYGDSEYVATHELCELRADLLR----LRFQAMEC

4b9wA1

0.30

0.23

7.05

1.78

MUSTER

----------------KDDALEKLDDLNQSLADYCAQKPPNG----FKAEIGRPCCAFFDGNWYRALVKEILPSGNVKVHFVDYGNVEEVTTDQLQAILPQFLL----LPFQG---

5ygbA

0.22

6.78

2.25

HHsearch

VYVSAVASPTKFWVQLIGPQSKKLASMVQEMTSYYSSAENRAKHVLTAPYVGQIVAAVFDEKWYRAEIVDIMPNQVIDLYFVDYGDSEYISPADICELRTDFL----TLRFQAVEC

5ygbA

0.22

6.78

1.67

FFAS-3D

VYVSAVASPTKFWVQLIGPQSKKLASMVQEMTSYYSSAENRAKHVLTAPYVGQIVAAVFDEKWYRAEIVDIPKEQVIDLYFVDYGDSEYISPADICELRTDFLT----LRFQAVEC

5vqgA

0.18

0.17

5.63

1.00

EigenThreader

YVSAVSSP-SRFWVQFVGPQVAQLDDLVAHMTEYYSKKENREAHTLRHVSVGQVVAAVFDGRWYRARVHDNEFDQVADVFYLDYGDSEYVATHELCELRADLLR--LRFQAMECFL

5ygbA

0.21

6.55

1.88

CNFpred

VYVSAVASPTKFWVQLIGPQSKKLASMVQEMTSYYSSAENRAKHVLTAPYVGQIVAAVFKEKWYRAEIVDIMPEQVIDLYFVDYGDSEYISPADICELRT----DFLTLRFQAVEC

3bdlA

0.24

0.23

7.24

1.33

DEthreader

VFVTEITDDLHFYVQDVE-TGTQLEKLMENMRNDIASH-PPVEGSY-APRRGEFCIAKFDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFS--TRVLPAQATEY

(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	0.8426

(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	5vqgA	0.90	1.18	0.223	0.966	model1_5vqgA.pdb.gz
2	5ygbA	0.90	1.22	0.214	0.966	model1_5ygbA.pdb.gz
3	4b9wA	0.85	1.37	0.296	0.931	model1_4b9wA.pdb.gz
4	3bdlA	0.85	1.85	0.234	0.957	model1_3bdlA.pdb.gz
5	2wacA	0.84	1.87	0.213	0.931	model1_2wacA.pdb.gz
6	5j39A	0.84	1.62	0.204	0.931	model1_5j39A.pdb.gz
7	5m9nA	0.81	1.87	0.241	0.931	model1_5m9nA.pdb.gz
8	4q5yA	0.79	1.49	0.184	0.888	model1_4q5yA.pdb.gz
9	3nthA	0.79	1.62	0.183	0.897	model1_3nthA.pdb.gz
10	2diqA	0.66	2.60	0.200	0.819	model1_2diqA.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:1901363	0.93	heterocyclic compound binding
GO:0097159	0.93	organic cyclic compound binding
GO:0003676	0.91	nucleic acid binding
GO:0003723	0.90	RNA binding
GO:0044822	0.89	poly(A) RNA binding
GO:0003729	0.88	mRNA 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:0048869	1.00	cellular developmental process
GO:0044767	1.00	single-organism developmental process
GO:0007276	1.00	gamete generation
GO:0007283	0.99	spermatogenesis
GO:0065007	0.98	biological regulation
GO:0050789	0.98	regulation of biological process
GO:0010468	0.97	regulation of gene expression
GO:0010608	0.91	posttranscriptional regulation of gene expression
GO:0070306	0.90	lens fiber cell differentiation
GO:0002089	0.90	lens morphogenesis in camera-type eye

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:0035770	1.00	ribonucleoprotein granule
GO:0044444	0.61	cytoplasmic 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	0.060	2djfC	0.237	3.82	0.019	0.371	3.4.14.1	85
2	0.060	2gfiA	0.461	3.78	0.010	0.716	3.1.3.8	NA
3	0.060	7pckD	0.433	4.09	0.039	0.698	3.4.22.38	NA
4	0.060	3exeA	0.441	4.06	0.026	0.672	1.2.4.1	72
5	0.060	1eb6A	0.441	4.44	0.059	0.724	3.4.24.39	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	0.22	3omcA	0.850	1.63	0.252	0.957	0.65	III	complex1.pdb.gz	2,5,15,20,64,81,84,86
2	0.15	3nthA	0.792	1.62	0.183	0.897	0.51	III	complex2.pdb.gz	81,84,86
3	0.15	3ntiA	0.794	1.60	0.183	0.897	0.45	III	complex3.pdb.gz	15,24,25,28,64,81,84
4	0.01	2uyqA	0.452	4.34	0.042	0.724	0.43	SAM	complex4.pdb.gz	53,79,80,82,83

	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.