D-I-TASSER A0AVF1-D4

D-I-TASSER results for A0AVF1-D4

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

Input Sequence in FASTA format

>A0AVF1 (68 residues)
NDDIFNFNYAQAKAATGNTSEGEEAFLLIQSEKMKNDYIYLSWLARCYIMNKKPRLAWEL
YLKMETSG

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| NDDIFNFNYAQAKAATGNTSEGEEAFLLIQSEKMKNDYIYLSWLARCYIMNKKPRLAWELYLKMETSG
Prediction	CCCHHHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCC
Confidence	95313489999999757899999999984497775217899999999998199999999999544789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| NDDIFNFNYAQAKAATGNTSEGEEAFLLIQSEKMKNDYIYLSWLARCYIMNKKPRLAWELYLKMETSG
Prediction	87652423302021334425404420240435614642210211030202264163004112435688
	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

                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCC
NDDIFNFNYAQAKAATGNTSEGEEAFLLIQSEKMKNDYIYLSWLARCYIMNKKPRLAWELYLKMETSG

2r5sA

0.14

0.13

4.50

1.33

DEthreader

--DEQLLKQVSELLQQGEHAQALNVIQTLS-DELQSRGDVKLAKADCLLETKQFELAQELLATI--PL

2fi7A3

0.16

5.37

1.37

SPARKS-K

RNARVLNNYGGFLYEQKRYEEAYQRLLEASQDTYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN

5i9dA3

0.19

6.15

1.36

MUSTER

-DVVTYNTLIDGLCKAGKLDEALKLFEEMVEKGIKPDVVTYSTLIDGLCKAGKLDEALKLFEEMVEKG

2r5sA1

0.14

0.13

4.50

1.33

DEthreader

--DEQLLKQVSELLQQGEHAQALNVIQTLS-DELQSRGDVKLAKADCLLETKQFELAQELLATI--PL

2hyzA1

0.17

0.16

5.32

1.36

SPARKS-K

--AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD

6i57A

0.09

3.37

0.45

MapAlign

KECAIYTNRALCYLKLCQFEEAKQDCDQAL-QLADGNVKAFYRRALAHKGLKNYQKSLIDLNKVILLD

6i57A

0.09

3.37

0.30

CEthreader

KECAIYTNRALCYLKLCQFEEAKQDCDQAL-QLADGNVKAFYRRALAHKGLKNYQKSLIDLNKVILLD

4leuA2

0.18

5.74

1.33

MUSTER

--DVFMYKDLIVSLAKKRMDEAMALWEKMKKENLFPDSQTYTEVIRGFLRDGCPADAMNVYEDMLKSP

6gmhQ

0.16

5.35

0.47

HHsearch

KNLYAANGIGAVLAHKGYFREARDVFAQVR-EATADISDVWLNLAHIYVEQKQYISAVQMYENCLRKF

2xcbA1

0.13

0.12

4.10

0.96

FFAS-3D

DTLEQLYALGFNQYQAGKWDDAQKIFQALC-MLDHYDARYFLGLGACRQSLGLYEQALQSYSYG----

(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	0.7537

(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	4rg6A	0.86	1.48	0.104	0.985	model1_4rg6A.pdb.gz
2	2pl2A	0.86	1.07	0.169	0.956	model1_2pl2A.pdb.gz
3	2vq2A	0.86	1.15	0.121	0.971	model1_2vq2A.pdb.gz
4	6tntX	0.85	1.24	0.147	0.985	model1_6tntX.pdb.gz
5	6yj6A2	0.85	1.15	0.061	0.971	model1_6yj6A2.pdb.gz
6	1w3bA	0.85	1.26	0.152	0.971	model1_1w3bA.pdb.gz
7	4ui9C1	0.85	1.47	0.104	0.985	model1_4ui9C1.pdb.gz
8	2gw1A1	0.83	1.27	0.152	0.971	model1_2gw1A1.pdb.gz
9	3as4A2	0.81	1.40	0.152	0.971	model1_3as4A2.pdb.gz
10	1kt1A	0.81	1.38	0.091	0.971	model1_1kt1A.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	0.42	enzyme binding
GO:0019902	0.39	phosphatase binding
GO:1901363	0.33	heterocyclic compound binding
GO:0097159	0.33	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:0044763	1.00	single-organism cellular process
GO:0006810	0.95	transport
GO:0098840	0.94	protein transport along microtubule
GO:0042073	0.94	intraciliary transport
GO:0065007	0.83	biological regulation
GO:0050789	0.83	regulation of biological process
GO:0050794	0.82	regulation of cellular process
GO:0007165	0.80	signal transduction
GO:0016043	0.79	cellular component organization
GO:0007224	0.79	smoothened signaling pathway
GO:0032502	0.78	developmental process
GO:0044767	0.77	single-organism developmental process
GO:0030030	0.76	cell projection organization
GO:0010927	0.75	cellular component assembly involved in morphogenesis
GO:0006996	0.75	organelle organization
GO:1902589	0.74	single-organism organelle organization
GO:0030031	0.74	cell projection assembly
GO:0042384	0.73	cilium assembly

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:0030992	1.00	intraciliary transport particle B
GO:0044464	0.99	cell part
GO:0043226	0.94	organelle
GO:0005929	0.92	cilium
GO:0072372	0.58	primary cilium
GO:0044424	0.57	intracellular part
GO:0044422	0.55	organelle 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	0.112	1tjcA	0.823	1.81	0.103	0.985	1.14.11.2	7,24,27,52,56
2	0.060	1kt1A	0.813	1.38	0.091	0.971	5.2.1.8	NA
3	0.060	1w6jA	0.618	3.19	0.030	0.971	5.4.99.7	NA
4	0.060	1a17A	0.803	1.47	0.152	0.971	3.1.3.16	NA
5	0.060	1slyA	0.688	1.97	0.123	0.956	4.2.2.-	40

	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	3gz1A	0.811	1.48	0.152	0.971	0.52	III	complex1.pdb.gz	7,11,14,26,37,46,49,50,61
2	0.20	2qfcB	0.815	1.82	0.132	0.985	0.43	III	complex2.pdb.gz	11,12,14,15,39,42,43,46
3	0.19	3cvnA	0.820	1.35	0.121	0.971	0.48	III	complex3.pdb.gz	9,16,26,39,42,43,46
4	0.19	1fchA	0.795	1.48	0.136	0.971	0.40	III	complex4.pdb.gz	8,12,13,16,26,40,46,50
5	0.18	2v5fA	0.833	1.73	0.103	0.985	0.46	III	complex5.pdb.gz	14,15,17,40,43

	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.