D-I-TASSER Q96FV9-D2

D-I-TASSER results for Q96FV9-D2

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

Input Sequence in FASTA format

>Q96FV9 (83 residues)
TASTPFVLLGDVLDCLPLDQCDTIFTFVEKNVATWKSNTFYSAGKNYLLRMCNDLLRRLS
KSQNTVFCGRIQLFLARLFPLSE

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| TASTPFVLLGDVLDCLPLDQCDTIFTFVEKNVATWKSNTFYSAGKNYLLRMCNDLLRRLSKSQNTVFCGRIQLFLARLFPLSE
Prediction	CCCHHHHHHHHHHHCCCHHHHHHHHHHHHHCHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCC
Confidence	99605789999982354999999999998114664122334467623489999999985014573133489999997478989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| TASTPFVLLGDVLDCLPLDQCDTIFTFVEKNVATWKSNTFYSAGKNYLLRMCNDLLRRLSKSQNTVFCGRIQLFLARLFPLSE
Prediction	85523131113124233163045005203532542456334676432003202410442364532301120123114314478
	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

                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHCCCHHHHHHHHHHHHHCHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCC
TASTPFVLLGDVLDCLPLDQCDTIFTFVEKNVATWKSNTFYSAGKNYLLRMCNDLLRRLSKSQNTVFCGRIQLFLARLFPLSE

6vp9B3

0.07

2.92

1.33

DEthreader

SFKSLLDQLKDVFSKCLLENLVFFVETISVILWVSSCEPVFTSFQDYVTGLQTLISNVVDHILLLEMGELLKKRLETTKK---

7apkA1

0.97

0.78

21.95

1.33

SPARKS-K

VTSTPFVLLGDVLDCLPLDQCDTIFTFVEKNV------------KNYLLRMCNDLLRRLSKSQNTVFCGRIQLFLARLF----

7apxB

0.24

7.51

3.35

HHsearch

WGNTFFELFSTIIDLLNSSTFLKFWPYAESRIEWFKMNTSVEKQPLEKLRHWNDILAKLENNKHYNMKYKLENFLSELLPINE

7apkA1

0.97

0.77

21.61

1.35

FFAS-3D

-TSTPFVLLGDVLDCLPLDQCDTIFTFVEKN------------VKNYLLRMCNDLLRRLSKSQNTVFCGRIQLFLARLF----

3j7jA

0.07

2.95

1.33

DEthreader

VERLYHDIAQQAFKFCRKAEFRKLCDNLRMHLSIQHHINLNPESQSMHLETRLVQLDSAISMELWQEAFKAVEDIHGLFSLSP

7apkA

0.92

0.78

22.00

1.08

SPARKS-K

VTSTPFVLLGDVLDCLPLDQCDTIFTFVEKNV------------KNYLLRMCNDLLRRLSKSQNTVFCGRIQLFLARLFSIPI

6ahoA

0.09

0.08

3.18

0.84

MapAlign

TQEKVIRIINQVSSDAEEDTNGALMEVLSQVISYNPPHSRK-EILQAEFHLVFTISSEDP--ANVQVVVQSQECLEKL-----

6yleC

0.10

3.58

0.62

CEthreader

ELSFLVTKILKLIRSGNDFDLWKGCHTSVVTCAYNPL--VLSTHGGQLLAAIYSRLEQKTGFYGKQLFNTLISSVAIIIDLMK

5ifeC

0.11

3.89

0.48

MUSTER

EDSVMLNGFGTVVNAL-GKRVKPYLPQICGTVLWRLNNKSAK--RQQAADLISRTAVVMKTCQEEKLMGHLGVVLYEYLGEEY

7apkA1

0.97

0.78

21.95

2.99

HHsearch

VTSTPFVLLGDVLDCLPLDQCDTIFTFVEKNV------------KNYLLRMCNDLLRRLSKSQNTVFCGRIQLFLARLF----

(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	0.7393

(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	6vp9B	0.77	2.13	0.085	0.988	model1_6vp9B.pdb.gz
2	6ux2A1	0.77	2.23	0.108	1.000	model1_6ux2A1.pdb.gz
3	7apkA1	0.77	1.03	0.955	0.795	model1_7apkA1.pdb.gz
4	5oenB	0.75	2.36	0.096	1.000	model1_5oenB.pdb.gz
5	4u1dC	0.74	2.28	0.061	0.988	model1_4u1dC.pdb.gz
6	2xheB	0.73	2.31	0.084	1.000	model1_2xheB.pdb.gz
7	7cunB	0.72	2.30	0.111	0.964	model1_7cunB.pdb.gz
8	3u0rA	0.72	2.02	0.101	0.940	model1_3u0rA.pdb.gz
9	2x68A	0.72	2.40	0.122	0.988	model1_2x68A.pdb.gz
10	3c98B	0.72	2.35	0.060	1.000	model1_3c98B.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	0.56	heterocyclic compound binding
GO:0097159	0.56	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	1.00	cellular process
GO:0006810	0.92	transport
GO:0006950	0.91	response to stress
GO:0006406	0.91	mRNA export from nucleus
GO:0008152	0.90	metabolic process
GO:0044260	0.89	cellular macromolecule metabolic process
GO:0044238	0.89	primary metabolic process
GO:0090304	0.88	nucleic acid metabolic process
GO:0065007	0.79	biological regulation
GO:0050789	0.79	regulation of biological process
GO:0033554	0.79	cellular response to stress
GO:0044699	0.76	single-organism process
GO:0044763	0.75	single-organism cellular process
GO:0010468	0.74	regulation of gene expression
GO:0010605	0.73	negative regulation of macromolecule metabolic process
GO:0051704	0.72	multi-organism process
GO:0016070	0.68	RNA metabolic process
GO:0050794	0.67	regulation of cellular process
GO:0048518	0.63	positive regulation of biological process
GO:2000112	0.62	regulation of cellular macromolecule biosynthetic process
GO:0080090	0.62	regulation of primary metabolic process
GO:0051171	0.62	regulation of nitrogen compound metabolic process
GO:0048522	0.62	positive regulation of cellular process
GO:0051173	0.61	positive regulation of nitrogen compound metabolic process
GO:0048583	0.61	regulation of response to stimulus
GO:0031328	0.61	positive regulation of cellular biosynthetic process
GO:0031324	0.61	negative regulation of cellular metabolic process
GO:0010628	0.61	positive regulation of gene expression
GO:0010557	0.61	positive regulation of macromolecule biosynthetic process
GO:0006355	0.61	regulation of transcription, DNA-templated
GO:2000002	0.60	negative regulation of DNA damage checkpoint
GO:0048297	0.60	negative regulation of isotype switching to IgA isotypes
GO:0046784	0.60	viral mRNA export from host cell nucleus
GO:0032786	0.60	positive regulation of DNA-templated transcription, elongation
GO:0031297	0.60	replication fork processing
GO:0006915	0.60	apoptotic process
GO:0006396	0.55	RNA processing

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:0000347	1.00	THO complex
GO:0043229	0.92	intracellular organelle
GO:0005634	0.91	nucleus
GO:0000445	0.56	THO complex part of transcription export complex
GO:0000346	0.55	transcription export complex
GO:0044427	0.54	chromosomal part
GO:0044421	0.54	extracellular region part
GO:0005737	0.54	cytoplasm
GO:0005654	0.54	nucleoplasm
GO:0045171	0.53	intercellular bridge
GO:0000784	0.53	nuclear chromosome, telomeric region

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	1hcuB	0.618	3.08	0.101	0.928	3.2.1.113	NA
2	0.060	3evhA	0.662	2.80	0.087	0.964	4.2.2.3	NA
3	0.060	1byeA	0.611	3.18	0.063	0.940	2.5.1.18	NA
4	0.060	2gsqA	0.619	2.58	0.095	0.892	2.5.1.18	NA
5	0.060	3cegB	0.578	3.65	0.037	0.976	6.3.2.19	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	0.02	2grmA	0.672	2.31	0.104	0.916	0.26	III	complex1.pdb.gz	6,10,13,47,50,51

	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.