D-I-TASSER Q9Y2H2-D2

D-I-TASSER results for Q9Y2H2-D2

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

Input Sequence in FASTA format

>Q9Y2H2 (87 residues)
APRLGSRSQSLSSTDSSVHAPSEITVAHGSGLGKGQESPLKKSPSAGDVHILTGFAKPMD
IYCHRFVQDAQNKVTHLSETRSVSQQA

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| APRLGSRSQSLSSTDSSVHAPSEITVAHGSGLGKGQESPLKKSPSAGDVHILTGFAKPMDIYCHRFVQDAQNKVTHLSETRSVSQQA
Prediction	CCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Confidence	987676544322232245799568751467777787863346998540577743588323567888887663367623333355569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| APRLGSRSQSLSSTDSSVHAPSEITVAHGSGLGKGQESPLKKSPSAGDVHILTGFAKPMDIYCHRFVQDAQNKVTHLSETRSVSQQA
Prediction	755445444424446242534441424436535754654366444453233134244313220341154155443624545534678
	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

CCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
APRLGSRSQSLSSTDSSVHAPSEITVAHGSGLGKGQESPLKKSPSAGDVHILTGFAKPMDIYCHRFVQDAQNKVTHLSETRSVSQQA

3gd9A2

0.09

3.48

0.48

CEthreader

WNKYTGTDLIVTPFADRPDVRYTGRVSGGVRFTDGSGAVVTTFQKPDASSVFGCHRLLDAPPISRTLCAGFNRTTLLANPHQPDRSA

6agbD

0.07

2.86

0.53

EigenThreader

MDRTQTFIKDCLFTKCLEDPEKPFDKNSKIALREYINNCKKNTKKCLKLAYENKITDKEDLLHYIEEKHPMYKELWINYIKELLNIT

3bboK

0.24

0.20

6.10

0.26

FFAS-3D

GPALGSKGVNIMAFCKGFVIPVEITVFDDKGAEKGSKDPQMEKVGKITIDQLRGICTTIESAMRIIAGTAAN---------------

4btgA

0.15

5.01

0.88

SPARKS-K

TSYIGQTSAIDHMGQPSHVVVYEITAFTPVKLANNSNQRVEPGISDRMSATLAPIGNTFAV--SAFVKNRTAVYEAVSQRGTVNSNG

4areA

0.14

0.06

1.97

0.49

CNFpred

----------------------TFIIRAGDKVSEE------------KIKRLYWASREVKSQFHRVVGND-----------------

4gfhA

0.07

2.84

1.00

DEthreader

GALMGHIKLIINFLELLGFLLEFITPYNMYERSKQKYYTSVEYFNLDRHL-KILKEIP-IDFINKELILFSLADNIRSKPGQRVILL

1h3iA

0.09

3.48

0.79

MapAlign

YTYEDGGVLQGTYVDGELNGPAQEYDTDGRLIFKGQYKDNIRHGVCWIYYLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMI

5n5xA2

0.11

0.10

3.72

0.58

MUSTER

FNNADEREKESIGALVSQIKLKE------RERISRVQNLIEHENSHDEDKYLQDLGYRLSIATNELLESWQKTKDESILSGSLSHSK

4dwnA

0.28

0.09

2.82

0.75

HHsearch

----------------------------------------------------------DQTYCDRLVQDTPGRLSEQQVDRIILQLN

6hwjA1

0.03

1.93

0.48

CEthreader

LDLGEGHAVGVVRSADAARWTVPLVRDGAGGVRRSRPGDGTAEHLVAALARDFVLEAFTGAAPVTGERGIIVDESVIVGECAVVKWA

(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	0.542

(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	1zc6B2	0.47	3.92	0.082	0.816	model1_1zc6B2.pdb.gz
2	1r8iA	0.47	4.14	0.065	0.805	model1_1r8iA.pdb.gz
3	1zxoB	0.46	4.21	0.053	0.828	model1_1zxoB.pdb.gz
4	2xqoA	0.45	4.09	0.083	0.816	model1_2xqoA.pdb.gz
5	2e2oA2	0.45	4.09	0.078	0.828	model1_2e2oA2.pdb.gz
6	1zbsA2	0.44	4.29	0.079	0.828	model1_1zbsA2.pdb.gz
7	2ch5A	0.43	3.83	0.039	0.759	model1_2ch5A.pdb.gz
8	3jcrV	0.37	4.70	0.061	0.782	model1_3jcrV.pdb.gz
9	4o5fA	0.35	4.67	0.051	0.713	model1_4o5fA.pdb.gz
10	1gc5A	0.34	4.83	0.015	0.736	model1_1gc5A.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:0042803	1.00	protein homodimerization activity
GO:0016791	1.00	phosphatase activity
GO:0052866	0.81	phosphatidylinositol phosphate phosphatase activity
GO:0034596	0.80	phosphatidylinositol phosphate 4-phosphatase activity
GO:0052833	0.53	inositol monophosphate 4-phosphatase activity

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:0050794	1.00	regulation of cellular process
GO:1902532	0.86	negative regulation of intracellular signal transduction
GO:0001933	0.86	negative regulation of protein phosphorylation
GO:0006810	0.79	transport
GO:0009987	0.77	cellular process
GO:0051049	0.75	regulation of transport
GO:0044699	0.75	single-organism process
GO:0016192	0.75	vesicle-mediated transport
GO:2001135	0.74	regulation of endocytic recycling
GO:0072583	0.74	clathrin-mediated endocytosis
GO:0008152	0.72	metabolic process
GO:0071704	0.69	organic substance metabolic process
GO:0044763	0.69	single-organism cellular process
GO:0044238	0.69	primary metabolic process
GO:0044237	0.69	cellular metabolic process
GO:0044710	0.67	single-organism metabolic process
GO:0044255	0.64	cellular lipid metabolic process
GO:0048518	0.63	positive regulation of biological process
GO:0019637	0.63	organophosphate metabolic process
GO:0007165	0.63	signal transduction
GO:0006796	0.63	phosphate-containing compound metabolic process
GO:0050896	0.62	response to stimulus
GO:0048522	0.62	positive regulation of cellular process
GO:0046488	0.62	phosphatidylinositol metabolic process
GO:0051239	0.61	regulation of multicellular organismal process
GO:0035556	0.61	intracellular signal transduction
GO:0031325	0.61	positive regulation of cellular metabolic process
GO:0010604	0.61	positive regulation of macromolecule metabolic process
GO:0006950	0.61	response to stress
GO:2000026	0.60	regulation of multicellular organismal development
GO:0080135	0.60	regulation of cellular response to stress
GO:0060284	0.60	regulation of cell development
GO:0051241	0.60	negative regulation of multicellular organismal process
GO:0051129	0.60	negative regulation of cellular component organization
GO:0048015	0.60	phosphatidylinositol-mediated signaling
GO:0046856	0.60	phosphatidylinositol dephosphorylation
GO:0046434	0.60	organophosphate catabolic process
GO:0044242	0.60	cellular lipid catabolic process
GO:0031344	0.60	regulation of cell projection organization
GO:0023056	0.60	positive regulation of signaling
GO:0003008	0.60	system process
GO:2000145	0.59	regulation of cell motility
GO:0048681	0.59	negative regulation of axon regeneration
GO:0042518	0.59	negative regulation of tyrosine phosphorylation of Stat3 protein
GO:0031161	0.59	phosphatidylinositol catabolic process
GO:0014898	0.59	cardiac muscle hypertrophy in response to stress
GO:0001921	0.59	positive regulation of receptor recycling
GO:0051896	0.51	regulation of protein kinase B signaling

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:0055037	1.00	recycling endosome
GO:0045334	1.00	clathrin-coated endocytic vesicle
GO:0005769	1.00	early endosome
GO:0016020	0.87	membrane
GO:0044425	0.83	membrane part
GO:0005905	0.81	clathrin-coated pit
GO:0044422	0.63	organelle part
GO:0044446	0.62	intracellular organelle part
GO:0098588	0.54	bounding membrane of organelle
GO:0098805	0.52	whole membrane
GO:0005774	0.51	vacuolar membrane
GO:0010008	0.50	endosome membrane

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	1ea0A	0.421	4.36	0.038	0.816	1.4.1.13	NA
2	0.060	1wl4A	0.420	4.44	0.114	0.851	2.3.1.9	NA
3	0.060	2v2fF	0.406	4.35	0.064	0.793	3.4.16.4	62
4	0.060	1uj6A	0.408	4.11	0.114	0.782	5.3.1.6	NA
5	0.060	1xtzA	0.425	4.16	0.069	0.816	5.3.1.6	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	0.01	1txtB	0.430	4.56	0.074	0.839	0.10	CAA	complex1.pdb.gz	26,31,32
2	0.01	2ch6C	0.428	3.95	0.026	0.770	0.26	GLC	complex2.pdb.gz	24,69,76
3	0.01	1txtA	0.429	4.56	0.074	0.839	0.12	CAA	complex3.pdb.gz	5,26,31,32,43
4	0.01	1ofdA	0.433	4.46	0.050	0.828	0.22	F3S	complex4.pdb.gz	63,68,70

	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.