D-I-TASSER Q9Y343-D1

D-I-TASSER results for Q9Y343-D1

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

Input Sequence in FASTA format

>Q9Y343 (169 residues)
MEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPS
KHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNVRHLPSLPKAESCGSFDET
ESEESSKLSHQPVLLFLRDPYVLPAASDFPNVVIEGVLHGIFYPHLQPR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNVRHLPSLPKAESCGSFDETESEESSKLSHQPVLLFLRDPYVLPAASDFPNVVIEGVLHGIFYPHLQPR
Prediction	CSSSSCCSSSSSCCCCCCSSSSSSSSSSCCSSSSSSSSHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCSCCCSCCCCCCCC
Confidence	9689673489856898648999999998994999997578999999999985789999987677889899999999999999999754332148999748811112454211223444445555554101654455789875888753125553142032217899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNVRHLPSLPKAESCGSFDETESEESSKLSHQPVLLFLRDPYVLPAASDFPNVVIEGVLHGIFYPHLQPR
Prediction	6704045243446856431000102032774413021113102401530374153251453314433562145015102500441144464135202610517414534645425444534574434244322232444232424544024011411021013254458
	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 DeepPotential. 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                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSCCSSSSSCCCCCCSSSSSSSSSSCCSSSSSSSSHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCSCCCSCCCCCCCC
MEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNVRHLPSLPKAESCGSFDETESEESSKLSHQPVLLFLRDPYVLPAASDFPNVVIEGVLHGIFYPHLQPR

2dybA

0.20

0.16

5.11

1.00

DEthreader

ISANIADIEEKRG-F-TSHFVFVIEVKTGGSKYLIYRRYRQFHALQSKLEERFTLPTLPAKYVGVKQE-IAEMRIPALNAYMKSLLSLPVWLDEDVRIFFYQ---------SPYDEDLSSTPLLKDLL-LNYRDAEGDL-----------------M-RQARGLPW---

4az9A

1.00

0.60

16.90

2.21

SPARKS-K

MEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNV-------------------------------------------------------------------

6h7wB

0.16

5.31

1.05

MapAlign

FHITVGDPHKVG-DLATSHIVYSVRTTYKQPEFEVKRRYRDFLWLYNTLHSNNVVPPPPEKQVGRFESNFVESRRAALEKMLNKIAAHPTLQDADLKLFLESAEAAADFSASLHALSTVELSPTLSGPLDALSELQLAIRDVYERQAQQDVLTFGIIIEEYIRLIGSVK

6h7wB

0.16

5.31

0.85

CEthreader

FHITVGDPHKV-GDLATSHIVYSVRTKTTQPEFEVKRRYRDFLWLYNTLHSNNVVPPPPEKQAGRFESNFVESRRAALEKMLNKIAAHPTLQDADLKLFLESESFNIDVKHKERKENKFVEQDDWFHDRRVYLDALMDNMVAQRKAMAEAAADFSASLHALSTVELSPT

4az9A

1.00

0.60

16.90

1.73

MUSTER

MEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNV-------------------------------------------------------------------

2ettA

0.49

0.33

9.62

1.95

HHsearch

PSVGPEAEGPRQSP-EKSHMVFRVEVLCSGRRHTVPRRYSEFHALHKRIKKLYKVPDFPSKRLPNWRTRGLEQRRQGLEAYIQGILYLNQEVPKELLEFLRLRHFPTDPKASNWG------------------------------------------------------

4az9A

1.00

0.60

16.90

1.92

FFAS-3D

MEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNV-------------------------------------------------------------------

5gw0A

0.16

0.15

5.12

1.07

EigenThreader

PSTPTILGYEV--EERAKFTVYKILVKKTPESWVVFRRYTDFSRLNDKLKEFPGFRLALRWFKDNYNADFLEDRQLGLQAFLQNLVAHDIANCLAVREFLCLDDPPGPFDSLEESRAFCET--LEETNYRLQKELLEKQKEESLKKLLSEKQLHIDTLENRIRTLSLE-

4az9A

1.00

0.60

16.90

1.50

CNFpred

MEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNV-------------------------------------------------------------------

5gw0A

0.24

0.17

5.18

1.00

DEthreader

STPTILGYEV-E-E-RAKFTVYKILVKKTEESWVVFRRYTDFSRLNDKLKEFGFRLALPPKRWDNYNADFLEDRQLGLQAFLQNLVAHKDANCLAVREFLCLDDPP------EESRAFCETETNYRLQ-----------------------------------------

(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	0.6803

(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 DeepPotential, 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	5gw0A	0.62	2.48	0.222	0.710	model1_5gw0A.pdb.gz
2	2rakA2	0.60	2.28	0.144	0.692	model1_2rakA2.pdb.gz
3	2dybA	0.60	3.53	0.171	0.769	model1_2dybA.pdb.gz
4	4on3A	0.59	2.99	0.241	0.704	model1_4on3A.pdb.gz
5	1xteA	0.57	1.76	0.302	0.627	model1_1xteA.pdb.gz
6	2cskA	0.56	2.73	0.203	0.675	model1_2cskA.pdb.gz
7	3iq2A	0.56	1.97	0.181	0.621	model1_3iq2A.pdb.gz
8	1ocuA	0.56	2.03	0.267	0.621	model1_1ocuA.pdb.gz
9	2mxcA	0.55	3.19	0.216	0.686	model1_2mxcA.pdb.gz
10	3p0cA	0.53	2.00	0.300	0.592	model1_3p0cA.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:0008289	0.68	lipid binding
GO:0035091	0.67	phosphatidylinositol 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	0.91	cellular process
GO:0051179	0.85	localization
GO:0006810	0.84	transport
GO:0016192	0.78	vesicle-mediated transport
GO:0016043	0.78	cellular component organization
GO:0006996	0.75	organelle organization
GO:0065007	0.71	biological regulation
GO:0050789	0.71	regulation of biological process
GO:0044699	0.70	single-organism process
GO:0050794	0.68	regulation of cellular process
GO:0016050	0.68	vesicle organization
GO:0044763	0.64	single-organism cellular process
GO:0048518	0.58	positive regulation of biological process
GO:0007165	0.56	signal transduction
GO:0032879	0.55	regulation of localization
GO:0008152	0.54	metabolic process
GO:0071704	0.53	organic substance metabolic process
GO:0051128	0.53	regulation of cellular component organization
GO:0051049	0.53	regulation of transport
GO:0044237	0.53	cellular metabolic process
GO:0048522	0.52	positive regulation of cellular process
GO:0044238	0.52	primary metabolic process
GO:0023051	0.52	regulation of signaling
GO:0019222	0.51	regulation of metabolic process
GO:0010646	0.51	regulation of cell communication
GO:0060255	0.50	regulation of macromolecule metabolic process
GO:0009966	0.50	regulation of signal transduction

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:0044444	1.00	cytoplasmic part
GO:0043227	1.00	membrane-bounded organelle
GO:0043229	0.99	intracellular organelle
GO:0043231	0.98	intracellular membrane-bounded organelle
GO:0016020	0.93	membrane
GO:0005773	0.91	vacuole
GO:0005768	0.88	endosome
GO:0044425	0.81	membrane part
GO:0044422	0.79	organelle part
GO:0044446	0.78	intracellular organelle part
GO:0031090	0.67	organelle membrane
GO:0031982	0.63	vesicle
GO:0019898	0.62	extrinsic component of membrane
GO:0005737	0.62	cytoplasm
GO:0031410	0.56	cytoplasmic vesicle
GO:0032991	0.54	macromolecular complex
GO:0044437	0.53	vacuolar part
GO:0005774	0.51	vacuolar membrane
GO:0044440	0.50	endosomal part
GO:0043234	0.50	protein complex

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	1cc1L	0.552	4.42	0.020	0.823	1.12.99.6	25
2	0.060	2occN	0.450	4.93	0.020	0.734	1.9.3.1	NA
3	0.060	1kq3A	0.509	4.98	0.060	0.858	1.1.1.6	43
4	0.060	2qmiA	0.440	5.27	0.067	0.769	3.5.2.6	NA
5	0.060	1itwB	0.441	5.35	0.029	0.781	1.1.1.42	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:

No Binding sites was predicted

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

	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.