D-I-TASSER Q9NYY3-D3

D-I-TASSER results for Q9NYY3-D3

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

Input Sequence in FASTA format

>Q9NYY3 (132 residues)
SVFPATDAPEQFISQVTVLKYFSHYMEENLMDGGDLPSVTDIRRPRLYLLQWLKSDKALM
MLFNDGTFQVNFYHDHTKIIICSQNEEYLLTYINEDRISTTFRLTTLLMSGCSSELKNRM
EYALNMLLQRCN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| SVFPATDAPEQFISQVTVLKYFSHYMEENLMDGGDLPSVTDIRRPRLYLLQWLKSDKALMMLFNDGTFQVNFYHDHTKIIICSQNEEYLLTYINEDRISTTFRLTTLLMSGCSSELKNRMEYALNMLLQRCN
Prediction	CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCSSSSSSCCCSSSSSSSCCSSSSSSSCCCSSSSSCCCCCCSSSSSSCCCCCSSSSSHHHHHHHCCCHHHHHHHHHHHHHHHHHHC
Confidence	914520288789999999999999999987534787766544468840257886186799997099399998378649998489986189999299977998868888709999999999999999999729
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| SVFPATDAPEQFISQVTVLKYFSHYMEENLMDGGDLPSVTDIRRPRLYLLQWLKSDKALMMLFNDGTFQVNFYHDHTKIIICSQNEEYLLTYINEDRISTTFRLTTLLMSGCSSELKNRMEYALNMLLQRCN
Prediction	752336521650532020052036104620474453445666445312033024344000010234303010353313000036454100000167463331304404734237503500410250046428
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCSSSSSSCCCSSSSSSSCCSSSSSSSCCCSSSSSCCCCCCSSSSSSCCCCCSSSSSHHHHHHHCCCHHHHHHHHHHHHHHHHHHC
SVFPATDAPEQFISQVTVLKYFSHYMEENLMDGGDLPSVTDIRRPRLYLLQWLKSDKALMMLFNDGTFQVNFYHDHTKIIICSQNEEYLLTYINEDRISTTFRLTTLLMSGCSSELKNRMEYALNMLLQRCN

6mf4A

0.27

0.21

6.51

1.00

DEthreader

---------VIKS--------WVDY---------LSTEDADEYHKDVFLRRYTRYKPFVMFELSDGTFQFNFK-DHHKMAISDG--GKLVTYISPSHESTTYPLVEVLKYGEPSNFREKLTLIKEGLKQKST

3fvhA

0.33

9.78

2.23

SPARKS-K

SYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMA--AVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLS

3fvhA

0.33

0.32

9.55

0.95

MapAlign

--LTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDELAPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPL--MAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLL-

4rs6A

1.00

0.98

27.36

0.92

CEthreader

SVFPATDAPEQFISQVTVLKYFSHYMEENLMDGGDLPSVTDIRRPRLYLLQWLKSDKALMMLFNDGTFQVNFYHDHTKIIICSQNEEYLLTYINEDRISTTFRLTTLLMSGCSSELKNRMEYALNMLLQ---

4rs6A

1.00

0.98

27.36

1.96

MUSTER

SVFPATDAPEQFISQVTVLKYFSHYMEENLMDGGDLPSVTDIRRPRLYLLQWLKSDKALMMLFNDGTFQVNFYHDHTKIIICSQNEEYLLTYINEDRISTTFRLTTLLMSGCSSELKNRMEYALNMLLQ---

3fvhA

0.34

0.33

9.98

4.00

HHsearch

SYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITEGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMA--AVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLS

4rs6A

1.00

0.97

27.15

1.99

FFAS-3D

-VFPATDAPEQFISQVTVLKYFSHYMEENLMDGGDLPSVTDIRRPRLYLLQWLKSDKALMMLFNDGTFQVNFYHDHTKIIICSQNEEYLLTYINEDRISTTFRLTTLLMSGCSSELKNRMEYALNMLLQ---

3fvhA

0.32

0.31

9.37

1.17

EigenThreader

TYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDELARLLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLM--AAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLS

4rs6A

1.00

0.98

27.36

2.01

CNFpred

SVFPATDAPEQFISQVTVLKYFSHYMEENLMDGGDLPSVTDIRRPRLYLLQWLKSDKALMMLFNDGTFQVNFYHDHTKIIICSQNEEYLLTYINEDRISTTFRLTTLLMSGCSSELKNRMEYALNMLLQ---

3fvhA

0.30

0.24

7.36

1.00

DEthreader

----Y------FNDST---L--YF--YM-EH-LLKAA-PE--EARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLM--AAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLS

(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	0.7406

(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	3fvhA	0.92	1.23	0.331	0.985	model1_3fvhA.pdb.gz
2	4rs6A	0.92	1.23	1.000	0.977	model1_4rs6A.pdb.gz
3	6mf4A	0.76	2.16	0.264	0.871	model1_6mf4A.pdb.gz
4	6jp4A	0.60	4.25	0.062	0.970	model1_6jp4A.pdb.gz
5	3a0oA	0.59	3.90	0.041	0.864	model1_3a0oA.pdb.gz
6	4n7vA	0.59	2.55	0.143	0.697	model1_4n7vA.pdb.gz
7	2futA	0.58	4.57	0.123	0.955	model1_2futA.pdb.gz
8	4mmhA	0.58	4.00	0.048	0.856	model1_4mmhA.pdb.gz
9	4fnvA2	0.56	4.23	0.089	0.864	model1_4fnvA2.pdb.gz
10	5jmdA	0.53	4.62	0.056	0.901	model1_5jmdA.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:0016301	0.97	kinase activity
GO:0004672	0.94	protein kinase activity
GO:0004674	0.91	protein serine/threonine kinase 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:0009987	0.99	cellular process
GO:0050794	0.93	regulation of cellular process
GO:0044699	0.93	single-organism process
GO:0022402	0.87	cell cycle process
GO:1903047	0.85	mitotic cell cycle process
GO:0051726	0.82	regulation of cell cycle
GO:0048522	0.81	positive regulation of cellular process
GO:0010564	0.79	regulation of cell cycle process
GO:0048523	0.76	negative regulation of cellular process
GO:0071704	0.75	organic substance metabolic process
GO:0044238	0.75	primary metabolic process
GO:0044237	0.75	cellular metabolic process
GO:0000075	0.75	cell cycle checkpoint
GO:0044260	0.74	cellular macromolecule metabolic process
GO:0007346	0.74	regulation of mitotic cell cycle
GO:0044772	0.72	mitotic cell cycle phase transition
GO:0006796	0.72	phosphate-containing compound metabolic process
GO:0006464	0.72	cellular protein modification process
GO:0006468	0.71	protein phosphorylation
GO:0043066	0.70	negative regulation of apoptotic process
GO:0044763	0.68	single-organism cellular process
GO:0051128	0.67	regulation of cellular component organization
GO:0019222	0.67	regulation of metabolic process
GO:0007093	0.67	mitotic cell cycle checkpoint
GO:0080090	0.66	regulation of primary metabolic process
GO:0060255	0.66	regulation of macromolecule metabolic process
GO:0010604	0.64	positive regulation of macromolecule metabolic process
GO:0033043	0.63	regulation of organelle organization
GO:0051246	0.62	regulation of protein metabolic process
GO:0007165	0.62	signal transduction
GO:0051247	0.60	positive regulation of protein metabolic process
GO:0035556	0.58	intracellular signal transduction
GO:0045732	0.57	positive regulation of protein catabolic process
GO:0065008	0.53	regulation of biological quality
GO:0050896	0.53	response to stimulus
GO:0023051	0.53	regulation of signaling
GO:0010646	0.53	regulation of cell communication
GO:0016043	0.52	cellular component organization
GO:0000082	0.52	G1/S transition of mitotic cell cycle
GO:0051716	0.51	cellular response to stimulus
GO:0006950	0.51	response to stress
GO:0044087	0.50	regulation of cellular component biogenesis
GO:0033554	0.50	cellular response to stress

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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0043229	0.96	intracellular organelle
GO:0044446	0.94	intracellular organelle part
GO:0044430	0.90	cytoskeletal part
GO:0043232	0.87	intracellular non-membrane-bounded organelle
GO:0005815	0.87	microtubule organizing center
GO:0005813	0.82	centrosome
GO:0044444	0.73	cytoplasmic part
GO:0005737	0.62	cytoplasm
GO:0043231	0.56	intracellular membrane-bounded organelle
GO:0005634	0.53	nucleus

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	3elqB	0.485	4.88	0.033	0.841	2.8.2.22	NA
2	0.060	1i8qA	0.529	4.40	0.064	0.826	4.2.2.1	NA
3	0.060	1f1sA	0.517	4.38	0.049	0.833	4.2.2.1	NA
4	0.060	2w00B	0.501	5.14	0.086	0.924	3.1.21.3	NA
5	0.060	1hdhA	0.531	4.68	0.049	0.864	3.1.6.1	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	0.01	3kllA	0.509	4.48	0.071	0.833	0.21	MAL	complex1.pdb.gz	65,66,67

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.