D-I-TASSER Q13099-D3

D-I-TASSER results for Q13099-D3

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

Input Sequence in FASTA format

>Q13099 (56 residues)
YVELANDLEINKAVTYLRQKDYNQAVEILKVLEKKDSRVKSAAATNLSALYYMGKD

Predicted Secondary Structure

Sequence	20 40 \| \| YVELANDLEINKAVTYLRQKDYNQAVEILKVLEKKDSRVKSAAATNLSALYYMGKD
Prediction	CHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	66888999999999999837889999999999865299999999999999998279
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| YVELANDLEINKAVTYLRQKDYNQAVEILKVLEKKDSRVKSAAATNLSALYYMGKD
Prediction	65623551314302420455526402520441454355243411322111232568
	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

                   |                   |

SS
Seq

CHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
YVELANDLEINKAVTYLRQKDYNQAVEILKVLEKKDSRVKSAAATNLSALYYMGKD

1hz4A

0.04

1.96

1.50

DEthreader

WFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMVWHYALWSLIQQSEILFAQGS

1elrA1

0.19

0.18

5.77

1.38

SPARKS-K

--GKQALKEKELGNDAYKKKDFDTALKHYDKAKELDPT-NMTYITNQAAVYFEKGD

6t3hA

0.07

2.93

1.50

DEthreader

WNLEAIQCSLVVGINLYDMGRLDDADAYFRDALTAYDKPITKIYHNLGLVHWQKGS

6aitA3

0.18

5.80

1.37

SPARKS-K

DLRTNPVLQLNLANAYLQGGQPQEAANILNRYTFNNKD-DSNGWDLLAQAEAALNN

3qkyA

0.12

4.38

0.61

MapAlign

LRAKLARKQYEAARLYERRELYEAAAVTYEAVFDAYPPWADDALVGAMRAYIAYAE

3qkyA

0.12

4.38

0.36

CEthreader

LRAKLARKQYEAARLYERRELYEAAAVTYEAVFDAYPPWADDALVGAMRAYIAYAE

2xpiA

0.16

5.32

0.73

MUSTER

NEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLSTN-DANVHTAIALVYLHKKI

5o09C

0.16

5.34

0.49

HHsearch

QSARVASVYSLLAHLYDRWGRMDKAAEFYELALKIESDKVATIKNNLAMIFKQLRK

6aitA3

0.20

0.18

5.71

0.77

FFAS-3D

-----PVLQLNLANAYLQGGQPQEAANILNRYTFNNKD-DSNGWDLLAQAEAALNN

3nmwA3

0.12

4.38

0.37

EigenThreader

GDVANKATLCSALVAQLKSESQQVIASVLRNLSWADVNSKKTLREVALECALEVKK

(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	0.8181

(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	6t3hA	0.90	1.30	0.071	1.000	model1_6t3hA.pdb.gz
2	1hz4A	0.89	0.96	0.036	1.000	model1_1hz4A.pdb.gz
3	5b3gA1	0.89	0.95	0.089	1.000	model1_5b3gA1.pdb.gz
4	6xt4A	0.87	1.05	0.107	1.000	model1_6xt4A.pdb.gz
5	3ulqA2	0.87	1.30	0.125	1.000	model1_3ulqA2.pdb.gz
6	3q15A4	0.87	0.94	0.196	0.982	model1_3q15A4.pdb.gz
7	4gpkA	0.84	1.50	0.161	1.000	model1_4gpkA.pdb.gz
8	2if4A	0.82	1.57	0.130	0.964	model1_2if4A.pdb.gz
9	3sf4A	0.81	1.28	0.143	0.982	model1_3sf4A.pdb.gz
10	4gyoA3	0.79	1.77	0.054	1.000	model1_4gyoA3.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:0097159	0.41	organic cyclic compound binding
GO:1901363	0.40	heterocyclic compound binding
GO:0008092	0.39	cytoskeletal protein binding
GO:0019894	0.36	kinesin binding
GO:0036094	0.34	small molecule binding
GO:0032555	0.33	purine ribonucleotide binding
GO:0032550	0.33	purine ribonucleoside binding
GO:0035639	0.32	purine ribonucleoside triphosphate 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:0044767	1.00	single-organism developmental process
GO:0030030	1.00	cell projection organization
GO:0060271	0.89	cilium morphogenesis
GO:0065007	0.88	biological regulation
GO:1902589	0.87	single-organism organelle organization
GO:0042384	0.86	cilium assembly
GO:0050789	0.83	regulation of biological process
GO:0051179	0.82	localization
GO:0050794	0.82	regulation of cellular process
GO:0007017	0.82	microtubule-based process
GO:0008104	0.81	protein localization
GO:0035058	0.80	nonmotile primary cilium assembly
GO:0032501	0.77	multicellular organismal process
GO:0006928	0.72	movement of cell or subcellular component
GO:0007018	0.71	microtubule-based movement
GO:0006810	0.71	transport
GO:1902580	0.70	single-organism cellular localization
GO:0046907	0.70	intracellular transport
GO:0044765	0.70	single-organism transport
GO:0015031	0.70	protein transport
GO:0010970	0.70	establishment of localization by movement along microtubule
GO:0098840	0.69	protein transport along microtubule
GO:0042073	0.69	intraciliary transport
GO:0048518	0.66	positive regulation of biological process
GO:0048856	0.65	anatomical structure development
GO:0048522	0.65	positive regulation of cellular process
GO:0044707	0.65	single-multicellular organism process
GO:0050896	0.64	response to stimulus
GO:0009967	0.63	positive regulation of signal transduction
GO:0007368	0.63	determination of left/right symmetry
GO:0000226	0.63	microtubule cytoskeleton organization
GO:0060122	0.62	inner ear receptor stereocilium organization
GO:0048598	0.62	embryonic morphogenesis
GO:0009888	0.62	tissue development
GO:0008589	0.62	regulation of smoothened signaling pathway
GO:0022402	0.53	cell cycle process
GO:1903047	0.52	mitotic cell cycle process
GO:0051716	0.52	cellular response to stimulus
GO:0051640	0.52	organelle localization
GO:0045494	0.52	photoreceptor cell maintenance
GO:0003341	0.52	cilium movement
GO:0072019	0.51	proximal convoluted tubule development
GO:0071482	0.51	cellular response to light stimulus
GO:0060785	0.51	regulation of apoptosis involved in tissue homeostasis
GO:0045880	0.51	positive regulation of smoothened signaling pathway
GO:0042462	0.51	eye photoreceptor cell development
GO:0007369	0.51	gastrulation
GO:0003351	0.51	epithelial cilium movement
GO:0000132	0.51	establishment of mitotic spindle orientation

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:0043226	0.93	organelle
GO:0005929	0.92	cilium
GO:0044424	0.91	intracellular part
GO:0044422	0.86	organelle part
GO:0044446	0.85	intracellular organelle part
GO:0044430	0.76	cytoskeletal part
GO:0044441	0.72	ciliary part
GO:0036064	0.70	ciliary basal body
GO:0005930	0.55	axoneme

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	0.066	1wcrA	0.661	2.37	0.073	0.982	2.7.1.69	NA
2	0.066	1r1bA	0.549	2.15	0.087	0.786	6.1.1.15 6.1.1.17	NA
3	0.066	1fyjA	0.547	1.91	0.067	0.714	6.1.1.15 6.1.1.17	NA
4	0.060	1ihgA	0.806	1.72	0.164	0.982	5.2.1.8	NA
5	0.060	1w3bB	0.777	1.80	0.145	0.946	2.4.1.-	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:

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, 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.