D-I-TASSER Q5VTT5-D7

D-I-TASSER results for Q5VTT5-D7

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

Input Sequence in FASTA format

>Q5VTT5 (76 residues)
FSKVKYYNVEYMKTTWFHKDKRLESGDRIRTGTTLDEIWLHILDPKDSDKGKYTLEIAAG
KEVRQLSTDLSGQAFE

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| FSKVKYYNVEYMKTTWFHKDKRLESGDRIRTGTTLDEIWLHILDPKDSDKGKYTLEIAAGKEVRQLSTDLSGQAFE
Prediction	CCSSSSSCCCCSSSSSSSCCCCCCCCCCSSSCCCCCCSSSSSCCCCCCCCCSSSSSSSCCCCCSSSSSSCCCCCCC
Confidence	9535553013326798736631365552541688110899861688444833999998189844888872233269
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| FSKVKYYNVEYMKTTWFHKDKRLESGDRIRTGTTLDEIWLHILDPKDSDKGKYTLEIAAGKEVRQLSTDLSGQAFE
Prediction	7340432336414130335764144554244344443020302514775424120301347743433241445438
	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

                   |                   |                   |

SS
Seq

CCSSSSSCCCCSSSSSSSCCCCCCCCCCSSSCCCCCCSSSSSCCCCCCCCCSSSSSSSCCCCCSSSSSSCCCCCCC
FSKVKYYNVEYMKTTWFHKDKRLESGDRIRTGTTLDEIWLHILDPKDSDKGKYTLEIAAGKEVRQLSTDLSGQAFE

3bx7C

0.09

3.47

1.33

DEthreader

VCEYSPGKATEVRVTVLRQVTEVCLDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYYLGIGGTQIYVIDP-

2r15A1

0.44

0.43

12.71

1.36

SPARKS-K

YSFVT-YYVEDLKVNWSHNGSAIRYSDRVKTGVTGEQIWLQINEPTPNDKGKYVMELFDGKTGHQKTVDLSGQAYD

7kbmA

0.12

4.17

0.58

MapAlign

SCAASSLSTSGIGVTWVRQLEWLSVKGRFTISADKNTAYLQMNSLCAEDTAVYYCAQSATSAMDWGGTLVTVSS--

2nziA2

0.14

0.13

4.51

0.38

CEthreader

SIKIPFSGKPDPVITWQKGQDLIDNNGHYQVIVTRSFTSLVFPNVERKDAGFYVVCAKNRFGIDQKTVELDVA---

2r15A1

0.45

13.07

1.09

MUSTER

YSFVTYY-VEDLKVNWSHNGSAIRYSDRVKTGVTGEQIWLQINEPTPNDKGKYVMELFDGKTGHQKTVDLSGQAYD

2r15A1

0.45

13.07

0.93

HHsearch

YSFVTYY-VEDLKVNWSHNGSAIRYSDRVKTGVTGEQIWLQINEPTPNDKGKYVMELFDGKTGHQKTVDLSGQAYD

2r15A1

0.45

13.07

1.45

FFAS-3D

YSFVTYY-VEDLKVNWSHNGSAIRYSDRVKTGVTGEQIWLQINEPTPNDKGKYVMELFDGKTGHQKTVDLSGQAYD

2ednA

0.18

5.97

0.38

EigenThreader

VAKVNGKELDKPTIKWFKGWLELGSARFSFKESASNVYTVEIGKVVLGDRGYYRLEVKAKDTCDSCGFNIDVEAPR

2rjmA

0.20

6.33

1.14

CNFpred

TFKCHVTGTAPIKITWAKDNREIRPGGNYKMTLVENTATLTVLKVTKGDAGQYTCYASNVAGKDSCSAQLGVQAPP

1dqtA

0.12

4.18

1.17

DEthreader

PCEYSSHNTDEVRVTVLRQMTEVCFYPFCSGTFNESRVNLTIQGLRAVDTGLYLCKVELMYFVGMGGTQIYVIDP-

(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	0.7227

(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	3pucA	0.85	1.51	0.203	0.974	model1_3pucA.pdb.gz
2	1g1cA	0.85	1.71	0.173	0.987	model1_1g1cA.pdb.gz
3	3b43A6	0.84	1.71	0.160	0.987	model1_3b43A6.pdb.gz
4	1tlkA	0.83	1.67	0.147	0.974	model1_1tlkA.pdb.gz
5	2kkqA	0.83	1.72	0.211	0.987	model1_2kkqA.pdb.gz
6	2wwkO	0.82	1.57	0.118	0.974	model1_2wwkO.pdb.gz
7	4c4kO	0.82	1.48	0.178	0.961	model1_4c4kO.pdb.gz
8	3qp3A	0.82	1.76	0.189	0.974	model1_3qp3A.pdb.gz
9	6ygnA	0.82	1.77	0.145	0.974	model1_6ygnA.pdb.gz
10	2bk8A	0.81	1.51	0.145	0.961	model1_2bk8A.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:0005198	0.65	structural molecule activity
GO:0042803	0.52	protein homodimerization 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:0044699	0.87	single-organism process
GO:0009987	0.87	cellular process
GO:0044763	0.81	single-organism cellular process
GO:0065007	0.79	biological regulation
GO:0032501	0.79	multicellular organismal process
GO:0050789	0.77	regulation of biological process
GO:0016043	0.76	cellular component organization
GO:0003008	0.76	system process
GO:0050794	0.74	regulation of cellular process
GO:0006936	0.74	muscle contraction
GO:0006996	0.72	organelle organization
GO:1902589	0.71	single-organism organelle organization
GO:0032502	0.66	developmental process
GO:0044767	0.64	single-organism developmental process
GO:0030029	0.64	actin filament-based process
GO:0031032	0.63	actomyosin structure organization
GO:0008152	0.63	metabolic process
GO:0045214	0.62	sarcomere organization
GO:0048856	0.61	anatomical structure development
GO:0071704	0.60	organic substance metabolic process
GO:0044237	0.58	cellular metabolic process
GO:0048869	0.57	cellular developmental process
GO:0044238	0.57	primary metabolic process
GO:0043170	0.57	macromolecule metabolic process
GO:0044260	0.56	cellular macromolecule metabolic process
GO:0048646	0.55	anatomical structure formation involved in morphogenesis
GO:0009653	0.55	anatomical structure morphogenesis
GO:0006464	0.54	cellular protein modification process
GO:0055002	0.52	striated muscle cell development
GO:0048583	0.52	regulation of response to stimulus
GO:0010927	0.52	cellular component assembly involved in morphogenesis
GO:0007015	0.52	actin filament organization
GO:0006468	0.52	protein phosphorylation
GO:0080090	0.51	regulation of primary metabolic process
GO:0071822	0.51	protein complex subunit organization
GO:0055013	0.51	cardiac muscle cell development
GO:0055008	0.51	cardiac muscle tissue morphogenesis
GO:0048747	0.51	muscle fiber development
GO:0031323	0.51	regulation of cellular metabolic process
GO:0030239	0.51	myofibril assembly
GO:0007165	0.51	signal transduction
GO:0006928	0.51	movement of cell or subcellular component
GO:0071688	0.50	striated muscle myosin thick filament assembly
GO:0051179	0.50	localization
GO:0050896	0.50	response to stimulus
GO:0048739	0.50	cardiac muscle fiber development
GO:0006941	0.50	striated muscle contraction

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:0044422	0.92	organelle part
GO:0044449	0.91	contractile fiber part
GO:0031430	0.90	M band
GO:0043226	0.66	organelle
GO:0043229	0.63	intracellular organelle
GO:0043227	0.57	membrane-bounded organelle
GO:0043231	0.54	intracellular membrane-bounded organelle

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	0.228	2bk8A	0.812	1.51	0.145	0.961	2.7.11.1	15,38
2	0.171	2edwA	0.749	1.87	0.186	0.908	2.7.11.1	23,49,67
3	0.103	1u2hA	0.782	1.78	0.162	0.974	2.7.11.1	65
4	0.074	2cknA	0.695	2.00	0.118	0.895	2.7.10.1	NA
5	0.067	2gqhA	0.706	2.03	0.174	0.895	2.7.11.1	23,67

	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	0.04	3sdcC	0.750	2.23	0.160	0.974	0.68	3GB	complex1.pdb.gz	7,13,59,60
	2	0.03	1p6a1	0.794	2.28	0.118	1.000	0.42	III	complex2.pdb.gz	11,13,15,56,58,59,60,61

	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.