D-I-TASSER Q5VT52-D3

D-I-TASSER results for Q5VT52-D3

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

Input Sequence in FASTA format

>Q5VT52 (103 residues)
EVKVVANAYKTFANRVNNLKKKLDQLKSTLPDPEESPVPSPSMDAPSPTGSESPFQGMGG
EESQSPTMESEKSATPEPVTDNRDVEDMELSDVEDDGSKIIVE

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| EVKVVANAYKTFANRVNNLKKKLDQLKSTLPDPEESPVPSPSMDAPSPTGSESPFQGMGGEESQSPTMESEKSATPEPVTDNRDVEDMELSDVEDDGSKIIVE
Prediction	CSSSSHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCC
Confidence	9177524667789999999999998740188977899999888899999998633467777889976566678999999897303432476445667761139
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| EVKVVANAYKTFANRVNNLKKKLDQLKSTLPDPEESPVPSPSMDAPSPTGSESPFQGMGGEESQSPTMESEKSATPEPVTDNRDVEDMELSDVEDDGSKIIVE
Prediction	8343224115413530541354156236514637644144363624446447653543577645546456554657656544442452615545674452338
	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

                   |                   |                   |                   |                   |

SS
Seq

CSSSSHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCC
EVKVVANAYKTFANRVNNLKKKLDQLKSTLPDPEESPVPSPSMDAPSPTGSESPFQGMGGEESQSPTMESEKSATPEPVTDNRDVEDMELSDVEDDGSKIIVE

2dkjA

0.11

3.88

0.57

CEthreader

KVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGAAYLVVDMAHVVTSTTHKTLRGPRGGLVIAGKAVAFFEALQPEFKEYSRLVVENAIVTGGTDNHLFLVD

5mqfK

0.06

2.57

0.62

EigenThreader

WQECVNNSMAQLEHQAVRIENLEHMIEHAQKELQKLRKHIQDLNWQRKNMQLTAGSKLREMESNWVSLVSKNYEIERTIVQLENEIYQIKQQHGEANKENIRQ

1vs7J

0.10

3.56

0.41

FFAS-3D

RIRIRLKAFDH--RLIDQATAEIVETAKRTGAQVRGPIPLPTRKE-RFTVLISPHVNKDARDQYEIRT---HLRLVDIVEPTEKTVDALMRLDLAAGVDVQIS

2p7nA2

0.09

0.08

3.00

0.88

SPARKS-K

--------ANWIKLNVDALKAALEKLKKDFSLGDNLDNKKAVLFPAQSKDGGIQGGSPDAPPPGFSCVQKAADGNVDTPID--TIRDVGALGSGTLELDNAKF

4ecgA

0.19

0.05

1.56

0.44

CNFpred

---VALPTYKDMLTKMTAYKNAVDKFIAS--------------------------------------------------------------------------

6r9tA

0.08

0.07

2.71

0.83

DEthreader

QEALEEAVQMMTEAVEDLTTTLNEAASAAGVELQCSPD-YTKKELECREKVSHAAQNRGTQACITAALGDLSSAVMHRQNLELDHQLTGHK------------

6zydE

0.13

4.40

0.89

MapAlign

-LSGLLTFGGIGGLAVGMAGKDILSNFFSGIMLYFDRPFSIGDWIRSPDRNIEGTVAEIGWRITKITTFDNRPLYNHPAIDQRQTLLVYFNQFADSSLNIMVY

2ajqA

0.13

4.37

0.73

MUSTER

DTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTR----EYVAGAPYTPVEHVV

2pffB

0.21

0.19

6.17

0.45

HHsearch

LVTAVAISWESFFVSVRKAITVLFFIGVRCY--EAYPNTSLPEGVPSPMLSISTQEQVVNGAKNLPQLTLRKAQSRKLKFSNRFLPVA-----SPFHSHLLVP

1n2lA

0.13

4.41

0.48

CEthreader

GRGPFGDSLMELDAAVGTLMTAIGDLGLLETMRMSRGGCSGLLRCGKGTTYEGGVREPAHELASSLDLLPTLAALAGAPLPNVTLDGFDLSPLLLGTGKSPRQ

(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	0.4409

(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	3p5pA2	0.52	3.67	0.071	0.806	model1_3p5pA2.pdb.gz
2	3n0fA2	0.52	4.01	0.033	0.835	model1_3n0fA2.pdb.gz
3	3saeA	0.51	4.24	0.080	0.845	model1_3saeA.pdb.gz
4	2zq5A	0.51	3.55	0.035	0.786	model1_2zq5A.pdb.gz
5	3s9vA2	0.50	4.08	0.080	0.835	model1_3s9vA2.pdb.gz
6	2z6vA1	0.49	3.86	0.035	0.767	model1_2z6vA1.pdb.gz
7	2j5cB2	0.48	3.75	0.080	0.757	model1_2j5cB2.pdb.gz
8	2ongA2	0.46	3.95	0.067	0.738	model1_2ongA2.pdb.gz
9	1n1zA	0.46	4.33	0.066	0.786	model1_1n1zA.pdb.gz
10	1hxgA	0.46	4.46	0.033	0.786	model1_1hxgA.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:0003824	0.68	catalytic activity
GO:0046872	0.61	metal ion binding
GO:0016829	0.59	lyase activity
GO:0016838	0.58	carbon-oxygen lyase activity, acting on phosphates

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:0016070	1.00	RNA metabolic process
GO:0044271	0.59	cellular nitrogen compound biosynthetic process
GO:0009059	0.59	macromolecule biosynthetic process
GO:0032774	0.58	RNA biosynthetic process
GO:0034645	0.57	cellular macromolecule biosynthetic process
GO:0016071	0.57	mRNA metabolic process
GO:0006396	0.56	RNA processing
GO:0006351	0.56	transcription, DNA-templated
GO:0006397	0.55	mRNA processing
GO:0031124	0.51	mRNA 3'-end processing
GO:0009301	0.51	snRNA transcription
GO:0042795	0.50	snRNA transcription from RNA polymerase II promoter

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:0044428	1.00	nuclear part
GO:0032991	1.00	macromolecular complex
GO:0043234	0.75	protein complex
GO:1990234	0.72	transferase complex
GO:0044451	0.72	nucleoplasm part
GO:0061695	0.71	transferase complex, transferring phosphorus-containing groups
GO:0055029	0.70	nuclear DNA-directed RNA polymerase complex
GO:0016591	0.68	DNA-directed RNA polymerase II, holoenzyme

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	1occA	0.469	3.62	0.000	0.738	1.9.3.1	NA
2	0.060	2j5cB	0.503	4.09	0.068	0.845	4.2.3.-	NA
3	0.060	1e6yE	0.464	4.42	0.053	0.835	2.8.4.1	NA
4	0.060	2vuaA	0.321	5.36	0.011	0.699	3.4.24.69	NA
5	0.060	1ticB	0.470	4.21	0.030	0.796	3.1.1.3	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.