D-I-TASSER Q5VZ19-D3

D-I-TASSER results for Q5VZ19-D3

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

Input Sequence in FASTA format

>Q5VZ19 (152 residues)
VTEALHQNMQALFSTLAQAEEQQPYLEGSTVMRGTRCLAEYHLGDYGHAWNRCWVLDRVD
TWAVVMFIDFGQLATIPVQSLRSLDSDDFWTIPPLTQPFMLEKDILSSYEVVHRILKGKI
TGALNSAVTAPASNLAVVPPLLPLGCLQQAAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VTEALHQNMQALFSTLAQAEEQQPYLEGSTVMRGTRCLAEYHLGDYGHAWNRCWVLDRVDTWAVVMFIDFGQLATIPVQSLRSLDSDDFWTIPPLTQPFMLEKDILSSYEVVHRILKGKITGALNSAVTAPASNLAVVPPLLPLGCLQQAAA
Prediction	CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCSSSCCCCCCCCCSSSSSSSSSCCCSSSSSSSSCCCCCCCCHHHHHHCCCCCCCCCCCCCCCSSSCCCCCCCHHHHHHHHHCHSSCSSCCCCCCCCCCCSSCCCCCCHHHHHHHCC
Confidence	93589999999999999865218999825532660322542688889832689998863973899998458623112777442474000237865544242014332278999987301001111222466556331476653345555219
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VTEALHQNMQALFSTLAQAEEQQPYLEGSTVMRGTRCLAEYHLGDYGHAWNRCWVLDRVDTWAVVMFIDFGQLATIPVQSLRSLDSDDFWTIPPLTQPFMLEKDILSSYEVVHRILKGKITGALNSAVTAPASNLAVVPPLLPLGCLQQAAA
Prediction	74642353043015204415764431566304501410151325645342210002333432110100232333413253046154751141343333131454134336203421434023204441434254111122322221145358
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCSSSCCCCCCCCCSSSSSSSSSCCCSSSSSSSSCCCCCCCCHHHHHHCCCCCCCCCCCCCCCSSSCCCCCCCHHHHHHHHHCHSSCSSCCCCCCCCCCCSSCCCCCCHHHHHHHCC
VTEALHQNMQALFSTLAQAEEQQPYLEGSTVMRGTRCLAEYHLGDYGHAWNRCWVLDRVDTWAVVMFIDFGQLATIPVQSLRSLDSDDFWTIPPLTQPFMLEKDILSSYEVVHRILKGKITGALNSAVTAPASNLAVVPPLLPLGCLQQAAA

5m9nA

0.16

0.12

4.18

1.00

DEthreader

FC-QLQ-SGRKLAELQASLSKYCLPRSDFYPAIGDICCAQFS---EDDQWYRASVLAYSEESVLVGYVDYGNFEILSLMRLCPIIPK-LLELPMQAIKCVLAGVKPALMLVQIITV--KVVD---------------KLENSSLV-------

5m9nA

0.14

4.70

2.22

SPARKS-K

FFCQQLQSGRKLAELQASLSKYCDQLPPFYPAIGDICCAQFS---EDDQWYRASVLAYASESVLVGYVDYGNFEILSLMRLCPIIP-KLLELPMQAIKCVLAGVKPSLICLMKKLVQNKIITVKVVDKLENSSLVELKSETPHVSVSKVLLD

2wacA

0.18

0.17

5.57

0.89

MapAlign

FFAQSVESGSKLESLMSKLHADFPIAGSYTPKRGDLVAAQFT---LDNQWYRAKVERVQGSNATVLYIDYGNKETLPTNRLAALP-PAFSSEKPYAEYALALVALPTDNEDKEEALKVTGSPNLATLRDPTTKVDFGKQLVAEGLVLAE---

2wacA

0.19

0.18

5.95

0.66

CEthreader

QSVESGSKLESLMSKLHADFQSNPPIASYTPKRGDLVAAQFTL---DNQWYRAKVERVQGSNATVLYIDYGNKETLPTNRLAALP-PAFSSEKPYATEYALALVALPTLRAFSEDVLNHKVQLNVELKVTGSPNLATLRDPTTKVDFGKQLV

5m9nA

0.16

0.15

5.06

1.40

MUSTER

QQLQSGRKLAELQASLSKYCDQLPPRSDFYPAIGDICCAQFSE---DDQWYRASVLAYASESVLVGYVDYGNFEILSLMRLCPII-PKLLELPMQAIKCVLAGVKPSLICLMKKLVQNKIITVKVVDKLENSSLVEIDKSETPHVSVSKVDA

4q5yA

0.14

4.69

2.30

HHsearch

FYVQMESDVPALEQMTDKLLDAEQDPAFSDLKEGALCVAQFPE---DEVFYRAQIRKVLDGKCEVHFIDFGNNAVTQ--QFRQLPE-ELAKPARYSRHCELDASTISKLQSFIDTRFSETFQVEILATKGTTHVVRLFYQSKNISEKLQECQ

5m9nA

0.17

0.16

5.41

1.59

FFAS-3D

-QLQSGRKLAELQASLSKYCDQLPPRSDFYPAIGDICCAQFSEDD---QWYRASVLAYSEESVLVGYVDYGNFEILSLMRLCPIIPK-LLELPMQAIKCVLAGVKPSLICLMKKLVQNKIITVKVVDKLENSSLVKSETPHVSVSLLDAGFA

5vqgA

0.13

0.12

4.30

1.03

EigenThreader

G-PQVAQLDDLVAHMTEYYSENREAHTLRHVSVGQVVAAVF---RHDGRWYRARVHDIRFDVADVFYLDYGDSEYVATHELCELRADLLR-LRFQAMECFLAKWHPQAVERFEELTQKALVSRTCTYKKTKDKEIPG------IKLFDVTGE

5m9nA

0.15

0.14

4.85

1.99

CNFpred

-----GRKLAELQASLSKYCDQLPPRSDFYPAIGDICCAQFS---EDDQWYRASVLAYAEESVLVGYVDYGNFEILSLMRLCPIIP-KLLELPMQAIKCVLAGVKPSAICLMKKLVQNKIITVKVVDKLENSSLVELIDKHVSVSKVLLDAG

2wacA

0.21

0.17

5.43

1.00

DEthreader

N-VESGSKLESLMSKLHADFSNPPIAGSYTPKRGDLVAAQFTL---DNQWYRAKVERVQGSNATVLYIDYGNKETLPTNRLAALPP-AFSSEKPYATEYALALVAAAFSDVHKVQL--NVELKVTGS---------PNL-------------

(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	0.7121

(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	5m9nA	0.84	2.17	0.135	0.967	model1_5m9nA.pdb.gz
2	4b9wA	0.83	2.42	0.135	0.954	model1_4b9wA.pdb.gz
3	3bdlA	0.81	2.51	0.142	0.974	model1_3bdlA.pdb.gz
4	2wacA	0.81	2.49	0.178	0.961	model1_2wacA.pdb.gz
5	5j39A	0.79	2.70	0.196	0.974	model1_5j39A.pdb.gz
6	5ygbA	0.78	2.73	0.142	0.974	model1_5ygbA.pdb.gz
7	4q5yA	0.78	2.56	0.160	0.947	model1_4q5yA.pdb.gz
8	3nthA	0.76	2.78	0.147	0.941	model1_3nthA.pdb.gz
9	2diqA	0.53	2.63	0.208	0.632	model1_2diqA.pdb.gz
10	4q5wA1	0.51	1.73	0.151	0.566	model1_4q5wA1.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:0003723	0.76	RNA binding
GO:0044822	0.74	poly(A) RNA binding
GO:0003824	0.74	catalytic activity
GO:0016787	0.61	hydrolase 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	0.91	cellular process
GO:0044699	0.86	single-organism process
GO:0044763	0.77	single-organism cellular process
GO:0065007	0.74	biological regulation
GO:0050789	0.74	regulation of biological process
GO:0071704	0.73	organic substance metabolic process
GO:0044238	0.73	primary metabolic process
GO:0044237	0.73	cellular metabolic process
GO:0043170	0.72	macromolecule metabolic process
GO:0010468	0.70	regulation of gene expression
GO:0090304	0.69	nucleic acid metabolic process
GO:0048519	0.69	negative regulation of biological process
GO:0044767	0.69	single-organism developmental process
GO:0044260	0.68	cellular macromolecule metabolic process
GO:0010605	0.66	negative regulation of macromolecule metabolic process
GO:0031047	0.65	gene silencing by RNA
GO:0044702	0.63	single organism reproductive process
GO:0016070	0.60	RNA metabolic process
GO:0051641	0.57	cellular localization
GO:0050658	0.55	RNA transport
GO:0046907	0.55	intracellular transport
GO:0048869	0.54	cellular developmental process
GO:0007276	0.52	gamete generation
GO:0016043	0.51	cellular component organization
GO:0010608	0.51	posttranscriptional regulation of gene expression
GO:0043412	0.50	macromolecule modification
GO:0007283	0.50	spermatogenesis
GO:0006996	0.50	organelle organization
GO:0003006	0.50	developmental process involved in reproduction

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	0.99	cell part
GO:0044424	0.98	intracellular part
GO:0043226	0.96	organelle
GO:0043229	0.95	intracellular organelle
GO:0032991	0.86	macromolecular complex
GO:0043227	0.84	membrane-bounded organelle
GO:0043231	0.82	intracellular membrane-bounded organelle
GO:0044444	0.79	cytoplasmic part
GO:0005634	0.74	nucleus
GO:0030529	0.73	intracellular ribonucleoprotein complex
GO:0043232	0.71	intracellular non-membrane-bounded organelle
GO:0005737	0.70	cytoplasm
GO:0035770	0.62	ribonucleoprotein granule
GO:0036464	0.57	cytoplasmic ribonucleoprotein granule
GO:0043186	0.55	P granule

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	7aatA	0.446	5.26	0.052	0.809	2.6.1.1	NA
2	0.060	3gbxA	0.365	5.30	0.079	0.651	2.1.2.1	NA
3	0.060	3h0gA	0.430	5.08	0.027	0.750	2.7.7.6	12,49,71
4	0.060	2wk7A	0.435	5.60	0.070	0.803	2.3.-.-	NA
5	0.060	1eqbB	0.430	5.55	0.034	0.803	2.1.2.1	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	0.03	3nthA	0.756	2.78	0.147	0.941	0.65	III	complex1.pdb.gz	41,51,67,70,72

	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.