D-I-TASSER Q9P2V4-D2

D-I-TASSER results for Q9P2V4-D2

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

Input Sequence in FASTA format

>Q9P2V4 (95 residues)
ELHPGVASIRSLLGGTALLRCGATGVPGPEMSWRRANGRPLNGTVHQEVSSDGTSWTLLG
LPAVSHLDSGDYICQAKNFLGASETVISLIVTEPP

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| ELHPGVASIRSLLGGTALLRCGATGVPGPEMSWRRANGRPLNGTVHQEVSSDGTSWTLLGLPAVSHLDSGDYICQAKNFLGASETVISLIVTEPP
Prediction	CSSCCCCSSSSSCCCCSSSSSSSSSCCCCSSSSSSCCCSSCCCCCCSSSSSCCCCSSSSSSCCCCHHHCSSSSSSSSSCCCSSSSSSSSSSSCCC
Confidence	94627705999769429999999853898899996988517999739998569745699987778577779999999479729999999998499
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| ELHPGVASIRSLLGGTALLRCGATGVPGPEMSWRRANGRPLNGTVHQEVSSDGTSWTLLGLPAVSHLDSGDYICQAKNFLGASETVISLIVTEPP
Prediction	84546466241434561454140445351514742674531577543403544444334445504465465434404442442424045446448
	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

                   |                   |                   |                   |

SS
Seq

CSSCCCCSSSSSCCCCSSSSSSSSSCCCCSSSSSSCCCSSCCCCCCSSSSSCCCCSSSSSSCCCCHHHCSSSSSSSSSCCCSSSSSSSSSSSCCC
ELHPGVASIRSLLGGTALLRCGATGVPGPEMSWRRANGRPLNGTVHQEVSSDGTSWTLLGLPAVSHLDSGDYICQAKNFLGASETVISLIVTEPP

6efyA

0.20

6.39

1.50

DEthreader

VIQVPNQLVGAPLGTDVQIECHVEASPKSINYWIKDTGEMIVTHVQESSQSMYETKMSMIVRKFQKDDVGSYRCIAKNSLGEVDSSIRLYEIPH-

1u2hA

0.22

0.21

6.65

1.15

SPARKS-K

TFKVSLMDQSVREGQDVIMSIRVQGEPKPVVSWLRNRQPVRPDQRRFAEEAEGGL-CRLRILAAERGDAGFYTCKAVNEYGARQCEARLEVRG--

2ifgA3

0.16

5.25

1.65

FFAS-3D

-FPASVQLHTAVEMHHWCIPFSVDGQPAPSLRWLFNGSVLNETSFIFTEFLEPARHGCLRLNQPTHVNNGNYTLLAANPFGQASASIMAAFMDNP

2rikA

0.25

0.24

7.52

1.53

CNFpred

FFDLKPVSVDLALGESGTFKCHVTGTAPIKITWAKDNREIRPGGNYKMTLV--ENTATLTVLKVTKGDAGQYTCYASNVAGKDSCSAQLGVQEPP

6efyA3

0.20

6.39

1.50

DEthreader

VIQVPNQLVGAPLGTDVQIECHVEASPKSINYWIKDTGEMIVTHVQESSQSMYETKMSMIVRKFQKDDVGSYRCIAKNSLGEVDSSIRLYEIPH-

6hciA

0.17

5.53

1.14

SPARKS-K

MFKRLLANAECQEGQSVCFEIRVSGIPPPTLKWEKDGQPLSLGPNIEIIHEGLD-YYALHIRDTLPEDTGYYRVTATNTAGSTSCQAHLQVERL-

2e9wB

0.21

0.20

6.37

0.63

MapAlign

VVSVSKASYLLREGEEFTVTCTIKDVSSVYSTWKRENSQTL--QEKYNSWFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDK-

6eg0B

0.20

6.40

0.46

CEthreader

MITVQNQLIGAVEGKGVTLDCESEAYPKSINYWTRERGEIVPYSANVTEIGGYRNSMRLHINPLTQAEFGSYRCVAKNSLGDTDGTIKLYRIPHH

2kkqA

0.26

8.11

0.99

MUSTER

MFIYKPQSKKVLEGDSVKLECQISAIPPPKLFWKRNNEMVQFNTDRISLYQDNTGRVTLLIKDVNKKDAGWYTVSAVNEAGVTTCNTRLDVTARP

5xnpA

0.28

0.25

7.74

0.40

HHsearch

LITRHTHEMRVLEGQRATLRCKARGDPEPAIHWISPEGKLISNATRSLVYDNGT----LDILITTVKDTGAFTCIASNPAGEATQIVDLHI----

(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	0.9312

(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	6efyA	0.92	1.11	0.202	0.990	model1_6efyA.pdb.gz
2	6eg0B	0.92	1.24	0.200	1.000	model1_6eg0B.pdb.gz
3	6efzA3	0.89	1.12	0.220	0.958	model1_6efzA3.pdb.gz
4	2ednA	0.88	1.46	0.158	1.000	model1_2ednA.pdb.gz
5	2e9wB	0.87	1.45	0.138	0.990	model1_2e9wB.pdb.gz
6	4of8A2	0.87	1.27	0.207	0.968	model1_4of8A2.pdb.gz
7	1ya5A	0.86	1.09	0.295	0.926	model1_1ya5A.pdb.gz
8	3f8uD	0.86	1.65	0.232	1.000	model1_3f8uD.pdb.gz
9	2wwkO	0.86	1.08	0.284	0.926	model1_2wwkO.pdb.gz
10	3dmkA2	0.86	1.31	0.297	0.958	model1_3dmkA2.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:1901363	0.73	heterocyclic compound binding
GO:0097159	0.73	organic cyclic compound binding
GO:0097367	0.71	carbohydrate derivative binding
GO:0032555	0.69	purine ribonucleotide binding
GO:0042802	0.68	identical protein binding
GO:0035639	0.68	purine ribonucleoside triphosphate binding
GO:0032550	0.68	purine ribonucleoside binding
GO:0046983	0.64	protein dimerization activity
GO:0042803	0.63	protein homodimerization activity
GO:0005524	0.60	ATP binding
GO:0004872	0.54	receptor activity
GO:0019955	0.52	cytokine binding
GO:0003824	0.51	catalytic 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	0.92	single-organism process
GO:0009987	0.91	cellular process
GO:0044763	0.88	single-organism cellular process
GO:0065007	0.86	biological regulation
GO:0050789	0.85	regulation of biological process
GO:0050794	0.84	regulation of cellular process
GO:0032502	0.74	developmental process
GO:0044767	0.69	single-organism developmental process
GO:0008152	0.60	metabolic process
GO:0006928	0.60	movement of cell or subcellular component
GO:0051128	0.59	regulation of cellular component organization
GO:0050793	0.59	regulation of developmental process
GO:0050896	0.58	response to stimulus
GO:0048869	0.58	cellular developmental process
GO:0048518	0.58	positive regulation of biological process
GO:0071704	0.57	organic substance metabolic process
GO:0048583	0.57	regulation of response to stimulus
GO:0044238	0.57	primary metabolic process
GO:0016043	0.57	cellular component organization
GO:0048522	0.56	positive regulation of cellular process
GO:0044237	0.56	cellular metabolic process
GO:0022603	0.56	regulation of anatomical structure morphogenesis
GO:0048856	0.55	anatomical structure development
GO:0044260	0.55	cellular macromolecule metabolic process
GO:0023051	0.55	regulation of signaling
GO:0010646	0.55	regulation of cell communication
GO:0009653	0.55	anatomical structure morphogenesis
GO:0007411	0.55	axon guidance
GO:0022604	0.54	regulation of cell morphogenesis
GO:0019222	0.54	regulation of metabolic process
GO:0009966	0.54	regulation of signal transduction
GO:0007165	0.54	signal transduction
GO:0080090	0.53	regulation of primary metabolic process
GO:0031323	0.53	regulation of cellular metabolic process
GO:0060255	0.52	regulation of macromolecule metabolic process
GO:0019538	0.52	protein metabolic process
GO:0048584	0.51	positive regulation of response to stimulus
GO:0006796	0.51	phosphate-containing compound metabolic process
GO:0006464	0.51	cellular protein modification process
GO:1902531	0.50	regulation of intracellular signal transduction
GO:0065008	0.50	regulation of biological quality
GO:0001932	0.50	regulation of protein phosphorylation

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	0.98	cell part
GO:0044424	0.76	intracellular part
GO:0044444	0.53	cytoplasmic part
GO:0043226	0.46	organelle
GO:0044425	0.44	membrane part
GO:0044422	0.40	organelle part
GO:0044459	0.39	plasma membrane part
GO:0016021	0.38	integral component of membrane
GO:0016020	0.38	membrane
GO:0043229	0.36	intracellular organelle
GO:0043227	0.34	membrane-bounded organelle
GO:0005887	0.34	integral component of plasma membrane
GO:0097458	0.33	neuron part
GO:0042995	0.31	cell projection
GO:0044446	0.30	intracellular organelle part
GO:0005886	0.30	plasma membrane

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	0.290	2edwA	0.776	1.28	0.220	0.863	2.7.11.1	21,34,68,88
2	0.171	2wwmD	0.860	1.09	0.216	0.926	2.7.11.1	39
3	0.113	1ri8A	0.763	2.18	0.180	0.926	3.2.1.17	35,39
4	0.104	1zv5A	0.738	2.18	0.193	0.905	3.2.1.17	NA
5	0.104	2edrA	0.750	1.73	0.241	0.874	2.7.11.1	21,34,88

	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.05	1tlk0	0.858	1.22	0.225	0.937	0.90	III	complex1.pdb.gz	24,26,28,30,31,32,41
2	0.05	3sdxG	0.840	1.68	0.217	0.968	0.64	GCY	complex2.pdb.gz	28,29,79
3	0.05	2bnqD	0.830	1.74	0.217	0.968	0.64	III	complex3.pdb.gz	15,63,64,65,66,69,70
4	0.05	2pyeD	0.829	1.73	0.217	0.968	0.64	III	complex4.pdb.gz	36,74,86
5	0.04	1kj20	0.812	1.78	0.178	0.947	0.61	III	complex5.pdb.gz	29,33,35,71,73,77,79,80,81,82,84,88

	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.