D-I-TASSER Q9BVQ7-D6

D-I-TASSER results for Q9BVQ7-D6

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

Input Sequence in FASTA format

>Q9BVQ7 (102 residues)
PPDHKGRLSILKVCTKTMPIGPDVSLENLAAETCFFSGADLRNLCTEAALLALQENGLDA
TTVKQEHFLKSLKTVKPSLSCKDLALYENLFKKEGFSNVEGI

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| PPDHKGRLSILKVCTKTMPIGPDVSLENLAAETCFFSGADLRNLCTEAALLALQENGLDATTVKQEHFLKSLKTVKPSLSCKDLALYENLFKKEGFSNVEGI
Prediction	CCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCSSCHHHHHHHHHHHCCCCCHHHHHHCHHHHHHHHHHHCCCC
Confidence	978899999999981799898888999999629799879999999999999999758775413799999999984479786664309999998625632699
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| PPDHKGRLSILKVCTKTMPIGPDVSLENLAAETCFFSGADLRNLCTEAALLALQENGLDATTVKQEHFLKSLKTVKPSLSCKDLALYENLFKKEGFSNVEGI
Prediction	865472144004112572514771415400751541100001210430012003555464640436204502741454345632531471364222352477
	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

CCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCSSCHHHHHHHHHHHCCCCCHHHHHHCHHHHHHHHHHHCCCC
PPDHKGRLSILKVCTKTMPIGPDVSLENLAAETCFFSGADLRNLCTEAALLALQENGLDATTVKQEHFLKSLKTVKPSLSCKDLALYENLFKKEGFSNVEGI

6b5cA

0.31

0.29

8.88

1.33

DEthreader

LPTAKGRAELLKINLREVELDPDIQLEDIAEKIEGYSGADITNVCRDASLMAMRRRIELQMPVTKGDFELALKKIAKSVSAADLEKYEKWMVFGS-A-----

5e7pA6

0.33

0.29

8.84

1.83

SPARKS-K

PPDAAARRDILRTAGKSIPLADDVDLDSLADDLDGYSAADCVALLRESAMTAMRRSI-DAADVTAADVAKARETVRPSLDPAQVESLREFAEK---------

5e7pA

0.24

7.34

0.84

MapAlign

LPDATARRSLLEMLLRGVPSE-DLDLGDIADHTPGFVVADLAAVVREGALRAAARASSSDPVLRHADLEGALTVIRPLSSEKAVRELFARARDSAPSLVFLD

6b5cA

0.32

0.30

9.16

0.61

CEthreader

LPTAKGRAELLKINLREVELDPDIQLEDIAEKIEGYSGADITNVCRDASLMAMRRRIELQMPVTKGDFELALKKIAKSVSAADLEKYEKWMVEFGSA-----

5g4fA2

0.50

0.45

13.08

1.32

MUSTER

PPDKEARLSILKVHTKNMPLAPDVDLNDIAQRTEGYVGADLENLCREAGMNAYRENP-DATSVSQKNFLDALKTIRPSVDEEVIKFYRTLSET---------

5e7pA

0.33

0.29

8.84

1.38

HHsearch

PPDAAARRDILRTAGKSIPLADDVDLDSLADDLDGYSAADCVALLRESAMTAMRRS-IDAADVTAADVAKARETVRPSLDPAQVESLREFAEK---------

5e7pA6

0.32

0.28

8.57

1.72

FFAS-3D

-PDAAARRDILRTAGKSIPLADDVDLDSLADDLDGYSAADCVALLRESAMTAMRRSI-DAADVTAADVAKARETVRPSLDPAQVESLREFAEK---------

6b5cA

0.32

0.30

9.16

0.98

EigenThreader

LPTAKGRAELLKINLREVELDPDIQLEDIAEKIEGYSGADITNVCRDASLMAMRRRINGLMPVTKGDFELALKKIAKSVSAADLEKYEKWMVEFGSA-----

4lgmA

0.29

0.26

8.07

0.88

CNFpred

LPDYEQRLSLFKYYTSKIKLDTEVSLEELAKLTEGYTASDIRDIVQAAHIKVVKEMLGEPRTITLQDFKDILKVRMPSVNPELIKAYEAWTEKF--------

3cf1B

0.35

0.32

9.67

1.33

DEthreader

LPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIEEVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQT-L-Q-----

(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	0.8858

(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	6b5cA	0.87	1.56	0.320	0.951	model1_6b5cA.pdb.gz
2	3eihA	0.83	1.86	0.202	0.941	model1_3eihA.pdb.gz
3	3cf1B2	0.83	1.80	0.347	0.931	model1_3cf1B2.pdb.gz
4	4lcbA	0.83	1.36	0.290	0.912	model1_4lcbA.pdb.gz
5	5e7pA	0.82	1.43	0.326	0.902	model1_5e7pA.pdb.gz
6	4l15A	0.81	2.10	0.265	0.961	model1_4l15A.pdb.gz
7	5wc0A	0.80	1.71	0.263	0.931	model1_5wc0A.pdb.gz
8	5z6qA	0.80	2.08	0.301	0.912	model1_5z6qA.pdb.gz
9	1xwiA	0.79	2.18	0.214	0.941	model1_1xwiA.pdb.gz
10	3d8bA	0.78	2.09	0.271	0.931	model1_3d8bA.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:0016887	0.99	ATPase activity
GO:0042623	0.90	ATPase activity, coupled
GO:0097159	0.69	organic cyclic compound binding
GO:1901363	0.68	heterocyclic compound binding
GO:0097367	0.63	carbohydrate derivative binding
GO:0000166	0.63	nucleotide binding
GO:0035639	0.62	purine ribonucleoside triphosphate binding
GO:0032555	0.62	purine ribonucleotide binding
GO:0032550	0.62	purine ribonucleoside binding
GO:0005524	0.60	ATP binding
GO:0036402	0.54	proteasome-activating ATPase activity
GO:0017025	0.54	TBP-class protein 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:0009987	0.96	cellular process
GO:0008152	0.86	metabolic process
GO:0071704	0.85	organic substance metabolic process
GO:0044238	0.85	primary metabolic process
GO:0043170	0.84	macromolecule metabolic process
GO:0019538	0.82	protein metabolic process
GO:0006508	0.79	proteolysis
GO:0065007	0.78	biological regulation
GO:0044237	0.78	cellular metabolic process
GO:0050794	0.76	regulation of cellular process
GO:0044260	0.76	cellular macromolecule metabolic process
GO:0044699	0.75	single-organism process
GO:0044763	0.72	single-organism cellular process
GO:0019222	0.72	regulation of metabolic process
GO:0031323	0.71	regulation of cellular metabolic process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0080090	0.69	regulation of primary metabolic process
GO:0051171	0.68	regulation of nitrogen compound metabolic process
GO:0019219	0.67	regulation of nucleobase-containing compound metabolic process
GO:0009057	0.67	macromolecule catabolic process
GO:0048522	0.66	positive regulation of cellular process
GO:0044248	0.66	cellular catabolic process
GO:0030163	0.66	protein catabolic process
GO:0051128	0.65	regulation of cellular component organization
GO:0044265	0.65	cellular macromolecule catabolic process
GO:0031326	0.65	regulation of cellular biosynthetic process
GO:2001141	0.64	regulation of RNA biosynthetic process
GO:2000112	0.64	regulation of cellular macromolecule biosynthetic process
GO:0051603	0.64	proteolysis involved in cellular protein catabolic process
GO:0031325	0.64	positive regulation of cellular metabolic process
GO:0010604	0.64	positive regulation of macromolecule metabolic process
GO:0010468	0.64	regulation of gene expression
GO:1903506	0.63	regulation of nucleic acid-templated transcription
GO:0071840	0.63	cellular component organization or biogenesis
GO:0016043	0.62	cellular component organization
GO:0006511	0.62	ubiquitin-dependent protein catabolic process
GO:0044087	0.61	regulation of cellular component biogenesis
GO:0030433	0.61	ER-associated ubiquitin-dependent protein catabolic process
GO:0045944	0.58	positive regulation of transcription from RNA polymerase II promoter
GO:0051130	0.55	positive regulation of cellular component organization
GO:0006996	0.55	organelle organization
GO:0045899	0.54	positive regulation of RNA polymerase II transcriptional preinitiation complex assembly
GO:0044267	0.54	cellular protein metabolic process

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:0044424	1.00	intracellular part
GO:0044446	0.88	intracellular organelle part
GO:0044444	0.88	cytoplasmic part
GO:0043226	0.83	organelle
GO:0043229	0.82	intracellular organelle
GO:0043227	0.80	membrane-bounded organelle
GO:0043231	0.79	intracellular membrane-bounded organelle
GO:0016020	0.79	membrane
GO:0005634	0.70	nucleus
GO:0032991	0.61	macromolecular complex
GO:0044428	0.59	nuclear part
GO:0043234	0.58	protein complex

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	1d7lA	0.499	3.63	0.041	0.784	1.14.13.2	NA
2	0.060	2ptxA	0.491	3.53	0.043	0.716	4.2.1.11	NA
3	0.060	3iydD	0.525	3.64	0.031	0.824	2.7.7.6	NA
4	0.060	3bowB	0.488	3.13	0.050	0.735	3.4.22.53	12,38
5	0.060	1c0mA	0.520	3.81	0.118	0.853	2.7.7.49	40

	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	0.32	3cf0A	0.821	1.78	0.347	0.931	0.70	ADP	complex1.pdb.gz	10,14,38,39,42
	2	0.06	2dvw1	0.659	1.46	0.329	0.716	1.40	III	complex2.pdb.gz	4,5,8,22,23,24,25,27,28,32,55,61,62,64,65,66,69

	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.