D-I-TASSER Q86Z02-D6

D-I-TASSER results for Q86Z02-D6

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

Input Sequence in FASTA format

>Q86Z02 (77 residues)
IIVPPLKTQLGDCTVATQARAQRGGTSAAQPLNLSQNQQSSAAPTSQERSSNPAPRRQQA
FVAPLSQAPYTFQHGSP

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| IIVPPLKTQLGDCTVATQARAQRGGTSAAQPLNLSQNQQSSAAPTSQERSSNPAPRRQQAFVAPLSQAPYTFQHGSP
Prediction	CCCCCCHHHCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCHHHHSHSCCCCCCCCCCCCCCC
Confidence	94675100024651233321114787766766522444312456542346897630110000211139823478999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| IIVPPLKTQLGDCTVATQARAQRGGTSAAQPLNLSQNQQSSAAPTSQERSSNPAPRRQQAFVAPLSQAPYTFQHGSP
Prediction	74344244424513233434664545443442414534544446345545565444444222331352424265768
	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

CCCCCCHHHCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCHHHHSHSCCCCCCCCCCCCCCC
IIVPPLKTQLGDCTVATQARAQRGGTSAAQPLNLSQNQQSSAAPTSQERSSNPAPRRQQAFVAPLSQAPYTFQHGSP

2be1A2

0.09

3.45

0.74

CEthreader

SLSDILIAADVEGGLHASIQNVLDVPLALQNTFSKDGMCIAPFRDKSLLASDLDFRIADVFNDLRTNENILVPHPFN

6lq8A1

0.05

2.40

0.53

EigenThreader

DGGWDKVGLALQWALIEHILGANPAAYMYAMGPGMSEIFYNNGTDEQKKWATIAAERGWGLTEPDAGSDVGAGRTKA

1ffkC

0.14

0.13

4.45

0.33

FFAS-3D

VDLPPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRGQAHVPDGRARRVPQAHPPKTEKDRSLD----

5yfpE1

0.07

0.06

2.74

1.09

SPARKS-K

-SLYELDPKWKKLLKTDNFLGGLTVNEFVQELSKDHRNDVLIDANTKNLPTNEKDQDAIREAIWKQLDPKPYIRTFE

3sqrA

0.32

0.08

2.35

0.62

CNFpred

----------------------------------------------------------QCPIAPGDTLTYKFQVTQY

6wucI

0.04

2.04

0.83

DEthreader

V-RYIQTPPVLQSALCKWLVHYLWTIYVSSLKHLSVSSMLWKPILGTLHQLVGPDNKFVSFFQLENLYIKKGIILRK

2zc7A

0.06

2.75

0.82

MapAlign

VMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLAN

5w3nA

0.16

0.13

4.30

0.79

MUSTER

------SYSGYSQSTDTSGYGQSSYSSYGQSQNTGYGTQSTPQGYGSTGGYGSSQSSQSSY---GQQSSY-------

2lf0A

0.15

0.05

1.74

0.42

HHsearch

VVVHPMTALGREMGL-----EEMTGFSK---TTF-------------------------------------------

3d89A

0.04

2.05

0.59

CEthreader

AVVHDREVKGEYHAMDIRCYHSGGPLHLGEIEDFNGQSCIVCPWHKYKITLATGEGKQRIHTVKVDNGNIYVTLSKE

(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	0.5261

(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	6dt1A2	0.42	4.12	0.087	0.805	model1_6dt1A2.pdb.gz
2	5fjsA	0.42	3.84	0.014	0.753	model1_5fjsA.pdb.gz
3	3ghaA	0.41	4.39	0.029	0.831	model1_3ghaA.pdb.gz
4	4mlgA	0.41	4.09	0.059	0.766	model1_4mlgA.pdb.gz
5	1rfsA	0.40	3.99	0.049	0.740	model1_1rfsA.pdb.gz
6	1o98A2	0.40	3.80	0.076	0.766	model1_1o98A2.pdb.gz
7	3azcA	0.39	4.15	0.062	0.766	model1_3azcA.pdb.gz
8	2remC	0.38	4.41	0.014	0.818	model1_2remC.pdb.gz
9	4n30A	0.38	4.46	0.041	0.792	model1_4n30A.pdb.gz
10	4jr4A	0.36	3.78	0.051	0.662	model1_4jr4A.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	0.70	heterocyclic compound binding
GO:0097159	0.70	organic cyclic compound binding
GO:0003714	0.67	transcription corepressor activity
GO:0003676	0.61	nucleic acid binding
GO:0003677	0.58	DNA binding
GO:0003824	0.57	catalytic activity
GO:0016740	0.56	transferase activity
GO:0004672	0.55	protein kinase 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:0097190	1.00	apoptotic signaling pathway
GO:0048518	1.00	positive regulation of biological process
GO:0044699	1.00	single-organism process
GO:0009987	1.00	cellular process
GO:0009966	1.00	regulation of signal transduction
GO:0007166	0.90	cell surface receptor signaling pathway
GO:0044767	0.88	single-organism developmental process
GO:0044763	0.88	single-organism cellular process
GO:0008152	0.83	metabolic process
GO:0071704	0.82	organic substance metabolic process
GO:0044238	0.82	primary metabolic process
GO:0044237	0.82	cellular metabolic process
GO:0044260	0.81	cellular macromolecule metabolic process
GO:0080090	0.70	regulation of primary metabolic process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0031323	0.70	regulation of cellular metabolic process
GO:1902531	0.69	regulation of intracellular signal transduction
GO:0048522	0.69	positive regulation of cellular process
GO:0006355	0.69	regulation of transcription, DNA-templated
GO:0048523	0.68	negative regulation of cellular process
GO:0035556	0.68	intracellular signal transduction
GO:0044093	0.67	positive regulation of molecular function
GO:0033554	0.67	cellular response to stress
GO:0006468	0.67	protein phosphorylation
GO:0006357	0.67	regulation of transcription from RNA polymerase II promoter
GO:0051099	0.66	positive regulation of binding
GO:0042771	0.66	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0097191	0.65	extrinsic apoptotic signaling pathway
GO:0072577	0.65	endothelial cell apoptotic process
GO:0010803	0.65	regulation of tumor necrosis factor-mediated signaling pathway
GO:0051239	0.57	regulation of multicellular organismal process
GO:0044707	0.57	single-multicellular organism process
GO:0031324	0.57	negative regulation of cellular metabolic process
GO:0010605	0.57	negative regulation of macromolecule metabolic process
GO:0045766	0.56	positive regulation of angiogenesis
GO:0043388	0.56	positive regulation of DNA binding
GO:0009952	0.56	anterior/posterior pattern specification
GO:0008284	0.56	positive regulation of cell proliferation
GO:0007224	0.56	smoothened signaling pathway
GO:0000122	0.56	negative regulation of transcription from RNA polymerase II promoter
GO:0030154	0.54	cell differentiation

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:0005737	1.00	cytoplasm
GO:0043229	0.95	intracellular organelle
GO:0005634	0.94	nucleus
GO:0044446	0.89	intracellular organelle part
GO:0044428	0.88	nuclear part
GO:0016605	0.54	PML body

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	2pffD	0.396	4.31	0.000	0.805	2.3.1.86	NA
2	0.060	3f7kA	0.376	4.12	0.046	0.701	1.15.1.1	57
3	0.060	2zsgA	0.376	4.58	0.071	0.792	3.4.11.9	NA
4	0.060	1p9bA	0.382	4.66	0.075	0.805	6.3.4.4	NA
5	0.060	3gdeA	0.382	4.26	0.031	0.766	6.5.1.1	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:

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.