D-I-TASSER Q99572-D1

D-I-TASSER results for Q99572-D1

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

Input Sequence in FASTA format

>Q99572 (120 residues)
MPACCSCSDVFQYETNKVTRIQSMNYGTIKWFFHVIIFSYVCFALVSDKLYQRGKFDIIQ
LVVYIGSTLSYFGLAAVFIDFLIDTYSSNCCRSHIYPWCKCCQPCVVNEYYYRKKCESIV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPACCSCSDVFQYETNKVTRIQSMNYGTIKWFFHVIIFSYVCFALVSDKLYQRGKFDIIQLVVYIGSTLSYFGLAAVFIDFLIDTYSSNCCRSHIYPWCKCCQPCVVNEYYYRKKCESIV
Prediction	CCCCCCHHHHHSSCCCCSSSSSSSCSSSSSHHHHHHHHHHHHHHHHHHHHHHHCCCCSSSSSSSSCCCSSSSSHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSCHHHHHHHHHHCCCCC
Confidence	996322101203226727999743014652134668998886775330123205786599999844421575224653444321354411256656654534411134432332041259
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPACCSCSDVFQYETNKVTRIQSMNYGTIKWFFHVIIFSYVCFALVSDKLYQRGKFDIIQLVVYIGSTLSYFGLAAVFIDFLIDTYSSNCCRSHIYPWCKCCQPCVVNEYYYRKKCESIV
Prediction	733213133015252631240433432203032113123311310113432554514102011322432323211311031113334442144423320431442514531355415537
	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 AttentionPotential. 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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCHHHHHSSCCCCSSSSSSSCSSSSSHHHHHHHHHHHHHHHHHHHHHHHCCCCSSSSSSSSCCCSSSSSHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSCHHHHHHHHHHCCCCC
MPACCSCSDVFQYETNKVTRIQSMNYGTIKWFFHVIIFSYVCFALVSDKLYQRGKFDIIQLVVYIGSTLSYFGLAAVFIDFLIDTYSSNCCRSHIYPWCKCCQPCVVNEYYYRKKCESIV

6u9vA

0.52

14.94

1.54

SPARKS-K

CQPKYSFRRLDDKYTNES-LFPGYNFRYAKYYKENKRTLIKAFGVRFDILVFGGKFDIIQLVVYIGSTLSYFGLATVCIDLIINTYASTCCRSRVYPSCKCCEPCAVNEYYYRKKCEPIV

6u9vA

0.51

14.72

1.31

MUSTER

SHRCYSFRRLDDKYTNESL-FPGYNFRYAKYYKENKRTLIKAFGFDILVFGTGGKFDIIQLVVYIGSTLSYFGLATVCIDLIINTYASTCCRSRVYPSCKCCEPCAVNEYYYRKKCEPIV

6u9vA

0.52

14.94

4.94

HHsearch

CQPKYSFRRLDDKYTNESL-FPGYNFRYAKYYKEGKRTLIKAFGVRFDILGTGGKFDIIQLVVYIGSTLSYFGLATVCIDLIINTYASTCCRSRVYPSCKCCEPCAVNEYYYRKKCEPIV

1vt4I3

0.03

1.90

0.56

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

4onyA

0.03

1.89

0.48

EigenThreader

PVLPKHAINRDTFGNSTLEPPIGSGPYVVASVQPGQ-RIVYKRNKISIEYYRNETSLFESFKKRERELLADVMNGVPAKKAYDLLSQAGFQFGMAIDPTAKPFAFEIMTRYDMILGALAS

6u9vA3

0.73

0.27

7.57

0.70

FFAS-3D

------------------------------------------------------------------------GLATVCIDLIINTYASTCCRSRVYPSCKCCEPCAVNEYYYRKKC----

3h9vA

0.18

0.12

4.07

1.35

SPARKS-K

CVPRYTFRRLDNKDPDNNVA-PGYNFRFAKYYKNETRTLIKGYGIRFDVMVFGGKFNIIPTLLNIGAGLALLGLVNVICDWIVL------------------------------------

3i5dA

0.20

0.13

4.28

0.88

CNFpred

CVPRYTFRRLDNKDP-DNNVAPGYNFRFAKYYKTETRTLIKGYGIRFDVMVQAGKFNIIPTLLNIGAGLALLGLVNVICDWI--------------------------------------

6v6bB

0.05

0.04

1.96

0.83

DEthreader

---------RHLMDLAT--SLYLVFLWKREYIDIRAVH-I------HQMQYYI-TFEVLECSWDELWNKVAHEVFLDTIISRLDSDSRALLNQLRAVFDQIIFYQGI-VQQFLVLLTTDL

4zxaW

0.10

0.09

3.38

0.82

MapAlign

ASPPHAVTGYRSFQLGAFELSRDEYFARITWPAKGETRSHLIPA-----------DIFLRAMMRDVAWGFFPLIMATFKAILRDWTERFRIATKRMPGLQDDSPLRNDLPVNRQFADVSQ

(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	0.5757

(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 AttentionPotential, 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	2oryB	0.53	4.09	0.053	0.858	model1_2oryB.pdb.gz
2	4v00A	0.52	4.22	0.045	0.875	model1_4v00A.pdb.gz
3	6d9fA	0.51	4.32	0.028	0.808	model1_6d9fA.pdb.gz
4	2o78A2	0.50	4.01	0.046	0.792	model1_2o78A2.pdb.gz
5	3e1tA	0.50	3.96	0.083	0.800	model1_3e1tA.pdb.gz
6	1w27A	0.49	4.22	0.034	0.800	model1_1w27A.pdb.gz
7	2nyfA2	0.47	4.26	0.096	0.800	model1_2nyfA2.pdb.gz
8	2rjsB2	0.46	4.86	0.043	0.825	model1_2rjsB2.pdb.gz
9	2oalB	0.45	4.31	0.070	0.792	model1_2oalB.pdb.gz
10	3unvA2	0.44	4.97	0.043	0.833	model1_3unvA2.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:0004931	0.94	extracellular ATP-gated cation channel activity
GO:0001614	0.85	purinergic nucleotide receptor 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:0006811	0.76	ion transport
GO:0006812	0.73	cation transport
GO:0009987	0.69	cellular process
GO:0006461	0.64	protein complex assembly
GO:0033198	0.58	response to ATP
GO:0065008	0.57	regulation of biological quality
GO:0042391	0.56	regulation of membrane potential
GO:0010959	0.56	regulation of metal ion transport
GO:0051050	0.55	positive regulation of transport
GO:0048522	0.55	positive regulation of cellular process
GO:0006816	0.55	calcium ion transport
GO:0097190	0.53	apoptotic signaling pathway
GO:0051899	0.53	membrane depolarization
GO:0051239	0.53	regulation of multicellular organismal process
GO:0044763	0.53	single-organism cellular process
GO:0007166	0.53	cell surface receptor signaling pathway
GO:0051047	0.52	positive regulation of secretion
GO:0031325	0.52	positive regulation of cellular metabolic process
GO:0051130	0.50	positive regulation of cellular component organization
GO:0050718	0.50	positive regulation of interleukin-1 beta secretion
GO:0046931	0.50	pore complex assembly
GO:0042327	0.50	positive regulation of phosphorylation
GO:0032060	0.50	bleb assembly
GO:0010604	0.50	positive regulation of macromolecule metabolic process
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:0016021	0.94	integral component of membrane
GO:0044424	0.93	intracellular part
GO:0005639	0.90	integral component of nuclear inner 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	0.060	1w27A	0.488	4.22	0.034	0.800	4.3.1.24	NA
2	0.060	1l7qA	0.481	4.62	0.059	0.833	3.1.1.1	NA
3	0.060	1fokA	0.461	4.81	0.037	0.817	3.1.21.4	NA
4	0.060	1h0nA	0.480	4.66	0.036	0.833	1.17.4.1	NA
5	0.060	1biqB	0.458	4.52	0.079	0.808	1.17.4.1	78

	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	0.01	1ecgA	0.490	4.34	0.071	0.817	0.27	PIN	complex1.pdb.gz	76,77,79
2	0.01	2qkiD	0.340	5.62	0.038	0.717	0.10	III	complex2.pdb.gz	23,28,71,74
3	0.01	2qkiA	0.319	5.56	0.020	0.658	0.15	III	complex3.pdb.gz	1,2,27,30,40
4	0.01	1ecfA	0.492	4.29	0.089	0.817	0.30	PIN	complex4.pdb.gz	73,74,75
5	0.01	1sxj5	0.337	4.62	0.060	0.583	0.12	III	complex5.pdb.gz	61,62,65,74,77,80,81,84,87

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.