D-I-TASSER Q96PY5-D3

D-I-TASSER results for Q96PY5-D3

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

Input Sequence in FASTA format

>Q96PY5 (201 residues)
AQYAVTFDFESVESTVESSVDKSKPNSVGPTMGAASSGPLPPPPPPLPPSSDTPETVQNG
PVTPPMPPPPPPPPPKAQGPAIDLSSSKQKIPQKGSNKVTLLEANRAKNLAIFDDVVKYF
GENPKTTPPSVFFPVFVRFVKAYKQAEEENELRKKQEQALMEKLLEQEALMEQQDPKSPS
HKSKRQQQELIAELRRRQVKD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| AQYAVTFDFESVESTVESSVDKSKPNSVGPTMGAASSGPLPPPPPPLPPSSDTPETVQNGPVTPPMPPPPPPPPPKAQGPAIDLSSSKQKIPQKGSNKVTLLEANRAKNLAIFDDVVKYFGENPKTTPPSVFFPVFVRFVKAYKQAEEENELRKKQEQALMEKLLEQEALMEQQDPKSPSHKSKRQQQELIAELRRRQVKD
Prediction	CCSSSSSCCHHHCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCC
Confidence	970244242331234455411358876677667778999999999999866676655568988877887889755445862128999999999999999999999999999999999996899999999999999999999999999999999999999999999899887412012454310468999999999974039
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| AQYAVTFDFESVESTVESSVDKSKPNSVGPTMGAASSGPLPPPPPPLPPSSDTPETVQNGPVTPPMPPPPPPPPPKAQGPAIDLSSSKQKIPQKGSNKVTLLEANRAKNLAIFDDVVKYFGENPKTTPPSVFFPVFVRFVKAYKQAEEENELRKKQEQALMEKLLEQEALMEQQDPKSPSHKSKRQQQELIAELRRRQVKD
Prediction	852113131531453255425664443223333334644353444524364734642575230232614426463565446451452155026504631540363155036204400520022376252640042035005205504641453455454455444556555655556555665553135015403744678
	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                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCSSSSSCCHHHCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCC
AQYAVTFDFESVESTVESSVDKSKPNSVGPTMGAASSGPLPPPPPPLPPSSDTPETVQNGPVTPPMPPPPPPPPPKAQGPAIDLSSSKQKIPQKGSNKVTLLEANRAKNLAIFDDVVKYFGENPKTTPPSVFFPVFVRFVKAYKQAEEENELRKKQEQALMEKLLEQEALMEQQDPKSPSHKSKRQQQELIAELRRRQVKD

1v9dB2

0.15

0.12

4.04

1.12

SPARKS-K

AACEELRKSENFSSLLELTLLVGNYMNAGSRNAGAFGFNISRDTKSADRVSAENLQKSLDQMKKQIADVERDNFPAATDEKDKFVEKMTSFVKDAQEQYNKLRMMHSNMETLYKELGDYFVFDPKKLSVEEFFMDLHNFRNMFLQAVKENQKRRETEEKMRRAKL------------------------------------

5v8kA1

0.07

3.01

1.03

MapAlign

GAVLKAHINHLGNVAAMVSFILVHHLSWDPATQGVLWAPATMFYARLYQLGLDAVALSPDALFVARMHLLAAIILWGFGHVKSPAEEKFLEKVMGKALVAQFHFFALIATLWGLHMAFGIPTGLPITPATMAGNHVAFGAVFFLGGIFHEAVLSVSCQILAFHFATVVFAMIIWQHPQLGFGFMREYAVKMIAQSNPGLLV

2z6eB

0.23

0.19

6.08

3.41

HHsearch

LYFKKKFAVEAIRSGSE-EVFRSFGNNKGQ-RGNAYGFKISADTKSSIDKNITLLHYLITIVENKYPSVPQAAKSQPPQPGDKFVSVVSQFITVASFSFSDVEDLLAEAKDLFTKAVKHFGEEAGKIQPDEFFGIFDQFLQAVSEAKQENENMRKKKEEE-ERRARMEAQLK-----------------------------

1wqgA

0.07

0.05

2.22

0.52

CEthreader

MFSRITIDYYGAATPITQLASINVPEARLVVIKPYEANQLRAIETAIRNSDLGVNPTNDGALIRVAVPQLT-------------EERRRELVKQAKHKGEEAKVSVRNIRRKAMEELHRI-RKEGEAGEDEVGRAEKDLDKTTHQYVTQIDELVKHKEGELLEV-------------------------------------

4l3iA2

0.07

2.83

0.67

EigenThreader

-----------IAEEESLKERLIKSISVCQKELNTLCSELHVEPFQEEGETTILQLEKDLRTQVELRIDSASVPSHVTTLRETKASRREEFVSIKRQIILCQKLLRQLENEAVCEGLRTQIRGSKAKVRKALQLEVDRLEELKQYWDQCEQRQLLQLHDAEIVRLKNYYEVHKELFEGVQKWEETWRLFLEFERKASDPNR

1v9dB2

0.18

0.08

2.60

0.93

FFAS-3D

-------------------------------------------------------------------------FPAATDEKDKFVEKMTSFVKDAQEQYNKLRMMHSNMETLYKELGDYFVFDPKKLSVEEFFMDLHNFRNMFLQAVKENQKRRETEEKMRRAK-------------------------------------

2z6eB

0.16

0.14

4.61

1.06

SPARKS-K

RSGSEEVFRSGALKQLLEVVLAFGNYMNKGQRGNAYGFKISADTKSSIDKNITLLYPSVLNLNEELRDIPQYQKSQPPQPGDKFVSVVSQFITVASFSFSDVEDLLAEAKDLFTKAVKHFGEEAGKIQPDEFFGIFDQFLQAVSEAKQENENMRKKKEEEERRARMEAQLK------------------------------

3o4xE

0.15

0.11

3.71

0.96

CNFpred

--------------------------------------------------SAENLQKSLDQMKKQIADVERDNFPAATDEKDKFVEKMTSFVKDAQEQYNKLRMMHSNMETLYKELGDYFVFDPKKLSVEEFFMDLHNFRNMFLQAVKENQKRRETEEKMRRAKLAKEKAEKERLEKQQKREQLIVMDSLLEALQSGAAFR

6gmhQ

0.09

0.06

2.31

0.83

DEthreader

-----GGGGGGGGGGGGGGGGGGGGGGGGGGG-GGGGGGGG---------------------------------DALGIAVLAHKFHVEKALFKCGKLQECATSVLKDEK-SN-----------YHVARARKQDEEERELRAKQEQEKELLRQKLLKEQEEKRLREKEEQKKLLEQRAQYVEKTKNILM-FT---------

4l22A

0.05

2.48

0.79

MapAlign

GNGGLGRLASCFIDSMATKSKLDRIDILGYHKDSKNYLNLFDIDGLDYGLIKDGITFDKTEIKKNLTLFLYPDDSDKNGELLRIYQQYFMVSNAAQLLIDEALEHLVTIIEHLDRIVRSQYVQIIMAHMDIHKTVHEQLAKIKFNNKLALKRYLKENKQMNALYVIYKYLEIKKGNLPAQDIIHLILCLSELINSPYLNVF

(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	0.4344

(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	6q0xA	0.49	5.15	0.045	0.816	model1_6q0xA.pdb.gz
2	2rakA	0.47	5.02	0.080	0.736	model1_2rakA.pdb.gz
3	6h7wB	0.46	5.45	0.034	0.766	model1_6h7wB.pdb.gz
4	4akvA	0.46	5.27	0.054	0.756	model1_4akvA.pdb.gz
5	6j72A	0.46	4.56	0.070	0.667	model1_6j72A.pdb.gz
6	3cazB	0.45	4.05	0.055	0.637	model1_3cazB.pdb.gz
7	1gpjA	0.45	4.63	0.034	0.687	model1_1gpjA.pdb.gz
8	2j69A	0.44	5.25	0.063	0.711	model1_2j69A.pdb.gz
9	2v0oA	0.44	3.84	0.058	0.612	model1_2v0oA.pdb.gz
10	3haiA	0.42	5.20	0.046	0.702	model1_3haiA.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:0008092	0.37	cytoskeletal protein binding
GO:0003779	0.31	actin 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:0044699	0.95	single-organism process
GO:0009987	0.88	cellular process
GO:0044763	0.86	single-organism cellular process
GO:0016043	0.83	cellular component organization
GO:0050794	0.72	regulation of cellular process
GO:0051128	0.68	regulation of cellular component organization
GO:0022603	0.62	regulation of anatomical structure morphogenesis
GO:0006996	0.61	organelle organization
GO:0022604	0.59	regulation of cell morphogenesis
GO:0007010	0.58	cytoskeleton organization

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:0044444	1.00	cytoplasmic part
GO:0043229	1.00	intracellular organelle
GO:0043231	0.81	intracellular membrane-bounded organelle
GO:0005773	0.76	vacuole
GO:0044446	0.75	intracellular organelle part
GO:0005737	0.74	cytoplasm
GO:0016020	0.66	membrane
GO:0005829	0.65	cytosol
GO:0005768	0.65	endosome
GO:0031982	0.58	vesicle
GO:0031090	0.57	organelle membrane
GO:0031410	0.52	cytoplasmic vesicle
GO:0044425	0.50	membrane part

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	3c2wC	0.379	4.54	0.083	0.542	2.7.13.3	NA
2	0.060	3b8cA	0.412	5.12	0.038	0.637	3.6.3.6	NA
3	0.060	3i9wA	0.389	4.98	0.040	0.582	2.7.13.3	NA
4	0.060	3e04D	0.379	5.12	0.061	0.602	4.2.1.2	147
5	0.060	1yfeA	0.381	5.04	0.062	0.592	4.2.1.2	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	0.01	1czaN	0.303	5.55	0.040	0.507	0.15	GLC	complex1.pdb.gz	39,40,119,120,121

	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.