D-I-TASSER Q6ZWK6-D1

D-I-TASSER results for Q6ZWK6-D1

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

Input Sequence in FASTA format

>Q6ZWK6 (182 residues)
MMYAPVEFSEAEFSRAEYQRKQQFWDSVRLALFTLAIVAIIGIAIGIVTHFVVEDDKSFY
YLASFKVTNIKYKENYGIRSSREFIERSHQIERMMSRIFRHSSVGGRFIKSHVIKLSPDE
QGVDILIVLIFRYPSTDSAEQIKKKIEKALYQSLKTKQLSLTINKPSFRLTPIDSKKMRN
LL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MMYAPVEFSEAEFSRAEYQRKQQFWDSVRLALFTLAIVAIIGIAIGIVTHFVVEDDKSFYYLASFKVTNIKYKENYGIRSSREFIERSHQIERMMSRIFRHSSVGGRFIKSHVIKLSPDEQGVDILIVLIFRYPSTDSAEQIKKKIEKALYQSLKTKQLSLTINKPSFRLTPIDSKKMRNLL
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHSSSCCCSSSSSSSSSSCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCHCHSCCCSSSSSSCCCCCSSSSSSSSSSSCCCCCHHHHHHHHHHHHHHHHHHCCCCCSSCCCCSSSSSCCHHHHHHCC
Confidence	98766667766677544566665552467799999999999999999733124447416899999985973474447745888999999999999999971852010111189999707995799999999734678768999999999999987267773145884189836878775309
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MMYAPVEFSEAEFSRAEYQRKQQFWDSVRLALFTLAIVAIIGIAIGIVTHFVVEDDKSFYYLASFKVTNIKYKENYGIRSSREFIERSHQIERMMSRIFRHSSVGGRFIKSHVIKLSPDEQGVDILIVLIFRYPSTDSAEQIKKKIEKALYQSLKTKQLSLTINKPSFRLTPIDSKKMRNLL
Prediction	71333252455624555455544203111001133333333233213201102155433213020304616136615473164045115414530451155251453134120240356741020202010212437445303520450035305645341504152040361546505527
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHSSSCCCSSSSSSSSSSCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCHCHSCCCSSSSSSCCCCCSSSSSSSSSSSCCCCCHHHHHHHHHHHHHHHHHHCCCCCSSCCCCSSSSSCCHHHHHHCC
MMYAPVEFSEAEFSRAEYQRKQQFWDSVRLALFTLAIVAIIGIAIGIVTHFVVEDDKSFYYLASFKVTNIKYKENYGIRSSREFIERSHQIERMMSRIFRHSSVGGRFIKSHVIKLSPDEQGVDILIVLIFRYPSTDSAEQIKKKIEKALYQSLKTKQLSLTINKPSFRLTPIDSKKMRNLL

1ivzA

0.17

0.12

3.96

1.00

DEthreader

-----------------------------------------GSS--G-SS-GSSS--SQHFNLNFTITNLPYSQDIAQPSTTKYQQTKRSIENALNQLFRNSSIKSYFSDCQVLAFRSVNNHTGVDSLCNFSLAR-R-V--DRVAIYEEFLRMTHTQLLNFTLDRKSVFVDSGPSSG-----

1ivzA

0.17

0.12

3.81

1.76

SPARKS-K

-----------------------------------------------GSSGSSGSSSSQHFNLNFTITNLPYSQDIAQPSTTKYQQTKRSIENALNQLFRNSSIKSYFSDCQVLAFRSNNNHTGVDSLCNFSPLARRVD---RVAIYEEFLRMTHTQLLNFTLDRKSVFVDSGPSSG-----

1ivzA

0.18

0.12

3.74

1.13

MapAlign

--------------------------------------------------------SSQHFNLNFTITNLPYSQDIAQPSTTKYQQTKRSIENALNQLFRNSSIKSYFSDCQVLAFRSVNNHTGVDSLCNFSPL----ARRVRVAIYEEFLRMTGTQLLNFTLDRKSVFVDSGP--------

1ivzA

0.17

0.12

3.81

1.18

CEthreader

-----------------------------------------------GSSGSSGSSSSQHFNLNFTITNLPYSQDIAQPSTTKYQQTKRSIENALNQLFRNSSIKSYFSDCQVLAFRSVNNHTGVDSLCNFSPLA---RRVDRVAIYEEFLRMTHTQLLNFTLDRKSVFVDSGPSSG-----

2e7vA

0.29

0.18

5.52

1.35

MUSTER

-------------------------------------------------------KKAYFYHSSFQILNVEYTEALNSPATHEYRTLSERIEAMITDEFRGSSLKSEFIRTHVVKLRKEGTGVVADVVMKFRS----NRKVMKTRIQSVLRRL---SSGNLEIAPSNE-ITSLTDQD-----

2e7vA

0.30

0.19

5.68

3.80

HHsearch

-------------------------------------------------------KKAYFYHSSFQILNVEYTEALNSPATHEYRTLSERIEAMITDEFRGSSLKSEFIRTHVVKLRKEGTGVVADVVMKFRS----NRKVMKTRIQSVLR-RLSS-SGNLEIAPSNE-ITSLTDQD-----

2e7vA

0.30

0.19

5.68

1.55

FFAS-3D

-------------------------------------------------------KKAYFYHSSFQILNVEYTEALNSPATHEYRTLSERIEAMITDEFRGSSLKSEFIRTHVVKLRKEGTGVVADVVMKFR----SNRKVMKTRIQSVLRRLSSSGNLEIAPSNEITSLTDQD--------

6rbgA

0.10

0.08

3.06

0.68

EigenThreader

-DLIDLLVQLWRGKMTIII--------------------SVIVAIALAIGYLAVAKEKWTSTAIITQPDYNNAMNVIYGQADLQETLIGRFSSAFSALAETLDNQEEREKLTIEPS-VKNQQLPLTVSYVG--QTAEGA---QMKLAQYIQQVDDKVNLDIHA---YKPMLPRDSTLILAVL

1ivzA

0.18

0.12

3.76

1.13

CNFpred

--------------------------------------------------------SSQHFNLNFTITNLPYSQDIAQPSTTKYQQTKRSIENALNQLFRNSSIKSYFSDCQVLAFRSVNNHTGVDSLCNFSPL---ARRVDRVAIYEEFLRMTHTQLLNFTLDRKSVFVDSGPSSG-----

3ikmD

0.08

0.06

2.41

0.83

DEthreader

------PKRPQHLPG-H---PGWY--RK--------GP--H--SS-LILAMVQAPYTLVGADVSQWIAVLGDAGRIYGVSNWVVQSSAVDYLHLMLVAMKWLFEEGRFCISIHD-------------EVRYLVREEDR-YRAALALQITNLLTRCMFAYKLGDLPQVAFFAVDDCLRKDC--

(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

SpinHigh qualityWhite background

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6898

(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

/jmol//j2s/core/package.js

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script 1 started

FileManager.getAtomSetCollectionFromFile(model1_1ivzA.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q6ZWK6/Q6ZWK6-D1/model1_1ivzA.pdb.gz

/jmol//j2s/core/corezip.z.js

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The Resolver thinks Pdb

/jmol//j2s/core/corebio.z.js

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/jmol//j2s/J/shape/Mesh.js

-- required by J.renderbio.BioShapeRenderer ajax=true async=false

Time for openFile(model1_1ivzA.pdb.gz): 2391 ms

reading 4079 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

4079 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

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SpinHigh qualityWhite background

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1ivzA	0.60	2.30	0.165	0.676	model1_1ivzA.pdb.gz
2	5a22A	0.56	3.60	0.070	0.753	model1_5a22A.pdb.gz
3	3s5hA	0.54	4.53	0.056	0.819	model1_3s5hA.pdb.gz
4	2aj4A	0.53	4.72	0.081	0.819	model1_2aj4A.pdb.gz
5	2gewA	0.53	4.67	0.086	0.835	model1_2gewA.pdb.gz
6	1coyA	0.52	4.74	0.074	0.835	model1_1coyA.pdb.gz
7	1pieA	0.52	4.16	0.056	0.758	model1_1pieA.pdb.gz
8	4hacA	0.47	4.62	0.042	0.709	model1_4hacA.pdb.gz
9	3bg7A	0.47	4.65	0.039	0.747	model1_3bg7A.pdb.gz
10	2fgeA1	0.46	4.33	0.078	0.676	model1_2fgeA1.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:0003824	0.95	catalytic activity
GO:0008233	0.94	peptidase activity
GO:0070011	0.91	peptidase activity, acting on L-amino acid peptides
GO:0008236	0.87	serine-type peptidase activity
GO:0004175	0.52	endopeptidase 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:0044238	0.85	primary metabolic process
GO:0043170	0.85	macromolecule metabolic process
GO:0019538	0.84	protein metabolic process
GO:0006508	0.69	proteolysis
GO:0009987	0.62	cellular process
GO:0044699	0.54	single-organism 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:0044464	0.99	cell part
GO:0044424	0.74	intracellular part
GO:0043227	0.66	membrane-bounded organelle
GO:0016020	0.62	membrane
GO:0044425	0.58	membrane part
GO:0044444	0.54	cytoplasmic part
GO:0005576	0.54	extracellular region
GO:0005886	0.52	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

script 1 started

FileManager.getAtomSetCollectionFromFile(model1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q6ZWK6/Q6ZWK6-D1/model1.pdb.gz

The Resolver thinks Pdb

Time for openFile(model1.pdb.gz): 303 ms

reading 3049 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

3049 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

3049 atoms selected

spinX = 10

spinY = 10

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Jmol script terminated

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SpinHigh qualityWhite background

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	1nb7A	0.487	3.90	0.047	0.654	3.4.21.98	NA
2	0.060	2gewA	0.530	4.67	0.086	0.835	1.1.3.6	NA
3	0.060	1fi4A	0.478	4.73	0.097	0.764	4.1.1.33	NA
4	0.060	3ikmD	0.484	4.00	0.078	0.698	2.7.7.7	114
5	0.060	1s4eG	0.330	5.79	0.075	0.610	2.7.1.6	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

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language=en_US

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Jmol applet jmolApplet1__828790614159262__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(complex1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q6ZWK6/Q6ZWK6-D1/complex1.pdb.gz

The Resolver thinks Pdb

Time for openFile(complex1.pdb.gz): 285 ms

reading 3054 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

3054 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

3054 atoms selected

5 atoms selected

solventProbeRadius = 1.0

ambientPercent = 40

16 atoms selected

1 atoms selected

/jmol//j2s/core/coretext.z.js

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16 atoms selected

1 atoms selected

12 atoms selected

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spinX = 10

spinY = 10

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4079 atoms selected

1030 atoms selected

3049 atoms selected

ambientPercent = 40

Script completed

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SpinHigh qualityWhite background

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	1pieA	0.516	4.16	0.056	0.758	0.55	PO4	complex1.pdb.gz	67,123,124

	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.