D-I-TASSER A6NFQ2-D6

D-I-TASSER results for A6NFQ2-D6

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

Input Sequence in FASTA format

>A6NFQ2 (168 residues)
VWGPIHELGHNQQRHGWEFPPHTTEATCNLWSVYVHETVLGIPRAQAHEALSPPERERRI
KAHLGKGAPLCDWNVWTALETYLQLQEAFGWEPFTQLFAEYQTLSHLPKDNTGRMNLWVK
KFSEKVKKNLVPFFEAWGWPIQKEVADSLASLPEWQENPMQVYLRARK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| VWGPIHELGHNQQRHGWEFPPHTTEATCNLWSVYVHETVLGIPRAQAHEALSPPERERRIKAHLGKGAPLCDWNVWTALETYLQLQEAFGWEPFTQLFAEYQTLSHLPKDNTGRMNLWVKKFSEKVKKNLVPFFEAWGWPIQKEVADSLASLPEWQENPMQVYLRARK
Prediction	CCHHHHHHHHHHCCCCCCCCCCCSSSHHHHHHHHHHHHHCCCCCHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCHHHHCCCC
Confidence	951466776430546666799975314789999999998698715541343536899999999854886222565678999999999977799999999999815799996799999999999998888499999989998999999998489887652265414799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| VWGPIHELGHNQQRHGWEFPPHTTEATCNLWSVYVHETVLGIPRAQAHEALSPPERERRIKAHLGKGAPLCDWNVWTALETYLQLQEAFGWEPFTQLFAEYQTLSHLPKDNTGRMNLWVKKFSEKVKKNLVPFFEAWGWPIQKEVADSLASLPEWQENPMQVYLRARK
Prediction	760331122123133415144300000000100000222453444434531446413530341154445265342232010112023212440044005202735734554641132003100410633014005424041375036305714514663045215568
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHCCCCCCCCCCCSSSHHHHHHHHHHHHHCCCCCHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCHHHHCCCC
VWGPIHELGHNQQRHGWEFPPHTTEATCNLWSVYVHETVLGIPRAQAHEALSPPERERRIKAHLGKGAPLCDWNVWTALETYLQLQEAFGWEPFTQLFAEYQTLSHLPKDNTGRMNLWVKKFSEKVKKNLVPFFEAWGWPIQKEVADSLASLPEWQENPMQVYLRARK

7jtvB2

0.18

5.81

1.33

DEthreader

GWGESHQLGHNLQV-NRLKGGRSGEISNQIFPLHKDWRVLREG-NLDDTRVNYRNAYNLIVAGRAEGVYLWEDLNGERMAFYTQWVHYWGWDIWTLLYLHQRQVDRPGNSSTDGNDNLLLGLSWLTQRDQRPTFALWGIRTSAAAQAQVAGFAEQPAFFYLLDSPAWP

7js4A4

0.18

0.17

5.43

1.82

SPARKS-K

GWGVAHELGHNFDTGGRTIV----EVTNNMMPLFFESKYKT-KTRITDQNIWENNTYPKVGLYSNELYNKADSTHLAQLAPLWQLYLYDNT-FYGKFERQFRERDFGNKNREDIYKSWVVAASDAMELDLTEFFARHGIRVDDKVKEDLAKYPKPDKKIYYL------

7jtvB

0.17

5.45

1.08

MapAlign

GWGESHQLGHNLQVNRLKVYGRSGEISNQIFPLHKVLREFGQNL--DDTRV----NYRNAYNLIVAGVYWTYALNGERMAFYTQWVHYWGWDIWTLLYLHQRQVDGNSGDATDGNDNLLLGLSWLTQRDQRPTFALWGIRTSAAAQAQVAGFAEQ-PAFFYANNRTN-

7jtvB2

0.16

5.34

0.98

CEthreader

GWGESHQLGHNLQVNRLKVYGRSGEISNQIFPLHKDWRVLREGQNLDDTRVNYRNAYNLIVAGRAEADPLAGVLNGERMAFYTQWVHYWAWDIWTLLYLHQRQVDSGDASSTDGNDNLLLGLSWLTQRDQRPTFALWGIRTSAAAQAQVAAYGFAEQPAFFYANNRTN

4fcaA2

0.20

0.17

5.51

1.28

MUSTER

-------------QDTWLWD-GLGEVTVNIYSLAVQTTF-------HKTRLEQEGRYEAAFAYLGKPDAQEK---EFEKLVFWQLHLAYGDQFYPNLHQYRLLHDTELPKSDEEKKQFIY-TSKVAGQNLIPFFDKWGLSANDATREKIEKLPKLEKEIWSNPIREKQ

5kd2A

0.23

0.22

6.92

3.40

HHsearch

AWGPAHQIGHVHQA-AINWA-SSTESSNNLFSNFIIYKL-GKYKSRG-NGLGATARYANGQAWYNMGDTHQNEDTETHMRMNWQLWIYYKTDFWQTLFKLMREVNMTEGDPGKKQLEFAKMASKAANQNLTDFFEMWGFPVNREAKEYMAQFPAPKHAFQYIEDRKKS

7js4A4

0.20

0.18

5.91

1.98

FFAS-3D

-WGVAHELGHNFDTGGRT----IVEVTNNMMPLFFESKYKTKTRITDQNIWENNTYPKVGLDDYSNNELYNDSTHLAQLAPLWQLYL-YDNTFYGKFERQFRERDFGNKNREDIYKSWVVAASDAMELDLTEFFARHGIRVDDKVKEDLAKYPKPDK-KI-YYL----

7js4A4

0.20

0.18

5.71

1.37

EigenThreader

GWGVAHELGHNFDTGGRTI----VEVTNNMMPLFFESKYK-TKTRITDQNI----WENNTYPKVGSNNELYNKTHLAQLAPLWQLYLYD-NTFYGKFERQFRERDFGNKNREDIYKSWVVAASDAMELDLTEFFARHGIRVDDKVKEDLAKYPKPDKKIL--------

4fcaA

0.27

0.26

7.87

1.40

CNFpred

GWGPWHEVGHQHQQDTWLWD-GLGEVTVNIYSLAVQTTF------GHKTRLEQEGRYEAAFAYLGKPDAQEKMNEFEKLVMFWQLHLAYGDQFYPNLHQMYRLLHELPKSDEEKKQMFIYMTSKVAGQNLIPFFDKWGLSANDATREKIENLPKLEKEIWLSTDSNPI

7jtvB

0.18

5.81

1.33

DEthreader

GWGESHQLGHNLQV-NRLKGGRSGEISNQIFPLHKDWRVLREG-NLDDTRVNYRNAYNLIVAGRAEGVYLWEDLNGERMAFYTQWVHYWGWDIWTLLYLHQRQVDRPGNSSTDGNDNLLLGLSWLTQRDQRPTFALWGIRTSAAAQAQVAGFAEQPAFFYLLDSPAWP

(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	0.8309

(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

script 1 started

FileManager.getAtomSetCollectionFromFile(model1_4fcaA.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/A6NFQ2/A6NFQ2-D6/model1_4fcaA.pdb.gz

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The Resolver thinks Pdb

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Time for openFile(model1_4fcaA.pdb.gz): 3284 ms

reading 6518 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

6518 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	4fcaA	0.81	2.31	0.282	0.923	model1_4fcaA.pdb.gz
2	5kdvA2	0.80	2.97	0.179	0.994	model1_5kdvA2.pdb.gz
3	7jtvB	0.80	2.99	0.173	0.994	model1_7jtvB.pdb.gz
4	5kd2A	0.80	2.39	0.209	0.941	model1_5kd2A.pdb.gz
5	5kdjB	0.78	2.60	0.190	0.941	model1_5kdjB.pdb.gz
6	7jfsA	0.78	2.61	0.190	0.941	model1_7jfsA.pdb.gz
7	7js4A	0.78	2.64	0.190	0.941	model1_7js4A.pdb.gz
8	6xsxA	0.76	2.84	0.187	0.917	model1_6xsxA.pdb.gz
9	1z5hA	0.65	3.57	0.080	0.887	model1_1z5hA.pdb.gz
10	4kx7A	0.64	3.64	0.074	0.887	model1_4kx7A.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:0044325	0.82	ion channel 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:0090314	1.00	positive regulation of protein targeting to membrane
GO:0048519	1.00	negative regulation of biological process
GO:0030334	1.00	regulation of cell migration
GO:0010359	1.00	regulation of anion channel activity
GO:0030335	0.56	positive regulation of cell migration
GO:0010360	0.56	negative regulation of anion channel 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 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:0005886	1.00	plasma membrane
GO:0005634	0.99	nucleus

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

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FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/A6NFQ2/A6NFQ2-D6/model1.pdb.gz

The Resolver thinks Pdb

Time for openFile(model1.pdb.gz): 933 ms

reading 2741 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

2741 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

2741 atoms selected

spinX = 10

spinY = 10

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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	3fvyA	0.515	3.99	0.120	0.762	3.4.14.4	NA
2	0.060	3ebgA	0.610	3.80	0.073	0.875	3.4.11.-	NA
3	0.060	2p8uA	0.434	4.98	0.050	0.732	2.3.3.10	NA
4	0.060	1wdkC	0.438	5.09	0.056	0.768	2.3.1.16	NA
5	0.060	2jgdA	0.436	5.52	0.039	0.798	1.2.4.2	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

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language=en_US

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Jmol applet jmolApplet1__2825816023115979__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(complex1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/A6NFQ2/A6NFQ2-D6/complex1.pdb.gz

The Resolver thinks Pdb

Time for openFile(complex1.pdb.gz): 892 ms

reading 2742 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

2742 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

2742 atoms selected

1 atoms selected

solventProbeRadius = 1.0

ambientPercent = 40

17 atoms selected

1 atoms selected

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17 atoms selected

1 atoms selected

11 atoms selected

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spinX = 10

spinY = 10

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6518 atoms selected

3777 atoms selected

2741 atoms selected

ambientPercent = 40

Script completed

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SpinHigh qualityWhite background

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	0.14	1espA	0.575	3.77	0.109	0.809	1.05	ZN	complex1.pdb.gz	6,10,28
2	0.09	3ftwA	0.595	4.14	0.111	0.857	0.59	IMD	complex2.pdb.gz	5,6,9,34
3	0.07	3b2xA	0.621	3.80	0.048	0.881	0.78	NA	complex3.pdb.gz	6,7,8,9,29
4	0.06	1h19A	0.594	4.15	0.111	0.857	0.56	IMD	complex4.pdb.gz	6,9,10,13
5	0.04	2dqmA	0.622	3.80	0.048	0.881	0.52	BES	complex5.pdb.gz	3,6,7,10,24,25,75

	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.