D-I-TASSER results for P05161-D1

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

Input Sequence in FASTA format

>P05161 (79 residues)
MGWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPL
ASQGLGPGSTVLLVVDKCD

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MGWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKCD
Prediction	CCCSSSSSSCCCCSSSSSCCCCCCHHHHHHHHHHHHCCCHHHHSSSSCCCCCSCCCCCCHHHCCCCCCCSSSSSSSCCC
Confidence	9721799971895899985987629999999999859996780444425672011587046619999949999996079
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MGWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKCD
Prediction	8746031312645414041556331440253027537144432202236534325564404636146522010105528
	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

                   |                   |                   |

SS
Seq

CCCSSSSSSCCCCSSSSSCCCCCCHHHHHHHHHHHHCCCHHHHSSSSCCCCCSCCCCCCHHHCCCCCCCSSSSSSSCCC
MGWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKCD

5b83A

0.30

0.29

8.84

1.50

DEthreader

GGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF-A-GKQLEDGRTLSDYNIQKESTLHLVLRLRE

6jh0D2

0.25

0.24

7.46

2.15

SPARKS-K

DPLSILVRNNKGRSIAYEVWLTQTVAELKQQVCQQEHVQADLFWLTFE--GKPMEDKHQLGEYGLTPQCTVFMNLRLR-

1v5oA

0.22

6.77

0.47

MapAlign

SGMLITVYCVTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVY--MEQLLDDHCSLGSYGLKDGDMVVLLQKDN-

1v5oA

0.21

0.20

6.46

0.31

CEthreader

SGMLITVYCVRRDTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVY-MEQLLTDDHCSLGSYGLKDGDMVVLLQKDNV

1z2mA

0.99

0.96

26.95

1.61

MUSTER

--WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSD

3q3fA

0.30

0.29

8.84

1.23

HHsearch

YGGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLSDYNIQKESTLHLVLRLRG

1z2mA1

0.99

0.95

26.59

1.64

FFAS-3D

--WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKS-

2dafA

0.16

0.15

5.08

0.63

EigenThreader

SLATVKVVLIVGQEIVIPFKVDTILKYLKDHFSHLLGIPHSVLQIRYS--GKILKNNETLVQHGVKEIVQVEIFSTNPD

3rt3B

0.99

0.96

26.95

1.56

CNFpred

--WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSD

6jh0D

0.62

0.61

17.38

1.50

DEthreader

--GNLTVKMLGGEEFLVPLRDSMLASELKQQIALKTGVPAFQQRLATHPAGTVLQDGISLIRQGLCPGSTVLLVVKNSN

(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	0.9098

(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_5b83A.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/P05161/P05161-D1/model1_5b83A.pdb.gz

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The Resolver thinks Pdb

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

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

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

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

Time for openFile(model1_5b83A.pdb.gz): 2252 ms

reading 3586 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

3586 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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Jmol JavaScript applet jmolApplet2__682425156269976__ initializing

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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	5b83A	0.93	0.79	0.299	0.975	model1_5b83A.pdb.gz
2	6px3C	0.90	0.92	0.293	0.949	model1_6px3C.pdb.gz
3	6jh0D	0.90	1.05	0.623	0.975	model1_6jh0D.pdb.gz
4	2w9nA2	0.90	0.79	0.307	0.937	model1_2w9nA2.pdb.gz
5	7bbdB	0.89	1.32	0.286	0.975	model1_7bbdB.pdb.gz
6	2fazA	0.89	0.98	0.240	0.949	model1_2fazA.pdb.gz
7	4gswA	0.88	0.87	0.284	0.937	model1_4gswA.pdb.gz
8	1v5oA	0.88	1.35	0.205	0.987	model1_1v5oA.pdb.gz
9	2zvnC	0.88	1.10	0.289	0.962	model1_2zvnC.pdb.gz
10	3q3fA2	0.88	1.22	0.299	0.975	model1_3q3fA2.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	0.62	heterocyclic compound binding
GO:0097159	0.62	organic cyclic compound binding
GO:0003676	0.50	nucleic acid 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:0051234	0.71	establishment of localization
GO:0045184	0.70	establishment of protein localization
GO:0009987	0.70	cellular process
GO:0071816	0.69	tail-anchored membrane protein insertion into ER membrane
GO:0008152	0.63	metabolic process
GO:0071704	0.59	organic substance metabolic process
GO:0044238	0.58	primary metabolic process
GO:0044237	0.58	cellular metabolic process
GO:0043170	0.54	macromolecule metabolic process
GO:0044260	0.53	cellular macromolecule metabolic 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	0.98	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.90	cytoplasmic part
GO:0005829	0.86	cytosol
GO:0032991	0.75	macromolecular complex
GO:0043234	0.74	protein complex
GO:0071818	0.72	BAT3 complex

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.getAtomSetCollectionFromFile(model1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/P05161/P05161-D1/model1.pdb.gz

The Resolver thinks Pdb

Time for openFile(model1.pdb.gz): 291 ms

reading 1190 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

1190 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

1190 atoms selected

19 atoms selected

1 atoms selected

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

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19 atoms selected

1 atoms selected

11 atoms selected

1 atoms selected

19 atoms selected

1 atoms selected

spinX = 10

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Script completed

Jmol script terminated

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Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

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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	0.127	2jrhA	0.692	2.27	0.122	0.937	2.7.11.25	54,60,69,73
2	0.060	2wdqB	0.611	2.78	0.093	0.937	1.3.99.1	32
3	0.060	1mp8A	0.341	4.81	0.075	0.747	2.7.10.2 2.7.1.112	NA
4	0.060	2nptD	0.730	1.90	0.127	0.899	2.7.11.25	65,72
5	0.060	1dgjA	0.578	2.64	0.074	0.861	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

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callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

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FileManager.getAtomSetCollectionFromFile(complex1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/P05161/P05161-D1/complex1.pdb.gz

The Resolver thinks Pdb

Time for openFile(complex1.pdb.gz): 279 ms

reading 1792 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

1792 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

1792 atoms selected

602 atoms selected

solventProbeRadius = 1.0

ambientPercent = 40

23 atoms selected

2 atoms selected

19 atoms selected

2 atoms selected

15 atoms selected

2 atoms selected

16 atoms selected

2 atoms selected

24 atoms selected

2 atoms selected

14 atoms selected

2 atoms selected

30 atoms selected

2 atoms selected

27 atoms selected

2 atoms selected

20 atoms selected

2 atoms selected

17 atoms selected

2 atoms selected

spinX = 10

spinY = 10

Script completed

Jmol script terminated

3586 atoms selected

2396 atoms selected

1190 atoms selected

ambientPercent = 40

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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	0.28	1aar0	0.890	1.12	0.293	0.949	1.38	III	complex1.pdb.gz	10,11,46,51,52,53,72,74,75,76
2	0.22	3a9kA	0.891	1.29	0.293	0.949	1.49	III	complex2.pdb.gz	10,44,46,51,72,74
3	0.11	2hd51	0.868	1.35	0.293	0.937	1.37	III	complex3.pdb.gz	4,6,8,9,11,12,14,15,16,18,35,44,47,50,51,53,55,64,66,67,68,69,70,72,73,74,75,76
4	0.11	1q0wB	0.857	1.31	0.293	0.949	1.38	III	complex4.pdb.gz	10,44,46,47,48,51,53,66,72,73,74,75,76
5	0.07	2c7n1	0.878	0.77	0.301	0.924	1.44	III	complex5.pdb.gz	8,9,10,44,46,47,48,51,53,67,68,70,72,74,75,76,77
6	0.07	1wrd1	0.897	1.09	0.293	0.949	1.14	III	complex6.pdb.gz	10,44,46,51,52,72,74,77
7	0.05	2d071	0.835	1.24	0.160	0.949	1.27	III	complex7.pdb.gz	2,11,12,13,14,15,16,17,18,19,27,34,35,36
8	0.04	2rpqA	0.816	1.77	0.156	0.975	0.99	III	complex8.pdb.gz	2,15,16,17,18,19,20,22,23,24,27,28,31,32,35
9	0.04	2emtA	0.799	1.93	0.103	0.987	0.94	III	complex9.pdb.gz	12,13,14,15,16,17,18,20,31,35

	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.