D-I-TASSER results for Q96S21

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

Summary of the Protein

Uniprot ID: Q96S21
Protein Name: Ras-related protein Rab-40C
Gene Name: RAB40C

Input Sequence in FASTA format

>Q96S21 (281 residues)
MGSQGSPVKSYDYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDG
RRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYDITNRWSFDGIDRWIKEIDEHAPGVP
RILVGNRLHLAFKRQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSRIVLMRHGM
EKIWRPNRVFSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSFSMANGMNAVMMHGRS
YSLASGAGGGGSKGNSLKRSKSIRPPQSPPQNCSRSNCKIS

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q96S21-D1	1-189	189		MGSQGSPVKSYDYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYDITNRWSFDGIDRWIKEIDEHAPGVPRILVGNRLHLAFKRQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSRIVLMRHGMEKIWRPNRV
2	Q96S21-D2	190-281	92		FSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSFSMANGMNAVMMHGRSYSLASGAGGGGSKGNSLKRSKSIRPPQSPPQNCSRSNCKIS

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	0.56

(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_5ganC.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q96S21/model1_5ganC.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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-- 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_5ganC.pdb.gz): 1700 ms

reading 10853 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

10853 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

JSmol exec jmolApplet2 start applet null

Jmol JavaScript applet jmolApplet2__014432390695331__ initializing

Jmol getValue debug null

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Jmol getValue allowjavascript null

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setting document base to "https://zhanglab.comp.nus.edu.sg/HPmod/data/Q96S21/"

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callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

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Jmol getValue EVALCallback null

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Jmol getValue MINIMIZATIONCallback null

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	5ganC	0.65	4.36	0.100	0.865	model1_5ganC.pdb.gz
2	5mqfB	0.65	4.40	0.089	0.854	model1_5mqfB.pdb.gz
3	6u43A	0.64	4.31	0.103	0.829	model1_6u43A.pdb.gz
4	7lhtA	0.63	3.92	0.146	0.776	model1_7lhtA.pdb.gz
5	3jb9B	0.63	4.52	0.102	0.847	model1_3jb9B.pdb.gz
6	5anbK	0.62	4.56	0.070	0.833	model1_5anbK.pdb.gz
7	6s5fA	0.61	1.83	0.303	0.637	model1_6s5fA.pdb.gz
8	2f9mA	0.60	1.77	0.367	0.626	model1_2f9mA.pdb.gz
9	3bc1A	0.60	1.20	0.358	0.616	model1_3bc1A.pdb.gz
10	5lpnA	0.60	0.79	0.441	0.605	model1_5lpnA.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	0.72	heterocyclic compound binding
GO:0097159	0.72	organic cyclic compound binding
GO:0032555	0.69	purine ribonucleotide binding
GO:0032550	0.69	purine ribonucleoside binding
GO:0003824	0.69	catalytic activity
GO:0016787	0.67	hydrolase activity
GO:0017111	0.66	nucleoside-triphosphatase activity
GO:0003924	0.65	GTPase activity
GO:0035639	0.64	purine ribonucleoside triphosphate binding
GO:0032561	0.60	guanyl ribonucleotide binding
GO:0005525	0.55	GTP 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:0009987	0.70	cellular process
GO:0051179	0.69	localization
GO:0006810	0.67	transport
GO:0044699	0.63	single-organism process
GO:0065007	0.59	biological regulation
GO:0050789	0.57	regulation of biological process
GO:0050794	0.55	regulation of cellular process
GO:0044763	0.54	single-organism cellular 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	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.92	cytoplasmic part
GO:0043226	0.84	organelle
GO:0043227	0.82	membrane-bounded organelle
GO:0043229	0.80	intracellular organelle
GO:0043231	0.78	intracellular membrane-bounded organelle
GO:0016020	0.60	membrane
GO:0044446	0.55	intracellular organelle 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

script 1 started

FileManager.getAtomSetCollectionFromFile(model1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q96S21/model1.pdb.gz

The Resolver thinks Pdb

Time for openFile(model1.pdb.gz): 799 ms

reading 4403 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

4403 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

4403 atoms selected

17 atoms selected

1 atoms selected

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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	0.378	1aa9A	0.547	2.31	0.266	0.601	3.6.5.-	73
2	0.363	2bmeA	0.604	0.92	0.343	0.616	3.6.5.2	73
3	0.147	2atxA	0.569	1.70	0.250	0.601	3.6.5.2	73
4	0.139	3bc1A	0.597	1.20	0.358	0.616	3.6.5.2	NA
5	0.112	1m2oB	0.509	1.74	0.190	0.544	3.6.5.-	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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FileManager.getAtomSetCollectionFromFile(complex1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q96S21/complex1.pdb.gz

The Resolver thinks Pdb

Time for openFile(complex1.pdb.gz): 517 ms

reading 4431 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

4431 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

4431 atoms selected

28 atoms selected

solventProbeRadius = 1.0

ambientPercent = 40

12 atoms selected

1 atoms selected

16 atoms selected

1 atoms selected

7 atoms selected

1 atoms selected

22 atoms selected

1 atoms selected

7 atoms selected

1 atoms selected

15 atoms selected

1 atoms selected

10 atoms selected

1 atoms selected

14 atoms selected

1 atoms selected

24 atoms selected

1 atoms selected

17 atoms selected

1 atoms selected

19 atoms selected

1 atoms selected

11 atoms selected

1 atoms selected

14 atoms selected

1 atoms selected

19 atoms selected

1 atoms selected

spinX = 10

spinY = 10

Script completed

Jmol script terminated

10853 atoms selected

6450 atoms selected

4403 atoms selected

ambientPercent = 40

Script completed

Jmol script terminated

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	0.81	2rhdA	0.553	1.84	0.411	0.580	1.53	GDP	complex1.pdb.gz	24,25,26,27,28,29,39,126,127,129,130,156,157,158
2	0.18	1z0k0	0.582	1.08	0.345	0.598	1.45	III	complex2.pdb.gz	11,31,32,35,47,48,49,50,51,52,53,64,66,68,75,76,79,83
3	0.06	2bcg1	0.589	2.01	0.362	0.623	1.13	III	complex3.pdb.gz	51,68,69,71,80,81,82,83,85,116,117
4	0.05	2heiB	0.551	1.88	0.348	0.584	1.07	D1D	complex4.pdb.gz	20,70,77,79,80,83,108,111

	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.