D-I-TASSER O95256-D1

D-I-TASSER results for O95256-D1

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

Input Sequence in FASTA format

>O95256 (149 residues)
MLCLGWIFLWLVAGERIKGFNISGCSTKKLLWTYSTRSEEEFVLFCDLPEPQKSHFCHRN
RLSPKQVPEHLPFMGSNDLSDVQWYQQPSNGDPLEDIRKSYPHIIQDKCTLHFLTPGVNN
SGSYICRPKMIKSPYDVACCVKMILEVKP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MLCLGWIFLWLVAGERIKGFNISGCSTKKLLWTYSTRSEEEFVLFCDLPEPQKSHFCHRNRLSPKQVPEHLPFMGSNDLSDVQWYQQPSNGDPLEDIRKSYPHIIQDKCTLHFLTPGVNNSGSYICRPKMIKSPYDVACCVKMILEVKP
Prediction	CCHHHHHHHHHHCCCSSCCCCCCCCCCCCSSSSSSCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCHHHHHCCCCCCSCCCCSSSSCCCCCCCCSSSSSSCCCCCCCCCCCCSSSSSSSSCC
Confidence	93277878776306521210047762442135762378843899827998101145563335777776555567888620227887258999378875478650126866887151346662699802334686555433789997469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MLCLGWIFLWLVAGERIKGFNISGCSTKKLLWTYSTRSEEEFVLFCDLPEPQKSHFCHRNRLSPKQVPEHLPFMGSNDLSDVQWYQQPSNGDPLEDIRKSYPHIIQDKCTLHFLTPGVNNSGSYICRPKMIKSPYDVACCVKMILEVKP
Prediction	43231112001124441452424614444331413345643000103145556541354441454633642414546424304013347755334513752333345621020224425421110032453454453100030105248
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHCCCSSCCCCCCCCCCCCSSSSSSCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCHHHHHCCCCCCSCCCCSSSSCCCCCCCCSSSSSSCCCCCCCCCCCCSSSSSSSSCC
MLCLGWIFLWLVAGERIKGFNISGCSTKKLLWTYSTRSEEEFVLFCDLPEPQKSHFCHRNRLSPKQVPEHLPFMGSNDLSDVQWYQQPSNGDPLEDIRKSYPHIIQDKCTLHFLTPGVNNSGSYICRPKMIKSPYDVACCVKMILEVKP

5dzoA

0.17

0.10

3.32

1.11

FFAS-3D

------------------------------MVKVGGEAGPSVTLPCHY---------------------------SGAVTSMCWNRGSCSLNGTHVTYRKDTRYKLLGDSLTIENTAVSDSGVYCCRVEHRGWFNDMK--ITVSLEIVP

5wy8B

0.18

0.13

4.36

1.33

CNFpred

--------------------SADGCTDWSIIKKYQVLVGEPVRIKCALFYG-----------YIRTNYSLAQS----AGLSLMWYKSSGPGDFEEPIAFDGSRMSKEEDSIWFRPTLLQDSGLYACVIRNS----TYCMKVSISLTVGE

5c6wJ

0.16

0.11

3.79

1.00

DEthreader

------------------QGLEMKQSALTQPASVSASPGQSITISCTG-TS----SDV---G-----A----------YDWVSWYQQHPGKAPKLLIRPVSHRFSGSKASLTISGLQAEDEADYYCASAT--L-LDTYVFGGTKVTVLG

2p1yA2

0.21

0.15

4.91

0.99

SPARKS-K

-----------SADDAKKDAAKKDGQVRQSPQSLTVWEGETAILNCSYEN--------------------------SAFDYFPWYQQFPGEGPALLISKEDGRFTEKKLSLHIADSQPGDSATYFCAAIDTN-AYKVIFGKGTHLHVLP

4mngE

0.16

0.13

4.23

0.82

MapAlign

-VTLNCLYETSWWSYYIFWYKQMIFLFCALGKSVIRQTGSSAEITCDL----------------------------AEGSYIHWYLHQEGKAPQRLLGISPGKYDTYNLRMILRNLIENDSGVYYCATWDEK--YYKKLFGGTKLIITD

4yfcB1

0.17

0.12

3.97

0.38

CEthreader

-----------------------CTDWSVDIKKYQVLVGEPVRIKCALFYGYI---------------RTNYSLAQSAGLSLMWYKSSGPGDFEEPIAFDGSRMSKEEDSIWFRPTLLQDSGLYACVIRN----STYCMKVSISLTVG-

3zyjA

0.16

0.14

4.70

0.75

MUSTER

NCDILWLSWWIKDMAPSNTACCARCNTPPNLKGRYIGN--------FTCYAPVIVEPPADLNVTEGMAAELKCRASTSLTSVSWIT--PNGTVMTHGAYKVRIAVLSDGTLNFTNVTVQDTGMYTCMVSNSVG----NTTASATLNVT-

3oq3B1

0.15

0.12

4.05

0.41

HHsearch

MIDIEITEFFRDTPAKDSKWLNPSCMFGGT-MNDMAALGEPFSAKCPPIEDS--LLSHR--Y-------------NDKDNVVNWEKIGKTR----RP----LNRRVKNGDLWIANYTSNDSHRYLCTVTT------KGDCVQGIVRSHI

4yfcB1

0.18

0.13

4.14

1.11

FFAS-3D

------------------------CTDSVDIKKYQVLVGEPVRIKCAL----------------FYGYIRTNYSLQSAGLSLMWYKSSGPGDFEEPIAFDGSRMSKEEDSIWFRPTLLQDSGLYACVIRNSTY----CMKVSISLTVG-

6jo7A2

0.13

0.09

3.27

0.38

EigenThreader

-----------------AAAS----SSLVSESVVSLAAGTQAVLRCQSPRMV----------------WTQDRLHDRAQQVVHWDRQGVSHDRADRLLYGPDRVSVNDFSLRIDELERADEGIYSCHLHHHYCG---LHERRVFHLQVT

(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

script 1 started

FileManager.getAtomSetCollectionFromFile(model1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/O95256/O95256-D1/model1.pdb.gz

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

-- required by ClazzNode ajax=true async=false

The Resolver thinks Pdb

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

-- required by ClazzNode ajax=true async=false

/jmol//j2s/J/render/MeshRenderer.js

-- 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.pdb.gz): 2652 ms

reading 2402 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

2402 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 jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__4499785543731596__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__4499785543731596__)

vwrOptions:

{ "name":"jmolApplet1","applet":true,"documentBase":"https://zhanglab.comp.nus.edu.sg/HPmod/data/O95256/O95256-D1/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1__4499785543731596__","codePath":"https:/jmol//j2s/","display":"jmolApplet1_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"4499785543731596","bgcolor":"#000000" }

setting document base to "https://zhanglab.comp.nus.edu.sg/HPmod/data/O95256/O95256-D1/"

Jmol Version: 14.2.13_2015.03.07 2015-03-07 10:45

java.vendor: Java2Script (HTML5)

java.version: 2015-03-01 07:13:29 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet1 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #000000

backgroundColor = "#000000"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet1__4499785543731596__ ready

SpinHigh qualityWhite background

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6682

(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

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	5c6wJ	0.61	2.39	0.146	0.718	model1_5c6wJ.pdb.gz
2	6uy3A	0.61	2.72	0.153	0.725	model1_6uy3A.pdb.gz
3	4buhA	0.61	2.58	0.138	0.718	model1_4buhA.pdb.gz
4	6cbpA	0.61	2.44	0.148	0.711	model1_6cbpA.pdb.gz
5	4nikB	0.61	2.47	0.131	0.711	model1_4nikB.pdb.gz
6	3omzA	0.61	2.72	0.113	0.725	model1_3omzA.pdb.gz
7	3uzeA	0.60	2.61	0.138	0.718	model1_3uzeA.pdb.gz
8	6ikma	0.60	2.70	0.156	0.711	model1_6ikma.pdb.gz
9	5yd5A	0.60	2.49	0.130	0.718	model1_5yd5A.pdb.gz
10	6pscA	0.60	2.49	0.149	0.705	model1_6pscA.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:0004872	0.56	receptor activity
GO:0042007	0.54	interleukin-18 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:0006950	1.00	response to stress
GO:0065007	0.69	biological regulation
GO:0050789	0.69	regulation of biological process
GO:0009987	0.68	cellular process
GO:0050794	0.61	regulation of cellular process
GO:0010033	0.57	response to organic substance
GO:0071310	0.55	cellular response to organic substance
GO:1901700	0.54	response to oxygen-containing compound
GO:0071345	0.54	cellular response to cytokine stimulus
GO:0002376	0.54	immune system process
GO:0070301	0.53	cellular response to hydrogen peroxide
GO:0007165	0.53	signal transduction
GO:0006955	0.50	immune response
GO:0006952	0.50	defense response

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

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

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	0.067	1rv6Y	0.480	2.48	0.100	0.571	2.7.10.1	NA
2	0.066	2eo1A	0.495	2.30	0.143	0.564	2.7.11.1	85
3	0.066	1zv5A	0.523	2.87	0.121	0.644	3.2.1.17	110,123
4	0.066	1ri8A	0.539	2.82	0.080	0.658	3.2.1.17	30,124
5	0.066	2edrA	0.476	2.25	0.178	0.550	2.7.11.1	35,46

	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

/jmol//j2s/core/package.js

-- required by ClazzNode ajax=false async=true

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

-- required by ClazzNode ajax=false async=true

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__4499785543731596__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__4499785543731596__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://zhanglab.comp.nus.edu.sg/HPmod/data/O95256/O95256-D1/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__4499785543731596__","codePath":"https:/jmol//j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"4499785543731596","bgcolor":"#000000" }

setting document base to "https://zhanglab.comp.nus.edu.sg/HPmod/data/O95256/O95256-D1/"

Jmol Version: 14.2.13_2015.03.07 2015-03-07 10:45

java.vendor: Java2Script (HTML5)

java.version: 2015-03-01 07:13:29 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

/jmol//j2s/core/corescript.z.js

-- required by ClazzNode ajax=true async=false

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #000000

backgroundColor = "#000000"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__4499785543731596__ ready

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	0.08	2f54D	0.573	2.15	0.173	0.658	0.49	III	complex1.pdb.gz	92,122,123,124
2	0.06	2pcpD	0.560	2.54	0.102	0.658	0.81	1PC	complex2.pdb.gz	87,89,92,123,125,142,143,144
3	0.04	1a6wH	0.581	2.59	0.079	0.678	0.51	NIP	complex3.pdb.gz	87,89,90,122,124,144
4	0.04	1xgyH	0.556	2.75	0.092	0.658	0.43	III	complex4.pdb.gz	88,92,123
5	0.03	1fptH	0.576	2.63	0.099	0.678	0.45	III	complex5.pdb.gz	88,90,122,123,124,145,146
6	0.03	2bnrD	0.579	2.22	0.162	0.664	0.54	III	complex6.pdb.gz	92,122,124
7	0.01	1oarK	0.424	2.18	0.125	0.483	0.43	AZN	complex7.pdb.gz	86,88,94

	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.