2OTR | Genus

Total Genus 14

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus	14
sequence length	90
structure length	90
Chain Sequence	MLTIETSKKFDKDLKILVKNGFDLKLLYKVVGNLATEQPLAPKYKDHPLKGGLKDFRECHLKPDLLLVYQIKKQENTLFLVRLGSHSELF

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

loadScript /static/js/j2s/core/package.js

loadScript /static/js/j2s/core/corejmol.z.js

loadScript /static/js/j2s/core/corescript.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__1427951973470827__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__1427951973470827__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2OTR/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__1427951973470827__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"1427951973470827","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2OTR/A/"

Jmol Version: 14.29.13 2018-04-17 17:17

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (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 getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

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 AUDIOCallback 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__1427951973470827__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd65f2d84f7d86633eb411/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd65f2d84f7d86633eb411/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd65f2d84f7d86633eb411/pdb.gz)

loadScript /static/js/j2s/core/corezip.z.js

The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/file/5cfd65f2d84f7d86633eb411/pdb.gz): 386 ms

reading 90 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 Jmol

90 atoms created

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

Time for creating model: 17 ms

Adding embedded #jmolscript: select ({0:89});backbone only;select *;

platformSpeed = 8

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

loadScript /static/js/j2s/core/corescriptcmd.z.js

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

Script completed

Jmol script terminated

loadScript /static/js/j2s/J/g3d/HermiteRenderer.js

loadScript /static/js/j2s/J/renderbio/BioMeshRenderer.js

loadScript /static/js/j2s/J/render/MeshRenderer.js

loadScript /static/js/j2s/J/shape/Mesh.js

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

publication title	Solution structure of conserved hypothetical protein HP0892 from Helicobacter pylori. pubmed doi rcsb
molecule keywords	Hypothetical protein HP0892
molecule tags	Structural genomics, unknown function
source organism	Helicobacter pylori
total genus	14
structure length	90
sequence length	90
ec nomenclature
pdb deposition date	2007-02-09

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF05016	ParE_toxin	ParE toxin of type II toxin-antitoxin system, parDE

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	2otrA00

4Q2UB 2OTRA 5CW7B 4MMJA 4LSYA 2KC9A 4ML2A 5CZEB 4MMGA 3G5OB 2A6QE 2KC8A 2A6SA 2A6RA 5CEGB 3OEIC 4LTTA 4MCXB 4NRNA 4FXED 4LS4A 4ML0B 4PX8A 1WMIA 4FXIA 5CZFC 5IXLA 4MCTB 5IWHA 4YY3Y 1Z8MA 3KXEA 4FXHA 2KHEA 3BPQB
chains in the Genus database with same CATH superfamily

4Q2UB 2OTRA 5CW7B 4MMJA 4LSYA 2KC9A 4ML2A 2A8KA 2FHZB 5CZEB 2PD0A 3HI2B 4MMGA 3G5OB 2A6QE 2KC8A 2A6SA 2A6RA 5CEGB 3OEIC 4LTTA 4MCXB 4NRNA 4FXED 3VJ7A 4LS4A 4ML0B 4PX8A 2DFXE 1WMIA 4FXIA 4FBDA 1XQBA 5CZFC 5IXLA 4MCTB 5IWHA 4YY3Y 1Z8MA 2DJHA 3KXEA 4FXHA 3AO9A 2KHEA 3BPQB
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4Q2U B;  2OTR A;  5CW7 B;  4MMJ A;  4LSY A;  2KC9 A;  4ML2 A;  5CZE B;  4MMG A;  3G5O B;  2A6Q E;  2KC8 A;  2A6S A;  2A6R A;  5CEG B;  3OEI C;  4LTT A;  4MCX B;  4NRN A;  4FXE D;  4LS4 A;  4ML0 B;  4PX8 A;  1WMI A;  4FXI A;  5CZF C;  5IXL A;  4MCT B;  5IWH A;  4YY3 Y;  1Z8M A;  3KXE A;  4FXH A;  2KHE A;  3BPQ B; 
#chains in the Genus database with same CATH topology
 4Q2U B;  2OTR A;  5CW7 B;  4MMJ A;  4LSY A;  2KC9 A;  4ML2 A;  2A8K A;  2FHZ B;  5CZE B;  2PD0 A;  3HI2 B;  4MMG A;  3G5O B;  2A6Q E;  2KC8 A;  2A6S A;  2A6R A;  5CEG B;  3OEI C;  4LTT A;  4MCX B;  4NRN A;  4FXE D;  3VJ7 A;  4LS4 A;  4ML0 B;  4PX8 A;  2DFX E;  1WMI A;  4FXI A;  4FBD A;  1XQB A;  5CZF C;  5IXL A;  4MCT B;  5IWH A;  4YY3 Y;  1Z8M A;  2DJH A;  3KXE A;  4FXH A;  3AO9 A;  2KHE A;  3BPQ B; 
#chains in the Genus database with same CATH homology
 4Q2U B;  2OTR A;  5CW7 B;  4MMJ A;  4LSY A;  2KC9 A;  4ML2 A;  5CZE B;  4MMG A;  3G5O B;  2A6Q E;  2KC8 A;  2A6S A;  2A6R A;  5CEG B;  3OEI C;  4LTT A;  4MCX B;  4NRN A;  4FXE D;  4LS4 A;  4ML0 B;  4PX8 A;  1WMI A;  4FXI A;  5CZF C;  5IXL A;  4MCT B;  5IWH A;  4YY3 Y;  1Z8M A;  3KXE A;  4FXH A;  2KHE A;  3BPQ B;

...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

2OTRA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations