3HJL | Genus

Total Genus 121

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	121
sequence length	321
structure length	321
Chain Sequence	KSALSKAQKAAVLLLSLPEEVSMNIVKELSEEELQKLFALAKDLESVPEEEIENIAEELLDEIKKAGIKIKKPEEFIENIKKVIPPTLAEKFRGILELGDAEKILKEIEKVDSRILASLLKNEHPQTIALFLSQLSPKKSAEIIQNLPEELKKEVVKRIATLENVNVQYVKELAQILLEEISSLGAKEALKLEGTAVAAELLNTLDKETRELILQSIGQEDPLLEERIREKMFTFEDIRKLSDRDIIEILKVVDKNTLMIALLGAPEDIKQKFLSNMSKRAAKLFLEDMEALGPVKKSEIEKAQRQVVNIIRKMIDEGKIE

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__9376287714777933__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__9376287714777933__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3HJL/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__9376287714777933__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"9376287714777933","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3HJL/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__9376287714777933__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cff0dac8586470d9bcecc73/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cff0dac8586470d9bcecc73/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cff0dac8586470d9bcecc73/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/5cff0dac8586470d9bcecc73/pdb.gz): 217 ms

reading 321 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

321 atoms created

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

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:320});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

molecule tags	Proton transport
source organism	Aquifex aeolicus
publication title	Structure of the torque ring of the flagellar motor and the molecular basis for rotational switching pubmed doi rcsb
molecule keywords	Flagellar motor switch protein fliG
total genus	121
structure length	321
sequence length	321
ec nomenclature
pdb deposition date	2009-05-22

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01706	FliG_C	FliG C-terminal domain
A	PF14841	FliG_M	FliG middle domain
A	PF14842	FliG_N	FliG N-terminal domain

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.220.30	Mainly Alpha	Orthogonal Bundle	Annexin V; domain 1	Annexin V; domain 1	3hjlA04
1.10.220.30	Mainly Alpha	Orthogonal Bundle	Annexin V; domain 1	Annexin V; domain 1	3hjlA01
1.10.220.30	Mainly Alpha	Orthogonal Bundle	Annexin V; domain 1	Annexin V; domain 1	3hjlA02

3USWA 4FQ0C 1LKVX 1QC7A 3HJLA 3USYA 3SOHB 4FHRB 3AJCA
chains in the Genus database with same CATH superfamily

1AIIA 3USWA 1HAKA 1DK5A 2R0DA 4HREA 2XO2A 1W45A 2HYWA 1W7BA 1HVFA 1PBVA 2HYUA 1YGMA 4KMUX 2VXGA 2H0LA 4A4PA 2HYVA 2ZOCA 1M9IA 4MDUA 4Q2SA 1HVDA 3LTLA 1C1KA 2QEZA 1N42A 1ALAA 1I4AA 2XO3A 1BC9A 2HSNA 2RANA 2ZHJA 3SWVA 4C0AA 1AXNA 1BC3A 1UPTB 2H0KA 3AJCA 2II2A 4JMOA 1G5NA 1HVGA 4D7RA 1XT0B 1AVHA 1QC7A 1Q8DA 1S9DE 1A8BA 1BCWA 3ABOA 4Z21A 1HVEA 2R09A 3AO0A 1BC0A 4FQ0C 2OY9A 4EVHA 1BO9A 3USYA 1ANNA 1YIIA 2IE6A 4JK1X 1BCZA 4MDVA 3SOHB 3ABRA 1AEIA 2H0MA 1KU1A 2K6XA 1HM6A 1N44A 1RE0B 1R8QE 1R8SE 2Q4CA 4OIYA 1LKVX 2ZHIA 1SAVA 1AOWA 2IE7A 1R4AE 1DM5A 1YCNA 3BRXA 1AVRA 4X9PA 3ANYA 1XJLA 1XSZA 3HJLA 4JXHA 1ANXA 3L8NA 4JWLA 1N41A 4EVFA 1MCXA 3TW5A 1BC1A 1BCYA 1ANWA 2IICA 4KN7X 1AVCA 1W3WA 3ABQA 4FHRB 1R8ME 1N00A 4KN4X 1A8AA 4C7PA 4D7QA 4L5MA 4JMIA 3ABSA 1YJ0A
chains in the Genus database with same CATH topology

3USWA 4JMOA 4D7RA 1XT0B 1QC7A 2R0DA 1XSZA 1KU1A 3HJLA 4JXHA 2K6XA 3L8NA 4JWLA 1S9DE 1Q8DA 1RE0B 1R8QE 1PBVA 4Z21A 4KMUX 3TW5A 1R8SE 2R09A 4A4PA 4FQ0C 4OIYA 1LKVX 4KN7X 3LTLA 3USYA 4JK1X 4FHRB 1R8ME 1BC9A 2HSNA 3SWVA 4C0AA 4KN4X 4C7PA 3SOHB 4D7QA 4L5MA 3AJCA 4JMIA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 3USW A;  4FQ0 C;  1LKV X;  1QC7 A;  3HJL A;  3USY A;  3SOH B;  4FHR B;  3AJC A; 
#chains in the Genus database with same CATH topology
 1AII A;  3USW A;  1HAK A;  1DK5 A;  2R0D A;  4HRE A;  2XO2 A;  1W45 A;  2HYW A;  1W7B A;  1HVF A;  1PBV A;  2HYU A;  1YGM A;  4KMU X;  2VXG A;  2H0L A;  4A4P A;  2HYV A;  2ZOC A;  1M9I A;  4MDU A;  4Q2S A;  1HVD A;  3LTL A;  1C1K A;  2QEZ A;  1N42 A;  1ALA A;  1I4A A;  2XO3 A;  1BC9 A;  2HSN A;  2RAN A;  2ZHJ A;  3SWV A;  4C0A A;  1AXN A;  1BC3 A;  1UPT B;  2H0K A;  3AJC A;  2II2 A;  4JMO A;  1G5N A;  1HVG A;  4D7R A;  1XT0 B;  1AVH A;  1QC7 A;  1Q8D A;  1S9D E;  1A8B A;  1BCW A;  3ABO A;  4Z21 A;  1HVE A;  2R09 A;  3AO0 A;  1BC0 A;  4FQ0 C;  2OY9 A;  4EVH A;  1BO9 A;  3USY A;  1ANN A;  1YII A;  2IE6 A;  4JK1 X;  1BCZ A;  4MDV A;  3SOH B;  3ABR A;  1AEI A;  2H0M A;  1KU1 A;  2K6X A;  1HM6 A;  1N44 A;  1RE0 B;  1R8Q E;  1R8S E;  2Q4C A;  4OIY A;  1LKV X;  2ZHI A;  1SAV A;  1AOW A;  2IE7 A;  1R4A E;  1DM5 A;  1YCN A;  3BRX A;  1AVR A;  4X9P A;  3ANY A;  1XJL A;  1XSZ A;  3HJL A;  4JXH A;  1ANX A;  3L8N A;  4JWL A;  1N41 A;  4EVF A;  1MCX A;  3TW5 A;  1BC1 A;  1BCY A;  1ANW A;  2IIC A;  4KN7 X;  1AVC A;  1W3W A;  3ABQ A;  4FHR B;  1R8M E;  1N00 A;  4KN4 X;  1A8A A;  4C7P A;  4D7Q A;  4L5M A;  4JMI A;  3ABS A;  1YJ0 A; 
#chains in the Genus database with same CATH homology
 3USW A;  4JMO A;  4D7R A;  1XT0 B;  1QC7 A;  2R0D A;  1XSZ A;  1KU1 A;  3HJL A;  4JXH A;  2K6X A;  3L8N A;  4JWL A;  1S9D E;  1Q8D A;  1RE0 B;  1R8Q E;  1PBV A;  4Z21 A;  4KMU X;  3TW5 A;  1R8S E;  2R09 A;  4A4P A;  4FQ0 C;  4OIY A;  1LKV X;  4KN7 X;  3LTL A;  3USY A;  4JK1 X;  4FHR B;  1R8M E;  1BC9 A;  2HSN A;  3SWV A;  4C0A A;  4KN4 X;  4C7P A;  3SOH B;  4D7Q A;  4L5M A;  3AJC A;  4JMI A;

...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...

3HJLA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations