2K4Q | Genus

Total Genus 9

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	9
sequence length	156
structure length	156
Chain Sequence	GAMMPVPNPTMPVKGAGTTLWVYKGSGDPYANPLSDVDWSRLAKVKDLTPGELTAESYDDSYLDDEDADWTATGQGQKSAGDTSFTLAWMPGEQGQQALLAWFNEGDTRAYKIRFPNGTVDVFRGWVSSIGKAVTAKEVITRTVKVTNVGRPSMAE

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__994975810354191__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__994975810354191__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2K4Q/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__994975810354191__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"994975810354191","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2K4Q/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__994975810354191__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd4b27c468dab01de212d2/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd4b27c468dab01de212d2/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd4b27c468dab01de212d2/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/5cfd4b27c468dab01de212d2/pdb.gz): 514 ms

reading 156 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

156 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:155});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	The phage lambda major tail protein structure reveals a common evolution for long-tailed phages and the type VI bacterial secretion system. pubmed doi rcsb
molecule keywords	Major tail protein V
molecule tags	Viral protein
source organism	Enterobacteria phage lambda
total genus	9
structure length	156
sequence length	156
ec nomenclature
pdb deposition date	2008-06-16

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF16461	Phage_TTP_12	Lambda phage tail tube protein, TTP

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

cath code	Class	Architecture	Topology	Homology	Domain
2.30.110.60	Mainly Beta	Roll	Pnp Oxidase; Chain A	Pnp Oxidase; Chain A	2k4qA00

2K4QA
chains in the Genus database with same CATH superfamily

2PTFA 1G79A 5ESCA 4HX6A 4F07A 3U34A 1EJEA 2QEAA 2K4QA 3EAAA 3KYFA 2IG6A 1W3PA 1WLIA 4XJ2A 1FLMA 1YLNA 4Y9IA 3ZODA 3F7EA 4HMUA 1TY9A 2FURA 2L1TA 4IRAA 2ECRA 1USFA 3SWJA 1Y12A 2R6VA 3ZOGA 2ECUA 1I0RA 2HHZA 1RZ1A 2Q9KA 2VPAA 2R0XA 1WV4A 2X1KA 2P5ZX 1DNLA 4N7RC 4ZKYA 4HMVA 1I0SA 2RE7A 1USCA 2D5MA 3K86A 1RFEA 4HMTA 1XXOA 5BNCA 1W3OA 2I51A 3TGVA 3ZOHA 3R5ZA 3HMZA 1WGBA 3R5LA 1W3RA 4HMXA 2HTDA 2D38A 4HMWA 1RZ0A 3VYAA 4R82A 3R5PA 3VY5A 1G78A 2A2JA 3RH7A 3ZOCA 3U0IA 3VY2A 2FG9A 2OU5A 1JNWA 3BPKA 4W64A 1AXJA 2FHQA 4XHYA 2D37A 1G77A 2AQ6A 4Z85A 3V4HA 2ASFA 1CI0A 2OL5A 2X1JA 3HE1A 3PFTA 4UHVA 5JABA 1Y30A 3A6RA 1YOAA 3CP3A 4L82A 1WLKA 3A6QA 2I02A 2IABA 4TV4A 1T9MA 3DB0A 3NFWA 2GJGA 3K88A 4QVBA 2ED4A 3BA3A 3B5MA 2ARZA 2HTIA 3K87A 4HMSA 3KYGA 2HQ7A 3DNHA 3ZOEA 3U5WA 3ZOFA 3R5YA 2E83A 3FGEA 1W9AA 3AWHA 3H96A 3AMFA 1W3QA 3U35A 3CB0A 2QCKA 4MTKA 3GASA 2D36A 2NR4A 3EC6A 3HY8A 4HKHA 2GUJA 3DMBA 3IN6A 4YBNA 2HQ9A 1NRGA 1XHNA 5CHEC 3R5RA 5CHOA 2RDEA 3E4VA 3R5WA 3BNKA 3FKHA 2IMLA 3A20A 4YWNA 1G76A 1VL7A
chains in the Genus database with same CATH topology

2L1TA 2GUJA 4MTKA 2P5ZX 2K4QA 4UHVA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2K4Q A; 
#chains in the Genus database with same CATH topology
 2PTF A;  1G79 A;  5ESC A;  4HX6 A;  4F07 A;  3U34 A;  1EJE A;  2QEA A;  2K4Q A;  3EAA A;  3KYF A;  2IG6 A;  1W3P A;  1WLI A;  4XJ2 A;  1FLM A;  1YLN A;  4Y9I A;  3ZOD A;  3F7E A;  4HMU A;  1TY9 A;  2FUR A;  2L1T A;  4IRA A;  2ECR A;  1USF A;  3SWJ A;  1Y12 A;  2R6V A;  3ZOG A;  2ECU A;  1I0R A;  2HHZ A;  1RZ1 A;  2Q9K A;  2VPA A;  2R0X A;  1WV4 A;  2X1K A;  2P5Z X;  1DNL A;  4N7R C;  4ZKY A;  4HMV A;  1I0S A;  2RE7 A;  1USC A;  2D5M A;  3K86 A;  1RFE A;  4HMT A;  1XXO A;  5BNC A;  1W3O A;  2I51 A;  3TGV A;  3ZOH A;  3R5Z A;  3HMZ A;  1WGB A;  3R5L A;  1W3R A;  4HMX A;  2HTD A;  2D38 A;  4HMW A;  1RZ0 A;  3VYA A;  4R82 A;  3R5P A;  3VY5 A;  1G78 A;  2A2J A;  3RH7 A;  3ZOC A;  3U0I A;  3VY2 A;  2FG9 A;  2OU5 A;  1JNW A;  3BPK A;  4W64 A;  1AXJ A;  2FHQ A;  4XHY A;  2D37 A;  1G77 A;  2AQ6 A;  4Z85 A;  3V4H A;  2ASF A;  1CI0 A;  2OL5 A;  2X1J A;  3HE1 A;  3PFT A;  4UHV A;  5JAB A;  1Y30 A;  3A6R A;  1YOA A;  3CP3 A;  4L82 A;  1WLK A;  3A6Q A;  2I02 A;  2IAB A;  4TV4 A;  1T9M A;  3DB0 A;  3NFW A;  2GJG A;  3K88 A;  4QVB A;  2ED4 A;  3BA3 A;  3B5M A;  2ARZ A;  2HTI A;  3K87 A;  4HMS A;  3KYG A;  2HQ7 A;  3DNH A;  3ZOE A;  3U5W A;  3ZOF A;  3R5Y A;  2E83 A;  3FGE A;  1W9A A;  3AWH A;  3H96 A;  3AMF A;  1W3Q A;  3U35 A;  3CB0 A;  2QCK A;  4MTK A;  3GAS A;  2D36 A;  2NR4 A;  3EC6 A;  3HY8 A;  4HKH A;  2GUJ A;  3DMB A;  3IN6 A;  4YBN A;  2HQ9 A;  1NRG A;  1XHN A;  5CHE C;  3R5R A;  5CHO A;  2RDE A;  3E4V A;  3R5W A;  3BNK A;  3FKH A;  2IML A;  3A20 A;  4YWN A;  1G76 A;  1VL7 A; 
#chains in the Genus database with same CATH homology
 2L1T A;  2GUJ A;  4MTK A;  2P5Z X;  2K4Q A;  4UHV 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...

2K4QA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations