1VHK | Genus

Total Genus 69

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	69
Knots found	KnotProt 2.0: K +3₁
sequence length	252
structure length	235
Chain Sequence	QRYFIELTKQQIEEAPTFSITGEEVHHIVNVMRMNEGDQIICCSQDGFEAKCELQSVSKDKVSCLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKRERWTKIAKEAAEQSYRNEVPRVMDVHSFQQLLQRMQDFDKCVVAYESAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLR

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__375717215210486__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__375717215210486__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1vhk/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__375717215210486__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"375717215210486","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1vhk/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__375717215210486__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfc4703b10d181fa068ec40/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfc4703b10d181fa068ec40/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfc4703b10d181fa068ec40/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/5cfc4703b10d181fa068ec40/pdb.gz): 1690 ms

reading 235 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

235 atoms created

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

Time for creating model: 23 ms

Adding embedded #jmolscript: select ({0:234});backbone only;select *;

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	Structural genomics, unknown function
source organism	Bacillus subtilis
publication title	Structural analysis of a set of proteins resulting from a bacterial genomics project pubmed doi rcsb
molecule keywords	Hypothetical protein yqeU
total genus	69
structure length	235
sequence length	252
chains with identical sequence	B, C, D
other databases	KnotProt 2.0: K +3₁
ec nomenclature	ec 2.1.1.193: 16S rRNA (uracil(1498)-N(3))-methyltransferase.
pdb deposition date	2003-12-01

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF04452	Methyltrans_RNA	RNA methyltransferase

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

cath code	Class	Architecture	Topology	Homology	Domain
2.40.240.20	Mainly Beta	Beta Barrel	Ribosomal Protein L25; Chain P	Hypothetical PUA domain-like; domain 1	1vhkA01
3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	Alpha/beta knot	1vhkA02

4YQ3A 1Z85A 3KTYA 1X7OA 5GMBA 3QUVA 4YQ4A 3KW2A 3IC6A 3L8UA 5CO4A 2YY8A 1K3RA 4YQCA 1OY5A 3AIAA 3OIIA 4YQLA 1UAKA 2O3AA 1IPAA 5FAIA 4H3ZA 3KNUA 4YPYA 4H3YA 4YVHA 3AXZA 4CNFA 1VHKA 3BBEA 2V3JA 3KY7A 2EGWA 4YQSA 4IG6A 1V6ZA 5GMCA 4YVIA 4PZKA 4YQ1A 3AI9X 3GYQA 1UAMA 2EGVA 4YQAA 3DCMX 3N4KA 4YPXA 4YQOA 3ONPA 4YQ0A 4YQBA 3NK6A 4YPWA 3ILKA 3N4JA 1O6DA 4RG1A 4YQQA 4YVGA 4L69A 4MCCA 4YQ8A 3E5YA 2QMMA 1J85A 4FAKA 2I6DA 1TO0A 4YQ7A 1GZ0A 4MCDA 4XBOA 1NXZA 4CNEA 5D9FA 1UAJA 1P9PA 3IEFA 1NS5A 3BBDA 4CNDA 4YVJA 4YPZA 4YQGA 4JAKA 4YQPA 5GM8A 4MCBA 2NWAA 4CNGA 4X3LA 4YQ5A 4YQNA 3BBHA 4KDZA 2QWVA 4E8BA 1ZJRA 4JALA 4YVKA 1X7PA 4YQDA 1VH0A 2CX8A 1V2XA 2Z0YA 4YQ9A 3O7BA 4YQ2A 4YQKA 4YQ6A 3OINA 4YQTA 1VHYA 4KGNA 2HA8A 4YQJA 1MXIA 4X3MA 2V3KA 3NK7A 4J3CA 3OIJA 1UALA 4YQIA 4YQRA
chains in the Genus database with same CATH superfamily

4YQ3A 2G6GA 1Z85A 3KTYA 1QRTA 3CF5S 1X7OA 4WFAS 4IOCS 3QUVA 5GMBA 4YQ4A 3KW2A 3IC6A 3L8UA 5CO4A 4JXZA 2YY8A 3PIOS 1O0CA 1K3RA 5JVHS 4JYZA 3W2WB 1OY5A 3AIAA 3OIIA 4YQCA 4YQLA 1UAKA 2O3AA 3CZBA 1ZJWA 1IPAA 5FAIA 5BNZA 2RE8A 4H3ZA 2PJJA 1GTRA 3KNUA 4YPYA 5DM7S 1EUYA 4H3YA 1EUQA 4YVHA 3AXZA 4FMWA 4CNFA 3PIPS 2PNWA 5HL7S 1VHKA 2GAEA 2ZJQS 3BBEA 3DLLS 1B75A 2V3JA 3KY7A 2EGWA 4YQSA 1QRUA 4JWJA 5GAHW 5GAGW 4IG6A 1V6ZA 5GMCA 4YVIA 4PZKA 4YQ1A 3AI9X 3GYQA 1UAMA 2EGVA 4YQAA 3DCMX 3N4KA 4YPXA 1EXDA 3X1LB 3ONPA 4YQOA 4YQ0A 4YQBA 3NK6A 4JWFA 4YPWA 3ILKA 3N4JA 1O6DA 4RG1A 4YQQA 4YVGA 4L69A 4MCCA 1QRSA 2HZ7A 4IOAS 2QMMA 3E5YA 4YQ8A 1NYLA 4WFNS 4H4KA 1J85A 4FAKA 2I6DA 2G5DA 2PICA 1TO0A 4YQ7A 1GZ0A 4MCDA 5IZNA 4XBOA 1NXZA 4CNEA 5JVGS 5D9FA 1UDXA 1FEUA 3J7ZV 1UAJA 1P9PA 3IEFA 1NS5A 2RD2A 5GADW 3BBDA 4CNDA 4YVJA 4YPZA 4YQGA 4JAKA 4YQPA 5GM8A 4MCBA 2NWAA 4CNGA 4X3LA 1O0BA 2ZJPS 4YQ5A 4YQNA 2AE0X 3BBHA 4KDZA 2QWVA 4E8BA 1ZJRA 3W2VB 1QTQA 4JALA 4UY88 4YVKA 1X7PA 2ZJRS 4YQDA 1D6KA 5GAEW 1VH0A 4H3SA 2CX8A 4WCES 2Z0YA 4WF9S 1V2XA 1DFUP 3O7BA 4YQ9A 4JXXA 4YQ2A 4P2BA 4YQKA 4YQ6A 3OINA 2PI8A 5DM6S 4JWHA 4YQTA 1VHYA 4IO9S 4JWGA 4KGNA 2HA8A 4YQJA 1MXIA 4X3MA 2V3KA 3NK7A 1GTSA 3AIIA 4U67S 4V194 4J3CA 3OIJA 1UALA 4YQIA 4WFBS 4YQRA
chains in the Genus database with same CATH topology

4YQ3A 1Z85A 3KTYA 1X7OA 5GMBA 3QUVA 4YQ4A 3KW2A 3IC6A 3L8UA 5CO4A 2YY8A 1K3RA 4YQCA 1OY5A 3AIAA 3OIIA 4YQLA 1UAKA 2O3AA 1IPAA 5FAIA 4H3ZA 3KNUA 4YPYA 4H3YA 4YVHA 3AXZA 4FMWA 4CNFA 1VHKA 3BBEA 2V3JA 3KY7A 2EGWA 4YQSA 4JWJA 4IG6A 1V6ZA 5GMCA 4YVIA 4PZKA 4YQ1A 3AI9X 3GYQA 1UAMA 2EGVA 4YQAA 3DCMX 3N4KA 4YPXA 4YQOA 3ONPA 4YQ0A 4YQBA 3NK6A 4JWFA 4YPWA 3ILKA 3N4JA 1O6DA 4RG1A 4YQQA 4YVGA 4L69A 4MCCA 4YQ8A 3E5YA 2QMMA 1J85A 4FAKA 2I6DA 1TO0A 4YQ7A 1GZ0A 4MCDA 4XBOA 1NXZA 4CNEA 5D9FA 1UAJA 1P9PA 3IEFA 1NS5A 3BBDA 4CNDA 4YVJA 4YPZA 4YQGA 4JAKA 4YQPA 5GM8A 4MCBA 2NWAA 4CNGA 4X3LA 4YQ5A 4YQNA 3BBHA 4KDZA 2QWVA 4E8BA 1ZJRA 4JALA 4YVKA 1X7PA 4YQDA 1VH0A 2CX8A 1V2XA 2Z0YA 4YQ9A 3O7BA 4YQ2A 4YQKA 4YQ6A 3OINA 4JWHA 4YQTA 1VHYA 4JWGA 4KGNA 2HA8A 4YQJA 1MXIA 4X3MA 2V3KA 3NK7A 4J3CA 3OIJA 1UALA 4YQIA 4YQRA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 4YQ3 A;  1Z85 A;  3KTY A;  1X7O A;  5GMB A;  3QUV A;  4YQ4 A;  3KW2 A;  3IC6 A;  3L8U A;  5CO4 A;  2YY8 A;  1K3R A;  4YQC A;  1OY5 A;  3AIA A;  3OII A;  4YQL A;  1UAK A;  2O3A A;  1IPA A;  5FAI A;  4H3Z A;  3KNU A;  4YPY A;  4H3Y A;  4YVH A;  3AXZ A;  4CNF A;  1VHK A;  3BBE A;  2V3J A;  3KY7 A;  2EGW A;  4YQS A;  4IG6 A;  1V6Z A;  5GMC A;  4YVI A;  4PZK A;  4YQ1 A;  3AI9 X;  3GYQ A;  1UAM A;  2EGV A;  4YQA A;  3DCM X;  3N4K A;  4YPX A;  4YQO A;  3ONP A;  4YQ0 A;  4YQB A;  3NK6 A;  4YPW A;  3ILK A;  3N4J A;  1O6D A;  4RG1 A;  4YQQ A;  4YVG A;  4L69 A;  4MCC A;  4YQ8 A;  3E5Y A;  2QMM A;  1J85 A;  4FAK A;  2I6D A;  1TO0 A;  4YQ7 A;  1GZ0 A;  4MCD A;  4XBO A;  1NXZ A;  4CNE A;  5D9F A;  1UAJ A;  1P9P A;  3IEF A;  1NS5 A;  3BBD A;  4CND A;  4YVJ A;  4YPZ A;  4YQG A;  4JAK A;  4YQP A;  5GM8 A;  4MCB A;  2NWA A;  4CNG A;  4X3L A;  4YQ5 A;  4YQN A;  3BBH A;  4KDZ A;  2QWV A;  4E8B A;  1ZJR A;  4JAL A;  4YVK A;  1X7P A;  4YQD A;  1VH0 A;  2CX8 A;  1V2X A;  2Z0Y A;  4YQ9 A;  3O7B A;  4YQ2 A;  4YQK A;  4YQ6 A;  3OIN A;  4YQT A;  1VHY A;  4KGN A;  2HA8 A;  4YQJ A;  1MXI A;  4X3M A;  2V3K A;  3NK7 A;  4J3C A;  3OIJ A;  1UAL A;  4YQI A;  4YQR A; 
#chains in the Genus database with same CATH topology
 4YQ3 A;  2G6G A;  1Z85 A;  3KTY A;  1QRT A;  3CF5 S;  1X7O A;  4WFA S;  4IOC S;  3QUV A;  5GMB A;  4YQ4 A;  3KW2 A;  3IC6 A;  3L8U A;  5CO4 A;  4JXZ A;  2YY8 A;  3PIO S;  1O0C A;  1K3R A;  5JVH S;  4JYZ A;  3W2W B;  1OY5 A;  3AIA A;  3OII A;  4YQC A;  4YQL A;  1UAK A;  2O3A A;  3CZB A;  1ZJW A;  1IPA A;  5FAI A;  5BNZ A;  2RE8 A;  4H3Z A;  2PJJ A;  1GTR A;  3KNU A;  4YPY A;  5DM7 S;  1EUY A;  4H3Y A;  1EUQ A;  4YVH A;  3AXZ A;  4FMW A;  4CNF A;  3PIP S;  2PNW A;  5HL7 S;  1VHK A;  2GAE A;  2ZJQ S;  3BBE A;  3DLL S;  1B75 A;  2V3J A;  3KY7 A;  2EGW A;  4YQS A;  1QRU A;  4JWJ A;  5GAH W;  5GAG W;  4IG6 A;  1V6Z A;  5GMC A;  4YVI A;  4PZK A;  4YQ1 A;  3AI9 X;  3GYQ A;  1UAM A;  2EGV A;  4YQA A;  3DCM X;  3N4K A;  4YPX A;  1EXD A;  3X1L B;  3ONP A;  4YQO A;  4YQ0 A;  4YQB A;  3NK6 A;  4JWF A;  4YPW A;  3ILK A;  3N4J A;  1O6D A;  4RG1 A;  4YQQ A;  4YVG A;  4L69 A;  4MCC A;  1QRS A;  2HZ7 A;  4IOA S;  2QMM A;  3E5Y A;  4YQ8 A;  1NYL A;  4WFN S;  4H4K A;  1J85 A;  4FAK A;  2I6D A;  2G5D A;  2PIC A;  1TO0 A;  4YQ7 A;  1GZ0 A;  4MCD A;  5IZN A;  4XBO A;  1NXZ A;  4CNE A;  5JVG S;  5D9F A;  1UDX A;  1FEU A;  3J7Z V;  1UAJ A;  1P9P A;  3IEF A;  1NS5 A;  2RD2 A;  5GAD W;  3BBD A;  4CND A;  4YVJ A;  4YPZ A;  4YQG A;  4JAK A;  4YQP A;  5GM8 A;  4MCB A;  2NWA A;  4CNG A;  4X3L A;  1O0B A;  2ZJP S;  4YQ5 A;  4YQN A;  2AE0 X;  3BBH A;  4KDZ A;  2QWV A;  4E8B A;  1ZJR A;  3W2V B;  1QTQ A;  4JAL A;  4UY8 8;  4YVK A;  1X7P A;  2ZJR S;  4YQD A;  1D6K A;  5GAE W;  1VH0 A;  4H3S A;  2CX8 A;  4WCE S;  2Z0Y A;  4WF9 S;  1V2X A;  1DFU P;  3O7B A;  4YQ9 A;  4JXX A;  4YQ2 A;  4P2B A;  4YQK A;  4YQ6 A;  3OIN A;  2PI8 A;  5DM6 S;  4JWH A;  4YQT A;  1VHY A;  4IO9 S;  4JWG A;  4KGN A;  2HA8 A;  4YQJ A;  1MXI A;  4X3M A;  2V3K A;  3NK7 A;  1GTS A;  3AII A;  4U67 S;  4V19 4;  4J3C A;  3OIJ A;  1UAL A;  4YQI A;  4WFB S;  4YQR A; 
#chains in the Genus database with same CATH homology
 4YQ3 A;  1Z85 A;  3KTY A;  1X7O A;  5GMB A;  3QUV A;  4YQ4 A;  3KW2 A;  3IC6 A;  3L8U A;  5CO4 A;  2YY8 A;  1K3R A;  4YQC A;  1OY5 A;  3AIA A;  3OII A;  4YQL A;  1UAK A;  2O3A A;  1IPA A;  5FAI A;  4H3Z A;  3KNU A;  4YPY A;  4H3Y A;  4YVH A;  3AXZ A;  4FMW A;  4CNF A;  1VHK A;  3BBE A;  2V3J A;  3KY7 A;  2EGW A;  4YQS A;  4JWJ A;  4IG6 A;  1V6Z A;  5GMC A;  4YVI A;  4PZK A;  4YQ1 A;  3AI9 X;  3GYQ A;  1UAM A;  2EGV A;  4YQA A;  3DCM X;  3N4K A;  4YPX A;  4YQO A;  3ONP A;  4YQ0 A;  4YQB A;  3NK6 A;  4JWF A;  4YPW A;  3ILK A;  3N4J A;  1O6D A;  4RG1 A;  4YQQ A;  4YVG A;  4L69 A;  4MCC A;  4YQ8 A;  3E5Y A;  2QMM A;  1J85 A;  4FAK A;  2I6D A;  1TO0 A;  4YQ7 A;  1GZ0 A;  4MCD A;  4XBO A;  1NXZ A;  4CNE A;  5D9F A;  1UAJ A;  1P9P A;  3IEF A;  1NS5 A;  3BBD A;  4CND A;  4YVJ A;  4YPZ A;  4YQG A;  4JAK A;  4YQP A;  5GM8 A;  4MCB A;  2NWA A;  4CNG A;  4X3L A;  4YQ5 A;  4YQN A;  3BBH A;  4KDZ A;  2QWV A;  4E8B A;  1ZJR A;  4JAL A;  4YVK A;  1X7P A;  4YQD A;  1VH0 A;  2CX8 A;  1V2X A;  2Z0Y A;  4YQ9 A;  3O7B A;  4YQ2 A;  4YQK A;  4YQ6 A;  3OIN A;  4JWH A;  4YQT A;  1VHY A;  4JWG A;  4KGN A;  2HA8 A;  4YQJ A;  1MXI A;  4X3M A;  2V3K A;  3NK7 A;  4J3C A;  3OIJ A;  1UAL A;  4YQI A;  4YQR 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...

1VHKA

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations