1TIL | Genus

Total Genus 38

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	38
sequence length	117
structure length	117
Chain Sequence	HMSLAIDLEVKQDVLIVRLSGELDHHTAEELREQVTDVLENRAIRHIVLNLGQLTFMDASGLGVILGRYKQIKNVGGQMVVCAVSPAVKRLFDMSGLFKIIRVEADEQFALQALGVA

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__3852991532097647__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__3852991532097647__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1TIL/B/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__3852991532097647__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3852991532097647","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1TIL/B/"

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__3852991532097647__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfc178be7ef679294de02ab/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfc178be7ef679294de02ab/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfc178be7ef679294de02ab/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/5cfc178be7ef679294de02ab/pdb.gz): 62 ms

reading 117 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

117 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:116});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	Transcription
source organism	Geobacillus stearothermophilus
publication title	Crystal Structures of the ADP and ATP Bound Forms of the Bacillus Anti-sigma Factor SpoIIAB in Complex with the Anti-anti-sigma SpoIIAA. pubmed doi rcsb
molecule keywords	Anti-sigma F factor
total genus	38
structure length	117
sequence length	117
chains with identical sequence	D, F
ec nomenclature
pdb deposition date	2004-06-02

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
B	PF01740	STAS	STAS domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.750.24	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	STAS domain	1tilB00

3OIZA 1VC1A 4QTPA 1BUZA 5EZBA 1AUZA 3OIRA 3IH8A 4DGHA 3MGLA 5EUSA 1TILB 4DGFA 4HYLA 3IHBA 3LLOA 5EUXA 5EUWA 3F43A 1TH8B 3ZXNA 2KA5A 1H4YA 3AGDA 5EUUA 1H4XA 2VY9A 3ZTBA 4XS5A 3NY7A 3T6OA 1SBOA 3IHAA 3IH9A 3LKLA 2KLNA 5EUZA 1H4ZA 1TIDB 3AGEA 1THNB 1T6RA 3IF5A
chains in the Genus database with same CATH superfamily

1FC7A 5EUSA 2ZO9B 5EUWA 1WXXA 3C0KA 1WXWA 2KA5A 4L8KA 3AGDA 3QDQA 3D03A 4L1CA 1N6EA 2CWWA 3V8VA 3K50A 2ZOAA 3IHAA 2KLNA 1FC9A 1FC6A 3VSEA 1H4ZA 4DGHA 3DORA 1K32A 1VC1A 2DXNA 3LDFA 3OIRA 3IH8A 1N6DA 2RRLA 5EUXA 3GVJA 4AE2A 1TH8B 3D3UA 1H4YA 1V0FA 3GVKA 4XS5A 3IH9A 3LKLA 5EUZA 2B78A 3AGEA 4AEJA 3OIZA 1HF2A 5EZBA 3GVLA 3GMFA 1TILB 4DGFA 3IHBA 3LLOA 3F43A 3ZXNA 1N6FA 4JC0A 2AS0A 5EUUA 3GK7A 3DJAA 3NY7A 4HIZA 1SBOA 1TIDB 1BPLA 3EH7A 1T6RA 3IF5A 3GHFA 4QTPA 1FCFA 3JU4A 1BUZA 3MOGA 1AUZA 3MGLA 4HYLA 3V97A 1J7XA 3DUPA 2OASA 1V0EA 4GHNA 2VY9A 3ZTBA 3T6OA 2DXLA 1THNB 4DMGA 1H4XA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 3OIZ A;  1VC1 A;  4QTP A;  1BUZ A;  5EZB A;  1AUZ A;  3OIR A;  3IH8 A;  4DGH A;  3MGL A;  5EUS A;  1TIL B;  4DGF A;  4HYL A;  3IHB A;  3LLO A;  5EUX A;  5EUW A;  3F43 A;  1TH8 B;  3ZXN A;  2KA5 A;  1H4Y A;  3AGD A;  5EUU A;  1H4X A;  2VY9 A;  3ZTB A;  4XS5 A;  3NY7 A;  3T6O A;  1SBO A;  3IHA A;  3IH9 A;  3LKL A;  2KLN A;  5EUZ A;  1H4Z A;  1TID B;  3AGE A;  1THN B;  1T6R A;  3IF5 A; 
#chains in the Genus database with same CATH topology
 1FC7 A;  5EUS A;  2ZO9 B;  5EUW A;  1WXX A;  3C0K A;  1WXW A;  2KA5 A;  4L8K A;  3AGD A;  3QDQ A;  3D03 A;  4L1C A;  1N6E A;  2CWW A;  3V8V A;  3K50 A;  2ZOA A;  3IHA A;  2KLN A;  1FC9 A;  1FC6 A;  3VSE A;  1H4Z A;  4DGH A;  3DOR A;  1K32 A;  1VC1 A;  2DXN A;  3LDF A;  3OIR A;  3IH8 A;  1N6D A;  2RRL A;  5EUX A;  3GVJ A;  4AE2 A;  1TH8 B;  3D3U A;  1H4Y A;  1V0F A;  3GVK A;  4XS5 A;  3IH9 A;  3LKL A;  5EUZ A;  2B78 A;  3AGE A;  4AEJ A;  3OIZ A;  1HF2 A;  5EZB A;  3GVL A;  3GMF A;  1TIL B;  4DGF A;  3IHB A;  3LLO A;  3F43 A;  3ZXN A;  1N6F A;  4JC0 A;  2AS0 A;  5EUU A;  3GK7 A;  3DJA A;  3NY7 A;  4HIZ A;  1SBO A;  1TID B;  1BPL A;  3EH7 A;  1T6R A;  3IF5 A;  3GHF A;  4QTP A;  1FCF A;  3JU4 A;  1BUZ A;  3MOG A;  1AUZ A;  3MGL A;  4HYL A;  3V97 A;  1J7X A;  3DUP A;  2OAS A;  1V0E A;  4GHN A;  2VY9 A;  3ZTB A;  3T6O A;  2DXL A;  1THN B;  4DMG A;  1H4X A; 
#chains in the Genus database with same CATH homology
 3OIZ A;  1VC1 A;  4QTP A;  1BUZ A;  5EZB A;  1AUZ A;  3OIR A;  3IH8 A;  4DGH A;  3MGL A;  5EUS A;  1TIL B;  4DGF A;  4HYL A;  3IHB A;  3LLO A;  5EUX A;  5EUW A;  3F43 A;  1TH8 B;  3ZXN A;  2KA5 A;  1H4Y A;  3AGD A;  5EUU A;  1H4X A;  2VY9 A;  3ZTB A;  4XS5 A;  3NY7 A;  3T6O A;  1SBO A;  3IHA A;  3IH9 A;  3LKL A;  2KLN A;  5EUZ A;  1H4Z A;  1TID B;  3AGE A;  1THN B;  1T6R A;  3IF5 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...

1TILB

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations