1SPH | Genus

Total Genus 25

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	25
sequence length	87
structure length	87
Chain Sequence	AQKTFKVTADSGIHARPATVLVQTASKYDADVNLEYNGKTVNLKDIMGVMSLGIAKGAEITISASGADENDALNALEETMKSEGLGE

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__762745990774335__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__762745990774335__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1SPH/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__762745990774335__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"762745990774335","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1SPH/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__762745990774335__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfc0654c642c33d94348f6c/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfc0654c642c33d94348f6c/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfc0654c642c33d94348f6c/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/5cfc0654c642c33d94348f6c/pdb.gz): 2197 ms

reading 87 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

87 atoms created

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

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:86});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	Phosphotransferase
source organism	Bacillus subtilis
publication title	Refined structures of the active Ser83-->Cys and impaired Ser46-->Asp histidine-containing phosphocarrier proteins. pubmed doi rcsb
molecule keywords	HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR
total genus	25
structure length	87
sequence length	87
chains with identical sequence	B
ec nomenclature
pdb deposition date	1994-11-03

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00381	PTS-HPr	PTS HPr component phosphorylation site

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.1340.10	Alpha Beta	2-Layer Sandwich	Histidine-containing Protein; Chain: A;	HPr-like	1sphA00

3OQOD 2RLZA 2JELP 3EZBB 5T17A 4XWJB 3OQND 3LE1A 1POHA 1MO1B 1QFRA 1VRCC 5T1OA 1PTFA 2LRLD 1SPHA 3LE3A 1PFHA 1KA5A 2HPRA 3LNWA 3EZEB 1MO1A 1Y4YA 1KKMH 2XDFC 1K1CA 5T1NA 1JEMA 2NZUL 1HDNA 1FU0A 2NZVL 3LFGA 1KKLH 1MU4A 3EZAB 1RZRL 1CM3A 2AK7A 3IHSA 2OENL 1J6TB 1ZVVJ 1QR5A 3CCDA 3LE5A 2LRKD 2FEPS 2HIDA 1CM2A 1OPDA 1PCHA 1TXEA 3OQMD 1GGRB 1Y51A 1Y50A
chains in the Genus database with same CATH superfamily

3OQOD 2RLZA 2JELP 3EZBB 5T17A 4XWJB 3OQND 3LE1A 1POHA 1MO1B 1QFRA 1VRCC 5T1OA 1PTFA 2LRLD 1SPHA 3LE3A 1PFHA 1KA5A 1J5YA 2HPRA 3LNWA 3EZEB 1MO1A 1Y4YA 1KKMH 2XDFC 1K1CA 5T1NA 1JEMA 2NZUL 1HDNA 1FU0A 2NZVL 3LFGA 1KKLH 1MU4A 3EZAB 1RZRL 1CM3A 2AK7A 3IHSA 2OENL 1J6TB 1ZVVJ 1QR5A 3CCDA 3LE5A 2LRKD 2FEPS 2HIDA 1CM2A 1OPDA 1PCHA 1TXEA 3OQMD 1GGRB 1Y51A 1Y50A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 3OQO D;  2RLZ A;  2JEL P;  3EZB B;  5T17 A;  4XWJ B;  3OQN D;  3LE1 A;  1POH A;  1MO1 B;  1QFR A;  1VRC C;  5T1O A;  1PTF A;  2LRL D;  1SPH A;  3LE3 A;  1PFH A;  1KA5 A;  2HPR A;  3LNW A;  3EZE B;  1MO1 A;  1Y4Y A;  1KKM H;  2XDF C;  1K1C A;  5T1N A;  1JEM A;  2NZU L;  1HDN A;  1FU0 A;  2NZV L;  3LFG A;  1KKL H;  1MU4 A;  3EZA B;  1RZR L;  1CM3 A;  2AK7 A;  3IHS A;  2OEN L;  1J6T B;  1ZVV J;  1QR5 A;  3CCD A;  3LE5 A;  2LRK D;  2FEP S;  2HID A;  1CM2 A;  1OPD A;  1PCH A;  1TXE A;  3OQM D;  1GGR B;  1Y51 A;  1Y50 A; 
#chains in the Genus database with same CATH topology
 3OQO D;  2RLZ A;  2JEL P;  3EZB B;  5T17 A;  4XWJ B;  3OQN D;  3LE1 A;  1POH A;  1MO1 B;  1QFR A;  1VRC C;  5T1O A;  1PTF A;  2LRL D;  1SPH A;  3LE3 A;  1PFH A;  1KA5 A;  1J5Y A;  2HPR A;  3LNW A;  3EZE B;  1MO1 A;  1Y4Y A;  1KKM H;  2XDF C;  1K1C A;  5T1N A;  1JEM A;  2NZU L;  1HDN A;  1FU0 A;  2NZV L;  3LFG A;  1KKL H;  1MU4 A;  3EZA B;  1RZR L;  1CM3 A;  2AK7 A;  3IHS A;  2OEN L;  1J6T B;  1ZVV J;  1QR5 A;  3CCD A;  3LE5 A;  2LRK D;  2FEP S;  2HID A;  1CM2 A;  1OPD A;  1PCH A;  1TXE A;  3OQM D;  1GGR B;  1Y51 A;  1Y50 A; 
#chains in the Genus database with same CATH homology
 3OQO D;  2RLZ A;  2JEL P;  3EZB B;  5T17 A;  4XWJ B;  3OQN D;  3LE1 A;  1POH A;  1MO1 B;  1QFR A;  1VRC C;  5T1O A;  1PTF A;  2LRL D;  1SPH A;  3LE3 A;  1PFH A;  1KA5 A;  2HPR A;  3LNW A;  3EZE B;  1MO1 A;  1Y4Y A;  1KKM H;  2XDF C;  1K1C A;  5T1N A;  1JEM A;  2NZU L;  1HDN A;  1FU0 A;  2NZV L;  3LFG A;  1KKL H;  1MU4 A;  3EZA B;  1RZR L;  1CM3 A;  2AK7 A;  3IHS A;  2OEN L;  1J6T B;  1ZVV J;  1QR5 A;  3CCD A;  3LE5 A;  2LRK D;  2FEP S;  2HID A;  1CM2 A;  1OPD A;  1PCH A;  1TXE A;  3OQM D;  1GGR B;  1Y51 A;  1Y50 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...

1SPHA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations