2Q0T | Genus

Total Genus 101

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	101
sequence length	258
structure length	258
Chain Sequence	GMTQTTPQPDPSRLRDELVRLHGKASPEWDSLVRLDPRFVDAYLKFAGVPQRRNHLDDKTRAFIALAADACATQLYAPGVARHIERALSFGATREELIEVLELVSTIGIHTSNVGVPVLLEVLEEEGLRKGAPPLDERRQKLKAEFETNRGYWHPTWEGLLELDPDLFEAYVEFSSVPWRTGVLSPKIKEFMYCAFDASATHLYVPGLKLHIRNALRYGATAEELMELLEIVSVTGIHGAELGAPLLEAALKRSGAAA

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

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Viewer cachePut cache://localLOAD_/file/5cfd7901fceb31809b2e5d16/pdb.gz

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The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/file/5cfd7901fceb31809b2e5d16/pdb.gz): 1126 ms

reading 258 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

258 atoms created

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

Time for creating model: 24 ms

Adding embedded #jmolscript: select ({0:257});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	Lyase
source organism	Burkholderia xenovorans
publication title	Crystal structure of putative gamma-carboxymuconolactone decarboxylase subunit (YP_554324.1) from Burkholderia xenovorans LB400 at 1.70 A resolution rcsb
molecule keywords	Putative gamma-carboxymuconolactone decarboxylase subunit
total genus	101
structure length	258
sequence length	258
chains with identical sequence	B, C
ec nomenclature
pdb deposition date	2007-05-22

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02627	CMD	Carboxymuconolactone decarboxylase family

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

cath code	Class	Architecture	Topology	Homology	Domain
1.20.1290.10	Mainly Alpha	Up-down Bundle	AhpD-like	AhpD-like	2q0tA01

4G9QA 1ME5A 5DIPA 2AF7A 1LW1A 2OYOA 2Q0TA 2O4DA 5DIKA 3C1LA 3LVYA 2CWQA 2IJCA 2GMYA 3BEYA 1GU9A 3D7IA 2PFXA 1P8CA 2OUWA 2PRRA 2QEUA 1KNCA 1VKEA
chains in the Genus database with same CATH superfamily

4G9QA 1ME5A 3AA1A 3LK41 5DIPA 3LK2A 2AF7A 4AKRA 1LW1A 2OYOA 3AAEA 2KXPA 2Q0TA 2KZ7A 2O4DA 5DIKA 5ADXK 3C1LA 3AA0A 3AAAA 3LVYA 2CWQA 3AA6A 2IJCA 2GMYA 3BEYA 1GU9A 3D7IA 2PFXA 1P8CA 2OUWA 2PRRA 2QEUA 3AA7A 2JN8A 2ES9A 3LK3A 5AFUK 1KNCA 1IZNA 1VKEA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4G9Q A;  1ME5 A;  5DIP A;  2AF7 A;  1LW1 A;  2OYO A;  2Q0T A;  2O4D A;  5DIK A;  3C1L A;  3LVY A;  2CWQ A;  2IJC A;  2GMY A;  3BEY A;  1GU9 A;  3D7I A;  2PFX A;  1P8C A;  2OUW A;  2PRR A;  2QEU A;  1KNC A;  1VKE A; 
#chains in the Genus database with same CATH topology
 4G9Q A;  1ME5 A;  3AA1 A;  3LK4 1;  5DIP A;  3LK2 A;  2AF7 A;  4AKR A;  1LW1 A;  2OYO A;  3AAE A;  2KXP A;  2Q0T A;  2KZ7 A;  2O4D A;  5DIK A;  5ADX K;  3C1L A;  3AA0 A;  3AAA A;  3LVY A;  2CWQ A;  3AA6 A;  2IJC A;  2GMY A;  3BEY A;  1GU9 A;  3D7I A;  2PFX A;  1P8C A;  2OUW A;  2PRR A;  2QEU A;  3AA7 A;  2JN8 A;  2ES9 A;  3LK3 A;  5AFU K;  1KNC A;  1IZN A;  1VKE A; 
#chains in the Genus database with same CATH homology
 4G9Q A;  1ME5 A;  3AA1 A;  3LK4 1;  5DIP A;  3LK2 A;  2AF7 A;  4AKR A;  1LW1 A;  2OYO A;  3AAE A;  2KXP A;  2Q0T A;  2KZ7 A;  2O4D A;  5DIK A;  5ADX K;  3C1L A;  3AA0 A;  3AAA A;  3LVY A;  2CWQ A;  3AA6 A;  2IJC A;  2GMY A;  3BEY A;  1GU9 A;  3D7I A;  2PFX A;  1P8C A;  2OUW A;  2PRR A;  2QEU A;  3AA7 A;  2JN8 A;  2ES9 A;  3LK3 A;  5AFU K;  1KNC A;  1IZN A;  1VKE A;

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similar chains in the Genus database (?% sequence similarity)

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similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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2Q0TA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations