5JFZ | Genus

Total Genus 65

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	65
sequence length	186
structure length	181
Chain Sequence	DPYLYPGLDIMRNRLNIHQQQRLEQAAYEMTALRAATIELGPLVRGLPHLRTIHRQLYQDIFDWAGQLREVDIPFCHFAYIEKEGNALMQDLEEEGYLVGLEKAKFVERLAHYYCEINVLHPFRVGSGLAQRIFFEQLAIHAGYQLSWQGIEKEAWNQANQSGAMGDLTALQMIFSKVVSE

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/5d013cd2f46574b869c1c46e/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d013cd2f46574b869c1c46e/pdb.gz): 1327 ms

reading 181 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

181 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:180});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	Transferase
source organism	Escherichia coli
publication title	Crystal Structure of the Escherichia coli Fic Toxin-Like Protein in Complex with Its Cognate Antitoxin. pubmed doi rcsb
molecule keywords	Probable adenosine monophosphate-protein transferase fic
total genus	65
structure length	181
sequence length	186
chains with identical sequence	C, E
ec nomenclature	ec 2.7.7.n1: Protein adenylyltransferase.
pdb deposition date	2016-04-19

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02661	Fic	Fic/DOC family

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.3290.10	Mainly Alpha	Orthogonal Bundle	Fic-like fold	Fido-like domain	5jfzA00

5CKLA 4U04A 3ZLMA 4M16A 4U0SA 5JJ6A 3ZC7A 4NPSA 5JJ7A 4LU4A 5JFFA 3LETA 4ITRA 2JK8A 2G03A 3CUCA 4PY3A 3ZCBA 4X2EA 5JFZA 4U0ZA 4WGJA 4XI8A 5CGLA 3S6AA 5CMTA 4N67A 5EU0A 4U0UA 2VY3A 2F6SA 2VZAA 4X2CA 3N3UA 4U07A 4X2DA 3SE5A 3SN9A 3SHGA
chains in the Genus database with same CATH superfamily

5CKLA 4U04A 3ZLMA 1NH1A 4M16A 4U0SA 5JJ6A 3SE5A 3ZC7A 4NPSA 5JJ7A 4LU4A 5JFFA 3LETA 4ITRA 2JK8A 2G03A 3CUCA 4PY3A 3ZCBA 4X2EA 5JFZA 4U0ZA 4WGJA 4XI8A 5CGLA 3S6AA 5CMTA 4N67A 5EU0A 4U0UA 2VY3A 2F6SA 2VZAA 4X2CA 3N3UA 4U07A 2NUNA 4X2DA 2NUDA 3SHGA 3SN9A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 5CKL A;  4U04 A;  3ZLM A;  4M16 A;  4U0S A;  5JJ6 A;  3ZC7 A;  4NPS A;  5JJ7 A;  4LU4 A;  5JFF A;  3LET A;  4ITR A;  2JK8 A;  2G03 A;  3CUC A;  4PY3 A;  3ZCB A;  4X2E A;  5JFZ A;  4U0Z A;  4WGJ A;  4XI8 A;  5CGL A;  3S6A A;  5CMT A;  4N67 A;  5EU0 A;  4U0U A;  2VY3 A;  2F6S A;  2VZA A;  4X2C A;  3N3U A;  4U07 A;  4X2D A;  3SE5 A;  3SN9 A;  3SHG A; 
#chains in the Genus database with same CATH topology
 5CKL A;  4U04 A;  3ZLM A;  1NH1 A;  4M16 A;  4U0S A;  5JJ6 A;  3SE5 A;  3ZC7 A;  4NPS A;  5JJ7 A;  4LU4 A;  5JFF A;  3LET A;  4ITR A;  2JK8 A;  2G03 A;  3CUC A;  4PY3 A;  3ZCB A;  4X2E A;  5JFZ A;  4U0Z A;  4WGJ A;  4XI8 A;  5CGL A;  3S6A A;  5CMT A;  4N67 A;  5EU0 A;  4U0U A;  2VY3 A;  2F6S A;  2VZA A;  4X2C A;  3N3U A;  4U07 A;  2NUN A;  4X2D A;  2NUD A;  3SHG A;  3SN9 A; 
#chains in the Genus database with same CATH homology
 5CKL A;  4U04 A;  3ZLM A;  4M16 A;  4U0S A;  5JJ6 A;  3ZC7 A;  4NPS A;  5JJ7 A;  4LU4 A;  5JFF A;  3LET A;  4ITR A;  2JK8 A;  2G03 A;  3CUC A;  4PY3 A;  3ZCB A;  4X2E A;  5JFZ A;  4U0Z A;  4WGJ A;  4XI8 A;  5CGL A;  3S6A A;  5CMT A;  4N67 A;  5EU0 A;  4U0U A;  2VY3 A;  2F6S A;  2VZA A;  4X2C A;  3N3U A;  4U07 A;  4X2D A;  3SE5 A;  3SN9 A;  3SHG 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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5JFZA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations