4A1J | Genus

Total Genus 46

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	46
sequence length	165
structure length	165
Chain Sequence	GMLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSAAHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINR

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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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	Bacillus subtilis
publication title	Structure of Ykud rcsb
molecule keywords	PUTATIVE L, D-TRANSPEPTIDASE YKUD
total genus	46
structure length	165
sequence length	165
chains with identical sequence	B
ec nomenclature	ec 2.-.-.-:
pdb deposition date	2011-09-15

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01476	LysM	LysM domain
A	PF03734	YkuD	L,D-transpeptidase catalytic domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	4a1jA02
3.10.350.10	Alpha Beta	Roll	Membrane-bound Lytic Murein Transglycosylase D; Chain A	LysM domain	4a1jA01

1E0GA 3U1PA 5DZPA 5E1IA 4A1IA 4GSRA 3TURA 3ZGPA 5BUMA 3VYPA 5DU7A 5DZJA 5E1GA 3U1QA 5D7HA 4A1JA 4Z7AA 5DCCA 3VYOA 3ZG4A 3ZQDA 4QRBA 4GSUA 4QR7A 4K73A 3VYNA 4QTFA 4HUCA 5K2LA 5DUJA 2L9YA 4ZFQA 4QRAA 5E51A 4GSQA 5C8QB 2MKXA 2DJPA 2MTZA 4LPQA 5LB1A 5DVPA 5E5LA 3VAEA 4A52A 4B9HA 5C8OA 5DC2A 1ZATA 4JMNA 1Y7MA 4LZHA 2HKLA 5K69A 4JMXA 4B8VA 4PXVA 4A1KA 4XVOA 3TX4A 5LBGA 5C8PA 2LTFA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1E0G A;  3U1P A;  5DZP A;  5E1I A;  4A1I A;  4GSR A;  3TUR A;  3ZGP A;  5BUM A;  3VYP A;  5DU7 A;  5DZJ A;  5E1G A;  3U1Q A;  5D7H A;  4A1J A;  4Z7A A;  5DCC A;  3VYO A;  3ZG4 A;  3ZQD A;  4QRB A;  4GSU A;  4QR7 A;  4K73 A;  3VYN A;  4QTF A;  4HUC A;  5K2L A;  5DUJ A;  2L9Y A;  4ZFQ A;  4QRA A;  5E51 A;  4GSQ A;  5C8Q B;  2MKX A;  2DJP A;  2MTZ A;  4LPQ A;  5LB1 A;  5DVP A;  5E5L A;  3VAE A;  4A52 A;  4B9H A;  5C8O A;  5DC2 A;  1ZAT A;  4JMN A;  1Y7M A;  4LZH A;  2HKL A;  5K69 A;  4JMX A;  4B8V A;  4PXV A;  4A1K A;  4XVO A;  3TX4 A;  5LBG A;  5C8P A;  2LTF A; 
#chains in the Genus database with same CATH topology
 1E0G A;  3U1P A;  5DZP A;  5E1I A;  4A1I A;  4GSR A;  3TUR A;  3ZGP A;  5BUM A;  3VYP A;  5DU7 A;  5DZJ A;  5E1G A;  3U1Q A;  5D7H A;  4A1J A;  4Z7A A;  5DCC A;  3VYO A;  3ZG4 A;  3ZQD A;  4QRB A;  4GSU A;  4QR7 A;  4K73 A;  3VYN A;  4QTF A;  4HUC A;  5K2L A;  5DUJ A;  2L9Y A;  4ZFQ A;  4QRA A;  5E51 A;  4GSQ A;  5C8Q B;  2MKX A;  2DJP A;  2MTZ A;  4LPQ A;  5LB1 A;  5DVP A;  5E5L A;  3VAE A;  4A52 A;  4B9H A;  5C8O A;  5DC2 A;  1ZAT A;  4JMN A;  1Y7M A;  4LZH A;  2HKL A;  5K69 A;  4JMX A;  4B8V A;  4PXV A;  4A1K A;  4XVO A;  3TX4 A;  5LBG A;  5C8P A;  2LTF A; 
#chains in the Genus database with same CATH homology
 1E0G A;  3U1P A;  5DZP A;  5E1I A;  4A1I A;  4GSR A;  3TUR A;  3ZGP A;  5BUM A;  3VYP A;  5DU7 A;  5DZJ A;  5E1G A;  3U1Q A;  5D7H A;  4A1J A;  4Z7A A;  5DCC A;  3VYO A;  3ZG4 A;  3ZQD A;  4QRB A;  4GSU A;  4QR7 A;  4K73 A;  3VYN A;  4QTF A;  4HUC A;  5K2L A;  5DUJ A;  2L9Y A;  4ZFQ A;  4QRA A;  5E51 A;  4GSQ A;  5C8Q B;  2MKX A;  2DJP A;  2MTZ A;  4LPQ A;  5LB1 A;  5DVP A;  5E5L A;  3VAE A;  4A52 A;  4B9H A;  5C8O A;  5DC2 A;  1ZAT A;  4JMN A;  1Y7M A;  4LZH A;  2HKL A;  5K69 A;  4JMX A;  4B8V A;  4PXV A;  4A1K A;  4XVO A;  3TX4 A;  5LBG A;  5C8P A;  2LTF 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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4A1JA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations