1Y7M | 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	164
structure length	164
Chain Sequence	MLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSAAHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINR

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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reading 164 atoms

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164 atoms created

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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	Structural genomics, unknown function
source organism	Bacillus subtilis subsp. subtilis str. 168
publication title	B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes. pubmed doi rcsb
molecule keywords	hypothetical protein BSU14040
total genus	38
structure length	164
sequence length	164
chains with identical sequence	B
ec nomenclature
pdb deposition date	2004-12-09

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	1y7mA02
3.10.350.10	Alpha Beta	Roll	Membrane-bound Lytic Murein Transglycosylase D; Chain A	LysM domain	1y7mA01

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

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

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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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1Y7MA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations