SUPERFAMILY 1.75 HMM library and genome assignments server

LysM domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   LysM domain [ 54105]
Superfamily:   LysM domain [ 54106]
Families:   LysM domain [ 54107] (2)


Superfamily statistics
Genomes (2,547) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 15,018 95,920 2
Proteins 10,226 62,246 2


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.5489 Moderately Informative Inherited
Biological Process (BP) organ development 0.7234 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.03675 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.4916 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.007668 Moderately Informative Inherited
Biological Process (BP) immune system process 0.01159 Moderately Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.00001709 Informative Direct
Biological Process (BP) regulation of defense response 0.000003596 Informative Direct
Biological Process (BP) regulation of immune response 0.000142 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00517 Informative Inherited
Biological Process (BP) defense response 0.005817 Informative Inherited
Biological Process (BP) response to bacterium 0.005582 Informative Inherited
Biological Process (BP) organ morphogenesis 0.002968 Informative Inherited
Biological Process (BP) post-embryonic development 0.0002592 Highly Informative Direct
Biological Process (BP) positive regulation of defense response 0.00000000391 Highly Informative Direct
Biological Process (BP) defense response to bacterium 0.000001251 Highly Informative Direct
Biological Process (BP) regulation of innate immune response 0.00003373 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 0.0000003697 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)In linear amides0.0000000000008018Moderately InformativeDirect
Enzyme Commission (EC)Glycosidases, i.e. enzymes hydrolyzing O- and S-gl0.00000000005106Moderately InformativeDirect
Enzyme Commission (EC)N-acetylmuramoyl-L-alanine amidase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.000000000000004283Least InformativeDirect
Enzyme Commission (EC)Glycosylases0.0001722Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.003927Moderately InformativeInherited
Enzyme Commission (EC)In linear amides0.000000000001025InformativeDirect
Enzyme Commission (EC)N-acetylmuramoyl-L-alanine amidase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.000000001889Moderately InformativeDirect
Biological processSporulation0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processVirulence0.0000002199InformativeDirect
Biological processSeptation0Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell wall0.000002784Highly InformativeDirect
DomainSignal0.0000000002705Least InformativeDirect
DomainRepeat0.0000006364Least InformativeDirect
Post-translational modificationHydrolase0.00000000000159Least InformativeDirect
Post-translational modificationProtease0.05404Moderately InformativeInherited
Post-translational modificationAntimicrobial0InformativeDirect
Post-translational modificationThiol protease0.0000003659InformativeDirect
Post-translational modificationGlycosidase0.0003722InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cell wall metabolism0.0000003402Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0.000005816Moderately InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 2 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a LysM domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 2 hidden Markov models representing the LysM domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]