SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (2,554) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 15,058 85,729 2
Proteins 10,263 57,708 2


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) response to stimulus 0.8519 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) immune system process 0.0000158 Moderately Informative Direct
Biological Process (BP) defense response 0.000009845 Moderately Informative Direct
Biological Process (BP) response to biotic stimulus 0.000005738 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.0007095 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.01276 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.005679 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.01199 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.1379 Moderately Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.0000000167 Informative Direct
Biological Process (BP) system process 0.00001448 Informative Direct
Biological Process (BP) response to temperature stimulus 0.0000000001082 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00001512 Informative Direct
Biological Process (BP) regulation of immune response 0.0000001375 Informative Direct
Biological Process (BP) defense response to other organism 0.0000000006062 Informative Direct
Biological Process (BP) response to bacterium 0.001902 Informative Inherited
Biological Process (BP) regulation of defense response 0.001211 Informative Inherited
Biological Process (BP) activation of innate immune response 0 Highly Informative Direct
Biological Process (BP) nervous system process 0.00000003251 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processVirulence0.000000000000006138Moderately InformativeDirect
Biological processCell cycle0.000000007456Moderately InformativeDirect
Biological processSporulation0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processPlant defense0.000004791InformativeDirect
Biological processSeptation0Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell wall0.00003343Highly InformativeDirect
DomainSignal0.0000000000001394Least InformativeDirect
DomainRepeat0.00000008021Least InformativeDirect
Molecular functionChitin-binding0Highly InformativeDirect
Post-translational modificationHydrolase0.00000000002959Least InformativeDirect
Post-translational modificationProtease0.06229Moderately InformativeInherited
Post-translational modificationAntimicrobial0InformativeDirect
Post-translational modificationThiol protease0.0000003288InformativeDirect
Post-translational modificationGlycosidase0.0002083InformativeDirect

Document: KW annotation of SCOP domains

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

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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]