SUPERFAMILY 1.75 HMM library and genome assignments server

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Pectin lyase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Single-stranded right-handed beta-helix [ 51125] (8)
Superfamily:   Pectin lyase-like [ 51126] (11)
Families:   Pectate lyase-like [ 51127] (2)
  Pectin lyase [ 51133]
  Galacturonase [ 51137] (2)
  Chondroitinase B [ 51144]
  iota-carrageenase [ 69333]
  Pectate transeliminase [ 101951]
  Dextranase, catalytic domain [ 101954]
  Pectin methylesterase [ 51147]
  P22 tailspike protein [ 51150]
  Virulence factor P.69 pertactin [ 51153]
  Filamentous hemagglutinin FhaB, secretion domain [ 101957]


Superfamily statistics
Genomes (2,373) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 31,250 189,263 36
Proteins 26,144 153,801 36


Functional annotation
General category Metabolism
Detailed category Polysaccharide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0.0003098Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1Least InformativeInherited
Enzyme Commission (EC)Carboxylic ester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Glycosidases, i.e. enzymes hydrolyzing O- and S-gl0Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0.2093Moderately InformativeInherited
Enzyme Commission (EC)Acting on polysaccharides0InformativeDirect
Enzyme Commission (EC)Alpha-galactosidase0.0001044Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Glycosylases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Carboxylic ester hydrolases0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0.001307InformativeInherited
Enzyme Commission (EC)Serine endopeptidases0.2437InformativeInherited
Enzyme Commission (EC)Acting on polysaccharides0Highly InformativeDirect
Enzyme Commission (EC)Acting on carbohydrates and derivatives0.000000006002Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR011050 SSF51126 Protein matches
Abstract

Microbial pectin and pectate lyases are virulence factors that degrade the pectic components of the plant cell wall [PubMed9195887]. When the backbone of pectin is methylated it is known as pectin and is cleaved by pectin lyase, and when it is demethylated it is known as pectate and is cleaved by pectate lyase. Pectin lyase from Aspergillus niger displays a single-stranded, right-handed parallel beta-helix topology , where each coil contains three beta-strands and three turn regions. Several other virulence factors share this beta-helix topology, although they vary in the number of coils, including bacterial pectate lyases, fungal and bacterial galacturonases (such as rhamnogalacturonase and polygalacturonase), chrondroitinase B from Flavobacterium sp., iota-carrageenase from Alteromonas sp., pectin methylesterase (PemA), P22 tailspike protein from Salmonella phage P22, and the virulence factor P.69 pertactin from Bordetella pertussis that mediates adhesion to target mammalian cells [PubMed9724625].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) ]

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 32 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 Pectin lyase-like 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 32 hidden Markov models representing the Pectin lyase-like 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 · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]