SUPERFAMILY 1.75 HMM library and genome assignments server

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 (2,366) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 31,139 105,011 36
Proteins 26,067 88,042 36


Functional annotation
General category Metabolism
Detailed category Polysaccharide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular component organization or biogenesis11Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)multicellular organismal process11Least InformativeInherited
Biological Process (BP)developmental process11Least InformativeInherited
Biological Process (BP)carbohydrate metabolic process00Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process00Moderately InformativeDirect
Biological Process (BP)reproduction0.72281Moderately InformativeInherited
Biological Process (BP)multi-organism process0.61830.1961Moderately InformativeInherited
Biological Process (BP)cell differentiation0.86521Moderately InformativeInherited
Biological Process (BP)anatomical structure morphogenesis0.3460.987Moderately InformativeInherited
Biological Process (BP)polysaccharide metabolic process00InformativeDirect
Biological Process (BP)carbohydrate catabolic process00InformativeDirect
Biological Process (BP)cell wall organization or biogenesis0.00033570.00000003895InformativeDirect
Biological Process (BP)multi-multicellular organism process0.0041110.005507InformativeInherited
Biological Process (BP)developmental process involved in reproduction0.20190.4116InformativeInherited
Biological Process (BP)growth0.016060.07448InformativeInherited
Biological Process (BP)cellular component morphogenesis0.06220.3194InformativeInherited
Biological Process (BP)cellular process involved in reproduction0.067030.4423InformativeInherited
Biological Process (BP)polysaccharide catabolic process00Highly InformativeDirect
Biological Process (BP)cell growth0.000026830.000006108Highly InformativeDirect
Biological Process (BP)external encapsulating structure organization0.0000035050.000000007733Highly InformativeDirect
Biological Process (BP)developmental growth0.0008750.0009982Highly InformativeDirect
Biological Process (BP)cell morphogenesis involved in differentiation0.014390.6555Highly InformativeInherited
Molecular Function (MF)hydrolase activity0.000088970.000000003903Least InformativeDirect
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds11Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on glycosyl bonds00InformativeDirect
Molecular Function (MF)carboxylic ester hydrolase activity0.00004740.000000000006262Highly InformativeDirect
Cellular Component (CC)membrane11Least InformativeInherited
Cellular Component (CC)intrinsic to membrane0.72551Moderately InformativeInherited
Cellular Component (CC)external encapsulating structure0.10160.00002086InformativeInherited
Cellular Component (CC)anchored to membrane0.00036680.00037Highly InformativeDirect

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) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.1961 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.987 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0 Informative Direct
Biological Process (BP) cell wall organization or biogenesis 0.00000003895 Informative Direct
Biological Process (BP) defense response 1 Informative Inherited
Biological Process (BP) response to bacterium 0.1092 Informative Inherited
Biological Process (BP) multi-multicellular organism process 0.005507 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.4116 Informative Inherited
Biological Process (BP) epithelium development 0.9486 Informative Inherited
Biological Process (BP) growth 0.07448 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.3194 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.4423 Informative Inherited
Biological Process (BP) single-organism behavior 0.6018 Informative Inherited
Biological Process (BP) synaptic transmission 0.53 Informative Inherited
Biological Process (BP) polysaccharide catabolic process 0 Highly Informative Direct
Biological Process (BP) cell growth 0.000006108 Highly Informative Direct
Biological Process (BP) external encapsulating structure organization 0.000000007733 Highly Informative Direct
Biological Process (BP) developmental growth 0.0009982 Highly Informative Direct
Biological Process (BP) defense response to bacterium 0.03825 Highly Informative Inherited
Biological Process (BP) epidermal cell differentiation 0.0292 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.6555 Highly Informative Inherited
Biological Process (BP) learning or memory 0.03319 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.000000003903 Least Informative Direct
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 0 Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.000000000006262 Highly Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cell projection 0.9965 Moderately Informative Inherited
Cellular Component (CC) intrinsic to membrane 1 Moderately Informative Inherited
Cellular Component (CC) external encapsulating structure 0.00002086 Informative Direct
Cellular Component (CC) anchored to membrane 0.00037 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)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

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)hematopoietic system phenotype0Least InformativeDirect

Document: MP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

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 (peptide hydrolases)1Moderately InformativeInherited
Enzyme Commission (EC)Carboxylic ester hydrolases0InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0.2012InformativeInherited
Enzyme Commission (EC)Acting on polysaccharides0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processHost-virus interaction0.09309Moderately InformativeInherited
Biological processPolysaccharide degradation0InformativeDirect
Biological processVirulence0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processViral immunoevasion0.001173InformativeInherited
Biological processModulation of host ubiquitin pathway by viral deubiquitinase0.000000007339Highly InformativeDirect
Biological processInhibition of host IRF3 by virus0.0000000143Highly InformativeDirect
Biological processActivation of host autophagy by virus0.000001175Highly InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentPeriplasm0InformativeDirect
Cellular componentCell outer membrane0InformativeDirect
Cellular componentCell wall0Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0.000476Moderately InformativeDirect
DiseaseAllergen0.00000000000000433Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainRepeat0.000414Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainTransmembrane beta strand0InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationProtease1Moderately InformativeInherited
Post-translational modificationGlycosidase0InformativeDirect
Post-translational modificationSerine protease0.00000001296InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0.00000000000005916Least InformativeDirect
Post-translational modificationZymogen0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)glycan metabolism0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis1Moderately InformativeInherited
UniPathway (UP)glycan degradation0InformativeDirect
UniPathway (UP)alginate biosynthesis0Highly InformativeDirect
UniPathway (UP)pectin degradation0Highly InformativeDirect
UniPathway (UP)cell surface structure biogenesis0.00005951Highly InformativeDirect

Document: UP 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · 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 24 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 24 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]