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Lipocalins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Lipocalins [ 50813]
Superfamily:   Lipocalins [ 50814] (9)
Families:   Retinol binding protein-like [ 50815] (21)
  Fatty acid binding protein-like [ 50847] (17)
  Thrombin inhibitor [ 50872]
  Hypothetical protein YodA [ 101863]
  Hypothetical protein YwiB [ 101866]
  Phenolic acid decarboxylase (PAD) [ 141469]
  Dinoflagellate luciferase repeat [ 141472]
  Rv2717c-like [ 141475] (2)
  All1756-like [ 159230]


Superfamily statistics
Genomes (1,876) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 7,589 38,210 119
Proteins 7,313 37,012 118


Functional annotation
General category Processes_IC
Detailed category Transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0.00000000000004383Least InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0Moderately InformativeDirect
Enzyme Commission (EC)Other intramolecular oxidoreductases0Highly InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.2813Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.6742Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.004972Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle physiology0.2057Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal triglyceride level0.08009InformativeInherited
Mammalian Phenotype (MP)abnormal fat-soluble vitamin level0.000001325Highly InformativeDirect
Mammalian Phenotype (MP)decreased triglyceride level0.0001121Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.01219Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.4423Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.6092Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.0715Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.1648Moderately InformativeInherited
Worm Phenotype (WP)lipid metabolism variant0.00000003869InformativeDirect
Worm Phenotype (WP)pesticide response variant0.002043InformativeInherited
Worm Phenotype (WP)pigmentation variant0.004373InformativeInherited
Worm Phenotype (WP)cell stress response variant0.1442InformativeInherited
Worm Phenotype (WP)fat content increased0.00001269Highly InformativeDirect
Worm Phenotype (WP)paraquat hypersensitive0.00002985Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)behavior defective0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA 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)portion of meristem tissue0Least 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)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately 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)Oxidoreductases0.002485Least InformativeInherited
Enzyme Commission (EC)Isomerases0.000000000008304Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Other intramolecular oxidoreductases0Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR011038 SSF50814 Protein matches
Abstract

Calycins form a large protein superfamily that share similar beta-barrel structures. Calycins can be divided into families that include lipocalins, fatty acid binding proteins, triabin, and thrombin inhibitor [PubMed11058743]. Of these families, the lipocalin family is the largest and functionally the most diverse. Lipocalins are extracellular proteins that share several common recognition properties such as ligand binding, receptor binding and the formation of complexes with other macromolecules. Lipocalins include the retinol binding protein, lipocalin allergen, aphrodisin (a sex hormone), alpha-2U-globulin, prostaglandin D synthase, beta-lactoglobulin, bilin-binding protein, and the nitrophorins [PubMed12432930, PubMed11058763, PubMed11058769, PubMed11058756].

This entry represents calycin as well as some other proteins that share a similar calycin beta-barrel structure, including two bacterial hypothetical proteins YodA from Escherichia coli and YwiB from bacillus subtilis. Part of the YodA hypothetical protein has a calycin-like structure [PubMed12909634].

Please be aware that some of the protein hits may be false positives.


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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 69 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 Lipocalins 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 69 hidden Markov models representing the Lipocalins 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]