SUPERFAMILY 1.75 HMM library and genome assignments server


Carboxypeptidase regulatory domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Prealbumin-like [ 49451] (7)
Superfamily:   Carboxypeptidase regulatory domain-like [ 49464] (2)
Families:   Carboxypeptidase regulatory domain [ 49465] (2)
  Pre-dockerin domain [ 141082]


Superfamily statistics
Genomes (1,103) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,543 45,787 3
Proteins 8,811 44,560 3


Functional annotation
General category Regulation
Detailed category Other regulatory function

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) regulation of cellular process 0.6426 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.137 Least Informative Inherited
Biological Process (BP) developmental process 0.00554 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6399 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.01679 Least Informative Inherited
Biological Process (BP) response to stimulus 0.7544 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.002859 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular component organization 8.272e-05 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.009807 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.002407 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.003985 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.02314 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.004486 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.006649 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.2029 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.0799 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.2366 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2316 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.6277 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.0004381 Informative Direct
Biological Process (BP) biological adhesion 7.187e-08 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0005966 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0004291 Informative Direct
Biological Process (BP) generation of neurons 1.104e-06 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 2.278e-07 Informative Direct
Biological Process (BP) regulation of cell development 0.0003226 Informative Direct
Biological Process (BP) cell projection organization 0.002264 Informative Inherited
Biological Process (BP) cellular component movement 0.006178 Informative Inherited
Biological Process (BP) locomotion 0.005622 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.1615 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.01939 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.01724 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.01412 Informative Inherited
Biological Process (BP) chemotaxis 0.0002002 Highly Informative Direct
Biological Process (BP) cell adhesion 5.319e-08 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in neuron differentiation 0.0001146 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0.0004687 Highly Informative Direct
Biological Process (BP) axon development 5.837e-05 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.01447 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1.867e-13 Least Informative Direct
Molecular Function (MF) binding 0.4255 Least Informative Inherited
Molecular Function (MF) peptidase activity 1.825e-11 Informative Direct
Molecular Function (MF) protein dimerization activity 5.088e-10 Informative Direct
Molecular Function (MF) exopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 5.682e-12 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0001517 Highly Informative Direct
Cellular Component (CC) membrane 2.752e-06 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.629 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.7154 Least Informative Inherited
Cellular Component (CC) plasma membrane 0.0007464 Moderately Informative Direct
Cellular Component (CC) vesicle 8.675e-05 Moderately Informative Direct
Cellular Component (CC) cell projection 7.628e-05 Moderately Informative Direct
Cellular Component (CC) extracellular region part 1.035e-09 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.2981 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.2451 Moderately Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.006495 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 3.346e-05 Informative Direct
Cellular Component (CC) integral to membrane 3.895e-06 Informative Direct
Cellular Component (CC) extracellular matrix 4.516e-05 Informative Direct
Cellular Component (CC) synapse part 4.555e-06 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 1.196e-05 Informative Direct
Cellular Component (CC) nucleoplasm part 0.002335 Informative Inherited
Cellular Component (CC) nuclear body 7.275e-07 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)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Metallocarboxypeptidases0Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)pericellular component development variant0Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant0InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus DEvelopment stage (XDE)embryonic stage0Least InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage0Least 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)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Metallocarboxypeptidases0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation6.946e-07Moderately InformativeDirect
Biological processCell adhesion4.392e-11InformativeDirect
Cellular componentMembrane2.647e-08Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell projection1.082e-12Moderately InformativeDirect
Cellular componentCytoplasmic vesicle2.882e-08Moderately InformativeDirect
Cellular componentCell junction2.029e-05Moderately InformativeDirect
Cellular componentSynapse1.791e-07InformativeDirect
Cellular componentExtracellular matrix0.0006662InformativeDirect
Cellular componentSynaptosome4.952e-12Highly InformativeDirect
Cellular componentPostsynaptic cell membrane4.054e-09Highly InformativeDirect
DomainSignal9.229e-16Least InformativeDirect
DomainEGF-like domain9.095e-14InformativeDirect
Molecular functionZinc3.555e-13Least InformativeDirect
Post-translational modificationHydrolase7.41e-09Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationRepressor7.777e-07Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0004351Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationCarboxypeptidase0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues1.136e-10Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008969 SSF49464 Protein matches
Abstract

This domain identifies a number of eukaryotic carboxypeptidases, these include carboxypeptidase D, E (H), N, X, X2 and Z. These are metallopeptidases belong to MEROPS peptidase family M14 (clan MC), subfamily M14B.

Carboxypeptidase D (CPD) is a new B-type metallocarboxypeptidase that is membrane bound and has an acidic pH optimum. A hydrophobic region at the N-terminus represents the signal peptide, and one near the C-terminus that probably represents the transmembrane anchor. A regulatory domain within the protein has been identified as a beta-sandwich, comprising 7 strands in 2 sheets in a greek-key topology. Some family members have an additional 1-2 strands to the common fold [PubMed11080148].

The bacterial and archaeal sequences having this signature are variously annotated, examples are:

  • Hypothetical/conserved/membrane/cell surface protein
  • N-acetylglucosamine deacetylase
  • Side tail fibre protein homolog from lambdoid prophage Rac
  • Hypothetical tonB-linked outer membrane receptor
  • OmpA-related protein
  • Putative outer membrane protein, probably involved in nutrient binding
  • TonB-dependent receptor


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-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · 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 3 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 Carboxypeptidase regulatory domain-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 3 hidden Markov models representing the Carboxypeptidase regulatory domain-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-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]