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 (1,104) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,548 45,787 3
Proteins 8,814 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) developmental process 0.006292 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.6833 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1705 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.05248 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.02629 Least Informative Inherited
Biological Process (BP) response to stimulus 0.789 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.003559 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.0001457 Moderately Informative Direct
Biological Process (BP) nervous system development 0.02629 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.02297 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.003963 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.002546 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.01454 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.11 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.005272 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.1465 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.3116 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.1664 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2556 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.2048 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.6797 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.0004619 Informative Direct
Biological Process (BP) biological adhesion 0.00000006468 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0004899 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0005623 Informative Direct
Biological Process (BP) generation of neurons 0.000001261 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0000002785 Informative Direct
Biological Process (BP) regulation of cell development 0.0002211 Informative Direct
Biological Process (BP) cellular component movement 0.00656 Informative Inherited
Biological Process (BP) cell projection organization 0.002512 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.01798 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.002567 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.005706 Informative Inherited
Biological Process (BP) locomotion 0.005981 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.1709 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.02281 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.02022 Informative Inherited
Biological Process (BP) chemotaxis 0.0001829 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0000000452 Highly Informative Direct
Biological Process (BP) neuron projection development 0.0004403 Highly Informative Direct
Biological Process (BP) positive regulation of cellular component biogenesis 0.0000458 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0.0005146 Highly Informative Direct
Biological Process (BP) positive regulation of neurogenesis 0.0000004266 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.0292 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-templated 0.01207 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0000000000002641 Least Informative Direct
Molecular Function (MF) binding 0.4771 Least Informative Inherited
Molecular Function (MF) peptidase activity 0.00000000001967 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0000000006076 Informative Direct
Molecular Function (MF) exopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 0.000000000006786 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0001523 Highly Informative Direct
Molecular Function (MF) cell adhesion molecule binding 0.00000002227 Highly Informative Direct
Cellular Component (CC) membrane 0.000004461 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.4415 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.7376 Least Informative Inherited
Cellular Component (CC) vesicle 0.0001021 Moderately Informative Direct
Cellular Component (CC) cell projection 0.0001211 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.000000001499 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.000008775 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.1818 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.2387 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.00000871 Informative Direct
Cellular Component (CC) extracellular matrix 0.00004516 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0003477 Informative Direct
Cellular Component (CC) synapse 0.0001947 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.00001549 Informative Direct
Cellular Component (CC) nuclear body 0.0000007327 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 processDifferentiation0.0000007254Moderately InformativeDirect
Biological processCell adhesion0.00000000004423InformativeDirect
Cellular componentMembrane0.00000002729Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell projection0.000000000001156Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.00000003002Moderately InformativeDirect
Cellular componentCell junction0.00002041Moderately InformativeDirect
Cellular componentSynapse0.0000001812InformativeDirect
Cellular componentExtracellular matrix0.0006644InformativeDirect
Cellular componentSynaptosome0.00000000000494Highly InformativeDirect
Cellular componentPostsynaptic cell membrane0.000000004035Highly InformativeDirect
DomainSignal9.217e-16Least InformativeDirect
DomainEGF-like domain0.00000000000008908InformativeDirect
Molecular functionZinc0.0000000000004161Least InformativeDirect
Post-translational modificationHydrolase0.000000007927Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationRepressor0.000000848Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.000432Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationCarboxypeptidase0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.0000000001119Moderately 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 ]