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 9,546 45,787 3
Proteins 8,812 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 0.6415 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.15 Least Informative Inherited
Biological Process (BP) developmental process 0.006141 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6733 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.01858 Least Informative Inherited
Biological Process (BP) response to stimulus 0.7839 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.003183 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.0001 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0101 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.002543 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.003971 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.02381 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.004827 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.008281 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.09027 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.2533 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.1629 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2458 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.2011 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.6455 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.0004717 Informative Direct
Biological Process (BP) biological adhesion 7.898e-08 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0005751 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.000481 Informative Direct
Biological Process (BP) generation of neurons 1.212e-06 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 2.352e-07 Informative Direct
Biological Process (BP) regulation of cell development 0.0003716 Informative Direct
Biological Process (BP) cell projection organization 0.002384 Informative Inherited
Biological Process (BP) cellular component movement 0.006461 Informative Inherited
Biological Process (BP) locomotion 0.005906 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.1679 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.02107 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.01881 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.01637 Informative Inherited
Biological Process (BP) chemotaxis 0.0001839 Highly Informative Direct
Biological Process (BP) cell adhesion 5.635e-08 Highly Informative Direct
Biological Process (BP) neuron projection development 0.0004297 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 0.3792 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.03188 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.01476 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 2.548e-13 Least Informative Direct
Molecular Function (MF) binding 0.4642 Least Informative Inherited
Molecular Function (MF) peptidase activity 1.842e-11 Informative Direct
Molecular Function (MF) protein dimerization activity 5.846e-10 Informative Direct
Molecular Function (MF) exopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 6.648e-12 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.000148 Highly Informative Direct
Cellular Component (CC) membrane 4.444e-06 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.6374 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.7345 Least Informative Inherited
Cellular Component (CC) plasma membrane 0.0008573 Moderately Informative Direct
Cellular Component (CC) vesicle 9.532e-05 Moderately Informative Direct
Cellular Component (CC) cell projection 9.924e-05 Moderately Informative Direct
Cellular Component (CC) extracellular region part 1.474e-09 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.297 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.2438 Moderately Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.005823 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 3.518e-05 Informative Direct
Cellular Component (CC) integral to membrane 3.717e-06 Informative Direct
Cellular Component (CC) extracellular matrix 5.107e-05 Informative Direct
Cellular Component (CC) synapse part 7.577e-06 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 1.268e-05 Informative Direct
Cellular Component (CC) nucleoplasm part 0.002395 Informative Inherited
Cellular Component (CC) nuclear body 7.329e-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 processDifferentiation7.254e-07Moderately InformativeDirect
Biological processCell adhesion4.423e-11InformativeDirect
Cellular componentMembrane2.729e-08Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell projection1.156e-12Moderately InformativeDirect
Cellular componentCytoplasmic vesicle3.002e-08Moderately InformativeDirect
Cellular componentCell junction2.041e-05Moderately InformativeDirect
Cellular componentSynapse1.812e-07InformativeDirect
Cellular componentExtracellular matrix0.0006644InformativeDirect
Cellular componentSynaptosome4.94e-12Highly InformativeDirect
Cellular componentPostsynaptic cell membrane4.035e-09Highly InformativeDirect
DomainSignal9.217e-16Least InformativeDirect
DomainEGF-like domain8.908e-14InformativeDirect
Molecular functionZinc4.161e-13Least InformativeDirect
Post-translational modificationHydrolase7.927e-09Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationRepressor8.48e-07Moderately 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 residues1.119e-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 ]