SUPERFAMILY 1.75 HMM library and genome assignments server


Mss4-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Mss4-like [ 51315]
Superfamily:   Mss4-like [ 51316] (4)
Families:   RabGEF Mss4 [ 51317]
  Translationally controlled tumor protein TCTP (histamine-releasing factor) [ 63873]
  SelR domain [ 75041] (2)
  Glutathione-dependent formaldehyde-activating enzyme, Gfa [ 117338]


Superfamily statistics
Genomes (2,042) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 7,312 15,415 10
Proteins 7,113 15,252 10


Functional annotation
General category Regulation
Detailed category Signal transduction

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)protein metabolic process0.20030.4828Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.50740.8342Least InformativeInherited
Molecular Function (MF)binding0.076780.8827Least InformativeInherited
Molecular Function (MF)cation binding1.539e-140Moderately InformativeDirect
Molecular Function (MF)oxidoreductase activity0.0070451.654e-06Moderately InformativeInherited
Molecular Function (MF)transition metal ion binding0.27520.353InformativeInherited
Molecular Function (MF)zinc ion binding5.688e-143.07e-15Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on a sulfur group of donors2.657e-130Highly InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle0.035870.2132Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.49530.7023Least InformativeInherited
Cellular Component (CC)protein complex0.22170.3633Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.23280.135Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.74380.8132Least InformativeInherited
Cellular Component (CC)cytoskeleton0.0012610.001449Moderately InformativeInherited
Cellular Component (CC)endosome0.00014150.001947InformativeInherited
Cellular Component (CC)late endosome4.383e-071.761e-06Highly 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) protein metabolic process 0.4828 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.8342 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) response to oxidative stress 8.916e-06 Informative Direct
Molecular Function (MF) binding 0.8827 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 1.654e-06 Moderately Informative Direct
Molecular Function (MF) cation binding 0 Moderately Informative Direct
Molecular Function (MF) transition metal ion binding 0.353 Informative Inherited
Molecular Function (MF) zinc ion binding 3.07e-15 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a sulfur group of donors 0 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.2132 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.7023 Least Informative Inherited
Cellular Component (CC) protein complex 0.3633 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.135 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.8132 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.001449 Moderately Informative Inherited
Cellular Component (CC) endosome 0.001947 Informative Inherited
Cellular Component (CC) late endosome 1.761e-06 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)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases0.02642Least InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0Moderately InformativeDirect
Enzyme Commission (EC)With a disulfide as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Carbon-sulfur lyases1Highly InformativeInherited

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence 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)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases0.03803Least InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0InformativeDirect
Enzyme Commission (EC)Carbon-sulfur lyases1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.8065Least InformativeInherited
Biological processElectron transport7.729e-05InformativeDirect
Cellular componentCytoplasm0.6683Least InformativeInherited
Cellular componentCytoskeleton8.132e-07Moderately InformativeDirect
Cellular componentMicrotubule2.978e-11InformativeDirect
Coding sequence diversitySelenocysteine5.279e-11InformativeDirect
DomainRedox-active center2.113e-13InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor8.255e-09InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)one-carbon metabolism0Moderately InformativeDirect
UniPathway (UP)formaldehyde degradation0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR011057 SSF51316 Protein matches
Abstract

This entry represents a structural domain with a complex fold consisting of several coiled beta-sheets. This domain exists as a duplication, consisting of a tandem repeat of two similar structural motifs. These domains can be found in:

  • Mss4, which contains a zinc-binding site.
  • Translationally controlled tumour-associated protein TCTP, which contains an insertion of an alpha-helix hairpin, and which lacks a zinc-binding site.
  • The C-terminal MsrB domain of peptide methionine sulphoxide reductase.

Mss4 is a conserved accessory factor for Rab GTPases, which function as ubiquitous regulators of intracellular membrane trafficking [PubMed11258916]. Mss4 acts to promote nucleotide release from exocytic but not endocytic Rab GTPases. Mss4 has a complex fold made of several coiled beta-sheets, and consists of a duplication of tandem repeats of two similar structural motifs. It contains a zinc-binding site.

Other proteins that show structure similarity to Mss4 include the translationally controlled tumour-associated proteins TCTPs, which contains an insertion of an alpha helical hairpin, and lacks the zinc-binding site. TCTPs are a highly conserved and abundantly expressed family of eukaryotic proteins that are implicated in both cell growth and the human acute allergic response [PubMed11473261].

The C-terminal MsrB domain of peptide methionine sulphoxide reductase PilB is structurally similar to Mss4. Methionine sulphoxide reductases protect against oxidative damage that can contribute to cell death. The tandem Msr domains (MsrA and MsrB) of the pilB protein from Neisseria gonorrhoeae each reduce different epimeric forms of methionine sulphoxide [PubMed11938352].


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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 8 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 Mss4-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 8 hidden Markov models representing the Mss4-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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]