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 (2,567) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 8,449 15,415 10
Proteins 8,254 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 process0.76211Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.95731Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.2521Least InformativeInherited
Biological Process (BP)single-organism cellular process0.95651Least InformativeInherited
Biological Process (BP)cellular component biogenesis0.01090.02922Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.0010660.001295Moderately InformativeInherited
Biological Process (BP)organelle organization0.017590.1876Moderately InformativeInherited
Biological Process (BP)actin filament-based process1.824e-071.348e-05InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly8.495e-074.691e-08InformativeDirect
Biological Process (BP)protein complex assembly3.338e-050.009561InformativeInherited
Biological Process (BP)cytoskeleton organization6.103e-050.001561InformativeInherited
Biological Process (BP)actin filament organization1.422e-102.669e-09Highly InformativeDirect
Biological Process (BP)protein polymerization6.642e-140Highly InformativeDirect
Molecular Function (MF)binding0.29051Least InformativeInherited
Molecular Function (MF)oxidoreductase activity8.037e-051.549e-08Moderately InformativeDirect
Molecular Function (MF)cation binding5.477e-116.179e-12Moderately InformativeDirect
Molecular Function (MF)cytoskeletal protein binding8.314e-091.562e-06InformativeDirect
Molecular Function (MF)transition metal ion binding0.3030.3762InformativeInherited
Molecular Function (MF)oxidoreductase activity, acting on a sulfur group of donors00Highly InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle0.0002320.03872Least InformativeInherited
Cellular Component (CC)protein complex0.64831Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.9271Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.93941Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)cytoskeleton1.537e-051.476e-05Moderately InformativeDirect
Cellular Component (CC)endosome0.0027230.02485InformativeInherited
Cellular Component (CC)late endosome1.867e-054.159e-05Highly 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) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular response to stress 0.4978 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.7629 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.02922 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.001295 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.1876 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 3.546e-05 Informative Direct
Biological Process (BP) actin filament-based process 1.348e-05 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 4.691e-08 Informative Direct
Biological Process (BP) protein complex assembly 0.009561 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.001561 Informative Inherited
Biological Process (BP) actin filament organization 2.669e-09 Highly Informative Direct
Biological Process (BP) protein polymerization 0 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 1.549e-08 Moderately Informative Direct
Molecular Function (MF) cation binding 6.179e-12 Moderately Informative Direct
Molecular Function (MF) cytoskeletal protein binding 1.562e-06 Informative Direct
Molecular Function (MF) transition metal ion binding 0.3762 Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on a sulfur group of donors 0 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.03872 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoskeleton 1.476e-05 Moderately Informative Direct
Cellular Component (CC) endosome 0.02485 Informative Inherited
Cellular Component (CC) late endosome 4.159e-05 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)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least 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)guard cell0Least 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)Lyases0.02275Least 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 processTransport0.8251Least InformativeInherited
Biological processInnate immunity1.29e-06InformativeDirect
Biological processElectron transport8.359e-05InformativeDirect
Cellular componentCytoplasm0.7181Least InformativeInherited
Cellular componentCytoskeleton7.837e-12Moderately InformativeDirect
Cellular componentMicrotubule3.333e-11InformativeDirect
Coding sequence diversitySelenocysteine5.574e-11InformativeDirect
DomainRedox-active center2.35e-13InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.0006498Moderately InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor9.348e-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 ]