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 (2,615) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,691 34,085 10
Proteins 8,482 33,757 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)cellular component organization or biogenesis0.30221Least InformativeInherited
Biological Process (BP)protein metabolic process0.78751Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.96581Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)cellular component biogenesis0.012390.03718Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.0042850.0284Moderately InformativeInherited
Biological Process (BP)single-organism organelle organization0.00092790.09479Moderately InformativeInherited
Biological Process (BP)actin filament-based process0.00000019020.00001664InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly0.00000098960.00000009076InformativeDirect
Biological Process (BP)cytoskeleton organization0.000037740.001892InformativeInherited
Biological Process (BP)actin filament organization0.00000000017430.0000000039Highly InformativeDirect
Biological Process (BP)protein polymerization0.00000000000018510.000000000000007248Highly InformativeDirect
Molecular Function (MF)binding0.44171Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.00030550.00000008131Moderately InformativeDirect
Molecular Function (MF)cation binding0.00000000080810.0000000001145Moderately InformativeDirect
Molecular Function (MF)cytoskeletal protein binding0.000000009490.000002237InformativeDirect
Molecular Function (MF)zinc ion binding0.00000000031340.00000000005211InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on a sulfur group of donors00Highly InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.0025520.1783Least InformativeInherited
Cellular Component (CC)protein complex0.66671Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.99951Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)cytoskeleton0.0000024980.00006131Moderately InformativeDirect
Cellular Component (CC)endosome0.0030850.02737InformativeInherited
Cellular Component (CC)late endosome0.000019660.00004855Highly 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) cellular component organization or biogenesis 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) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular component biogenesis 0.03718 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.0284 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.09479 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 0.00005031 Informative Direct
Biological Process (BP) actin filament-based process 0.00001664 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.00000009076 Informative Direct
Biological Process (BP) cytoskeleton organization 0.001892 Informative Inherited
Biological Process (BP) actin filament organization 0.0000000039 Highly Informative Direct
Biological Process (BP) protein polymerization 0.000000000000007248 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.00000008131 Moderately Informative Direct
Molecular Function (MF) cation binding 0.0000000001145 Moderately Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0.000002237 Informative Direct
Molecular Function (MF) zinc ion binding 0.00000000005211 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a sulfur group of donors 0 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.1783 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) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.00006131 Moderately Informative Direct
Cellular Component (CC) endosome 0.02737 Informative Inherited
Cellular Component (CC) late endosome 0.00004855 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)Lyases0.02279Least 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 processTransport0.8464Least InformativeInherited
Biological processInnate immunity0.000001584InformativeDirect
Biological processElectron transport0.00009108InformativeDirect
Cellular componentCytoplasm0.8097Least InformativeInherited
Cellular componentCytoskeleton0.00000000001136Moderately InformativeDirect
Cellular componentMicrotubule0.00000000003716InformativeDirect
Coding sequence diversitySelenocysteine0.00000000005829InformativeDirect
DomainRedox-active center0.0000000000002611InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.0008744Moderately InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0.00000000973InformativeDirect

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 ]