SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


Thioredoxin-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Thioredoxin fold [ 52832] (2)
Superfamily:   Thioredoxin-like [ 52833] (23)
Families:   Thioltransferase [ 52834] (15)
  PDI-like [ 52849] (2)
  Calsequestrin [ 52855]
  DsbA-like [ 100953] (3)
  Glutathione S-transferase (GST), N-terminal domain [ 52862] (18)
  Phosducin [ 52888]
  ERP29 N domain-like [ 52892] (2)
  spliceosomal protein U5-15Kd [ 52895]
  SH3BGR (SH3-binding, glutamic acid-rich protein-like) [ 102446]
  KaiB-like [ 102449] (2)
  DsbC/DsbG C-terminal domain-like [ 52898] (2)
  Glutathione peroxidase-like [ 52901] (28)
  Thioredoxin-like 2Fe-2S ferredoxin [ 52918]
  ArsC-like [ 69518] (3)
  Txnl5-like [ 110612]
  YuzD-like [ 117605]
  YKR049C-like [ 142395]
  Atu2684-like [ 142398]
  HyaE-like [ 142401]
  NQO2-like [ 142405]
  Mitochondrial ribosomal protein L51/S25/CI-B8 domain [ 142408]
  Selenoprotein W-related [ 142411] (3)
  UAS domain [ 159589]


Superfamily statistics
Genomes (3,255) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 135,619 814,729 301
Proteins 123,030 771,535 292


Functional annotation
General category Metabolism
Detailed category Redox

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0.000000004463Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)Acting on NADH or NADPH0.7939Moderately InformativeInherited
Enzyme Commission (EC)Peroxidases0InformativeDirect
Enzyme Commission (EC)NADH:ubiquinone reductase (H(+)-translocating)0.00000000009784InformativeDirect
Enzyme Commission (EC)With other acceptors0.0000000001562InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00000731InformativeDirect
Enzyme Commission (EC)Protein-histidine kinases0.0002113InformativeDirect
Enzyme Commission (EC)Protein-disulfide reductase0Highly InformativeDirect
Enzyme Commission (EC)Glutathione transferase0Highly InformativeDirect
Enzyme Commission (EC)Other oxidoreductases0.000000001046Highly InformativeDirect
Enzyme Commission (EC)Other intramolecular oxidoreductases0.000004643Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)nervous system disease0.05115Least InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.05096Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.4432Moderately InformativeInherited
Disease Ontology (DO)cell type cancer0.6005Moderately InformativeInherited
Disease Ontology (DO)malignant glioma0.7874InformativeInherited
Disease Ontology (DO)congenital hemolytic anemia0.00002639Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.4138Least InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.2232Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.6212Least InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.03245Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.3386Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.5971Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.2331InformativeInherited
Mammalian Phenotype (MP)abnormal redox activity0.000000005495Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thyroid hormone level0.03375Highly InformativeInherited
Mammalian Phenotype (MP)increased sensitivity to induced cell death0.2561Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.0001983Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.1443Least InformativeInherited
Worm Phenotype (WP)cell physiology variant1Least InformativeInherited
Worm Phenotype (WP)blast cell physiology variant1Least InformativeInherited
Worm Phenotype (WP)organism stress response variant0.00000004193Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0.9078Moderately InformativeInherited
Worm Phenotype (WP)body region morphology variant0.9487Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.9487Moderately InformativeInherited
Worm Phenotype (WP)developmental morphology variant0.9492Moderately InformativeInherited
Worm Phenotype (WP)adult body morphology variant0.95Moderately InformativeInherited
Worm Phenotype (WP)body morphology variant0.9663Moderately InformativeInherited
Worm Phenotype (WP)metal response variant0.001564InformativeInherited
Worm Phenotype (WP)pesticide response variant0.004215InformativeInherited
Worm Phenotype (WP)pericellular component morphology variant0.007452InformativeInherited
Worm Phenotype (WP)cell stress response variant0.04278InformativeInherited
Worm Phenotype (WP)enzyme activity reduced0Highly InformativeDirect
Worm Phenotype (WP)cadmium hypersensitive0.00004916Highly InformativeDirect
Worm Phenotype (WP)organism heat response variant0.8718Highly InformativeInherited

Document: WP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)tissue0.01205Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.05011Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.4285Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.754Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.004223Moderately InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)dermal system0.0001486InformativeDirect
Xenopus ANatomical entity (XAN)tail0.0002477InformativeDirect
Xenopus ANatomical entity (XAN)solid compound organ0.001345InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.001582InformativeInherited
Xenopus ANatomical entity (XAN)anatomical space0.4043InformativeInherited
Xenopus ANatomical entity (XAN)urinary system0.5369InformativeInherited
Xenopus ANatomical entity (XAN)bone tissue0.00001369Highly InformativeDirect
Xenopus ANatomical entity (XAN)pronephric tubule0.01893Highly InformativeInherited
Xenopus DEvelopment stage (XDE)post-embryonic stage0.000531Least InformativeDirect
Xenopus DEvelopment stage (XDE)climax stage0.3245Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 660.0006044InformativeDirect

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 cell0.000006185Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0.0002144Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.0009131Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0.001677Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.006762Least InformativeInherited
Plant ANatomical entity (PAN)flower0.02103Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.05835Least InformativeInherited
Plant ANatomical entity (PAN)whole plant0.09809Least InformativeInherited
Plant ANatomical entity (PAN)microsporophyll0.1702Least InformativeInherited
Plant ANatomical entity (PAN)megasporophyll0.6222Least InformativeInherited
Plant ANatomical entity (PAN)pollen0.0001963Moderately InformativeDirect
Plant ANatomical entity (PAN)portion of vascular tissue0.1448InformativeInherited
Plant ANatomical entity (PAN)phloem0.0005478Highly 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)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Isomerases0.000000000242Moderately InformativeDirect
Enzyme Commission (EC)Acting on a peroxide as acceptor0InformativeDirect
Enzyme Commission (EC)Acting on a sulfur group of donors0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Acting on NADH or NADPH0.496InformativeInherited
Enzyme Commission (EC)Catalysing the translocation of hydrons0.4973InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Carboxylic ester hydrolases1InformativeInherited
Enzyme Commission (EC)NADH dehydrogenase0.0000000000002519Highly InformativeDirect
Enzyme Commission (EC)NADH:ubiquinone reductase (H(+)-translocating)0.00000000005641Highly InformativeDirect
Enzyme Commission (EC)Other intramolecular oxidoreductases0.000001917Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.000003411Highly InformativeDirect
Enzyme Commission (EC)Protein-histidine kinases0.0003973Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.01866Highly InformativeInherited
Enzyme Commission (EC)Acting on hydrogen as donors0.1701Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationTransferase0.0000000003875Moderately InformativeDirect
Post-translational modificationEye lens protein0.000000000002569InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR012336 SSF52833 Protein matches
Abstract

Several biological processes regulate the activity of target proteins through changes in the redox state of thiol groups (S2 to SH2), where a hydrogen donor is linked to an intermediary disulphide protein. Such processes include the ferredoxin/thioredoxin system, the NADP/thioredoxin system, and the glutathione/glutaredoxin system [PubMed15862094]. Several of these disulphide proteins share a common structure, consisting of a three-layer alpha/beta/alpha core. Proteins that contain this thioredoxin fold include: 2Fe-2S ferredoxin, thioltransferase, phosducin, glutathione peroxidase-like enzymes, arsenate reductase, disulphide bond isomerase DsbC (C-terminal domain), disulphide bond facilitator DsbA (contains an alpha-helical insertion), glutathione S-transferase (N-terminal domain), Endoplasmic reticulum protein ERP29 (N-terminal domain), spliceosomal protein U5-15Kd, circadian oscillation regulator KaiB, protein disulphide isomerase PDI (contains two tandem repeats of this fold), and calsequestrin (contains three tandem repeats of this fold).

This entry differs from the thioredoxin fold protein, the classification of this fold is in the glutathione S-transferase enzymes, where this entry defines two regions containing this fold, and the thioredoxin fold protein defines only the N-terminal as containing this fold.


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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 489 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 Thioredoxin-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 489 hidden Markov models representing the Thioredoxin-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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]