SUPERFAMILY 1.75 HMM library and genome assignments server


FMN-binding split barrel superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Split barrel-like [ 50474] (3)
Superfamily:   FMN-binding split barrel [ 50475] (4)
Families:   PNP-oxidase like [ 50476] (16)
  NADH:FMN oxidoreductase-like [ 50482] (5)
  UbiD middle domain-like [ 141368]
  MTH863-like [ 159164] (3)


Superfamily statistics
Genomes (2,998) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 19,133 87,129 34
Proteins 18,957 86,498 34


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

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)nitrogen compound metabolic process0.95781Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.66261Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.36470.9158Least InformativeInherited
Biological Process (BP)biosynthetic process0.66560.8955Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.93630.9182Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.42930.8945Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.074990.1431Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.011680.000421Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.00022522.604e-07InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process0.00012484.932e-06InformativeDirect
Biological Process (BP)vitamin metabolic process0.0011687.953e-06InformativeInherited
Biological Process (BP)vitamin B6 metabolic process1.244e-071.088e-12Highly InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.00033240.0001949Moderately InformativeDirect
Molecular Function (MF)transcription factor binding4.241e-106.266e-05Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor9.482e-116.436e-10Highly InformativeDirect
Cellular Component (CC)external encapsulating structure0.0019310.002955InformativeInherited

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) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.9158 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.8955 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.9182 Least Informative Inherited
Biological Process (BP) cofactor metabolic process 0.000421 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.1431 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.8945 Moderately Informative Inherited
Biological Process (BP) vitamin metabolic process 7.953e-06 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 2.604e-07 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 4.932e-06 Informative Direct
Biological Process (BP) vitamin B6 metabolic process 1.088e-12 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.0001949 Moderately Informative Direct
Molecular Function (MF) transcription factor binding 6.266e-05 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor 6.436e-10 Highly Informative Direct
Cellular Component (CC) external encapsulating structure 0.002955 Informative Inherited

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)Acting on the CH-NH group of donors1.171e-12Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP 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)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral 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)Acting on the CH-NH(2) group of donors0InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH group of donors5.208e-15InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAromatic hydrocarbons catabolism3.2e-08InformativeDirect
Cellular componentMembrane1.629e-09Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionNAD2.244e-09Moderately InformativeDirect
Molecular functionFMN0InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationDecarboxylase0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009002 SSF50475 Protein matches
Abstract

Sulphate-reducing bacteria possess many redox proteins including some flavoproteins. Flavodoxins are a group of proteins with a tightly bound flavin mononucleotide (FMN) that mediate electron transfer at low redox potential. A novel FMN-binding protein from Desulphovibrio vulgaris has been cloned and crystallised and shown to be composed of 122 amino acids making it the smallest of the known proteins which bind FMN [PubMed10713530]. The exact function of this protein is unknown but it may take part in the electron-transfer pathway. The structure has been shown to contain a FMN-binding split barrel, which is related to the ferredoxin reductase-like FAD-binding domain.


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) · Yeast Phenotype (YP) · 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 30 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 FMN-binding split barrel 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 30 hidden Markov models representing the FMN-binding split barrel 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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]