SUPERFAMILY 1.75 HMM library and genome assignments server

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Formyltransferase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Formyltransferase [ 53327]
Superfamily:   Formyltransferase [ 53328]
Families:   Formyltransferase [ 53329] (4)


Superfamily statistics
Genomes (3,082) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,824 46,846 13
Proteins 8,796 46,821 13


Functional annotation
General category Metabolism
Detailed category Transferases

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 process0.004870.0000001661Least InformativeInherited
Biological Process (BP)biosynthetic process0.029050.0000000005581Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.0015350.0000007941Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.0024620.000002113Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.0014950.0000005431Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.0097580.0003104Least InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.00034060.00001839Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process0.0038280.00191Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.0053290.00003085Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.0011650.0005391Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.0059670.0002524Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.0037760.0002214Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.0077060.0008021Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.013160.0006415Moderately InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.00000210.0003824InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process0.00000029720.000000001316InformativeDirect
Molecular Function (MF)transferase activity0.00066970.0003987Least InformativeDirect
Molecular Function (MF)transferase activity, transferring one-carbon groups0.000000026660InformativeDirect
Molecular Function (MF)hydroxymethyl-, formyl- and related transferase activity0.000000000000096620Highly 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 aromatic compound metabolic process 0.0000007941 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000001661 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0000000005581 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0003104 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000005431 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000002113 Least Informative Direct
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 amino acid metabolic process 0.0005129 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.0002524 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0002214 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.0005391 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.00001839 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00007483 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.00003085 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0008021 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0006415 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.03692 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.00191 Moderately Informative Inherited
Biological Process (BP) gene expression 0.02293 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.2046 Moderately Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.0002078 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.0003824 Informative Direct
Biological Process (BP) pigment metabolic process 0.0002859 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.00007317 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.000000001316 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.6555 Informative Inherited
Biological Process (BP) translational initiation 0.0000003472 Highly Informative Direct
Biological Process (BP) folic acid-containing compound metabolic process 0.000000000000003741 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0.0000004189 Highly Informative Direct
Biological Process (BP) purine ribonucleotide biosynthetic process 0.00002212 Highly Informative Direct
Biological Process (BP) pigment biosynthetic process 0.0004756 Highly Informative Direct
Molecular Function (MF) transferase activity 0.0003987 Least Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0 Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.8967 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1141 Least Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Ligases1Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.000000003085Moderately InformativeDirect
Enzyme Commission (EC)Forming carbon-nitrogen bonds1Moderately InformativeInherited
Enzyme Commission (EC)In linear amides0.9421Moderately InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH group of donors0.06006Moderately InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)Other carbon--nitrogen ligases0.9519InformativeInherited
Enzyme Commission (EC)Cyclo-ligases0.006156InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.03395InformativeInherited
Enzyme Commission (EC)UDP-4-amino-4-deoxy-L-arabinose formyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Formyltetrahydrofolate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylamine--glycine ligase0.00000004785Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylglycinamide formyltransferase0.0000001658Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylformylglycinamidine cyclo-ligase0.0003963Highly InformativeDirect

Document: EC annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)intestine0Moderately 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)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve 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)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Acting on the CH-OH group of donors0.00000000366Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds1Moderately InformativeInherited
Enzyme Commission (EC)Ligases1Moderately InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0000000001915InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH group of donors0.0469InformativeInherited
Enzyme Commission (EC)In linear amides0.7278InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)Phosphoribosylamine--glycine ligase0.00000003429Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylglycinamide formyltransferase0.00000008458Highly InformativeDirect
Enzyme Commission (EC)Cyclo-ligases0.005225Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0.00000009307Moderately InformativeDirect
Biological processAntibiotic resistance0InformativeDirect
Biological processLipid biosynthesis0InformativeDirect
Biological processProtein biosynthesis0InformativeDirect
Biological processPurine biosynthesis0.00001542InformativeDirect
Biological processLipid A biosynthesis0Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis0Highly InformativeDirect
Molecular functionNAD0.00000001076Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationPhosphopantetheine0.00000109Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)lipopolysaccharide biosynthesis0InformativeDirect
UniPathway (UP)nucleotide-sugar biosynthesis1InformativeInherited
UniPathway (UP)UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR002376 SSF53328 Protein matches
Abstract A number of formyl transferases belong to this group. Methionyl-tRNA formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and by impairing its binding to EFTU-GTP. Formyltetrahydrofolate dehydrogenase produces formate from formyl- tetrahydrofolate. This is the N-terminal domain of these enzymes and is found upstream of the C-terminal domain .

The trifunctional glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide transformylase catalyses the second, third and fifth steps in de novo purine biosynthesis. The glycinamide ribonucleotide transformylase belongs to this group.


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) · 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 7 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 Formyltransferase 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 7 hidden Markov models representing the Formyltransferase 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]