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78  structures 3491  species 1  interaction 8204  sequences 29  architectures

Family: DegT_DnrJ_EryC1 (PF01041)

Summary: DegT/DnrJ/EryC1/StrS aminotransferase family

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

DegT/DnrJ/EryC1/StrS aminotransferase family Provide feedback

The members of this family are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA P72454 StsC P77952 and StsS [1]. The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase EC:2.6.1.50, which catalyses the first amino transfer in the biosynthesis of the streptidine subunit of streptomycin [1].

Literature references

  1. Ahlert J, Distler J, Mansouri K, Piepersberg W; , Arch Microbiol 1997;168:102-113.: Identification of stsC, the gene encoding the L-glutamine:scyllo-inosose aminotransferase from streptomycin-producing Streptomycetes. PUBMED:9238101 EPMC:9238101


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000653

This entry represents a family that are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA SWISSPROT, StsC SWISSPROT and StsS [PUBMED:9238101]. The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase EC, which catalyses the first amino transfer in the biosynthesis of the streptidine subunit of streptomycin [PUBMED:9238101].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan PLP_aminotran (CL0061), which has the following description:

This superfamily contains a variety of PLP-dependent enzymes.

The clan contains the following 15 members:

Alliinase_C Aminotran_1_2 Aminotran_3 Aminotran_5 Aminotran_MocR Beta_elim_lyase Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Met_gamma_lyase OKR_DC_1 Pyridoxal_deC SelA SHMT SLA_LP_auto_ag

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(38)
Full
(8204)
Representative proteomes NCBI
(27677)
Meta
(18092)
RP15
(739)
RP35
(1465)
RP55
(1821)
RP75
(2089)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(38)
Full
(8204)
Representative proteomes NCBI
(27677)
Meta
(18092)
RP15
(739)
RP35
(1465)
RP55
(1821)
RP75
(2089)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(38)
Full
(8204)
Representative proteomes NCBI
(27677)
Meta
(18092)
RP15
(739)
RP35
(1465)
RP55
(1821)
RP75
(2089)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_239 (release 3.0)
Previous IDs: DegT_DnrJ_EryC1_fam;
Type: Domain
Author: Finn RD, Bateman A, Parkhill J
Number in seed: 38
Number in full: 8204
Average length of the domain: 342.00 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 92.75 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.8 19.8
Trusted cut-off 19.8 19.8
Noise cut-off 19.7 19.7
Model length: 363
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There is 1 interaction for this family. More...

DegT_DnrJ_EryC1

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DegT_DnrJ_EryC1 domain has been found. There are 78 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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