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98  structures 870  species 4  interactions 993  sequences 8  architectures

Family: SOR_SNZ (PF01680)

Summary: SOR/SNZ family

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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.

SOR/SNZ family Provide feedback

Members of this family are enzymes involved in a new pathway of pyridoxine/pyridoxal 5-phosphate biosynthesis [1]. This family was formerly known as UPF0019.

Literature references

  1. Braun EL, Fuge EK, Padilla PA, Werner-Washburne M; , J Bacteriol 1996;178:6865-6872.: A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family. PUBMED:8955308 EPMC:8955308

  2. Ehrenshaft M, Bilski P, Li MY, Chignell CF, Daub ME; , Proc Natl Acad Sci U S A 1999;96:9374-9378.: A highly conserved sequence is a novel gene involved in de novo vitamin B6 biosynthesis. PUBMED:10430950 EPMC:10430950

  3. Osmani AH, May GS, Osmani SA; , J Biol Chem 1999;274:23565-23569.: The extremely conserved pyroA gene of Aspergillus nidulans is required for pyridoxine synthesis and is required indirectly for resistance to photosensitizers. PUBMED:10438537 EPMC:10438537


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001852

This entry represents a family of pyridoxal 5'-phosphate synthase subunit, known as pdxS/SNZ family. Proteins in this family occur in organisms in four kingdoms and form one of the most highly conserved family [PUBMED:10430950]. PdxS/SNZ proteins have a classic (beta/alpha)8-barrel fold, consisting of eight parallel beta-strands alternating with eight alpha helices [PUBMED:15911615]. They are involved in vitamin B6 biosynthesis.

The term vitamin B6 is used to refer collectively to the compound pyridoxine and its vitameric forms, pyridoxal, pyridoxamine, and their phosphorylated derivatives. Vitamin B6 is required by all organisms and plays an essential role as a co-factor for enzymatic reactions. Plants, fungi, bacteria, archaebacteria, and protists synthetize vitamin B6. Animals and some highly specialised obligate pathogens obtain it nutritionally. Vitamin B6 has two distinct biosynthetic pathways, which do not coexist in any organism. The pdxA/pdxJ pathway, that has been extensively characterised in Escherichia coli, is found in the gamma subdivision of the proteobacteria. A second pathway of vitamin B6 synthesis involving the pdxS/SNZ and pdxT/SNO protein families, which are completely unrelated in sequence to the pdxA/pdxJ proteins, is found in plants, fungi, protists, archaebacteria, and most bacteria.

PdxS/SNZ and pdxT/SNO proteins form a complex which serves as a glutamine amidotransferase to supply ammonia as a source of the ring nitrogen of vitamin B6 [PUBMED:14764090]. PdxT/SNO and pdxS/SNZ appear to encode respectively the glutaminase subunit, which produces ammonia from glutamine, and the synthase subunit, which combines ammonia with five- and three-carbon phosphosugars to form vitamin B6 [PUBMED:14762015].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(136)
Full
(993)
Representative proteomes UniProt
(3778)
NCBI
(4341)
Meta
(538)
RP15
(281)
RP35
(660)
RP55
(973)
RP75
(1245)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(136)
Full
(993)
Representative proteomes UniProt
(3778)
NCBI
(4341)
Meta
(538)
RP15
(281)
RP35
(660)
RP55
(973)
RP75
(1245)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(136)
Full
(993)
Representative proteomes UniProt
(3778)
NCBI
(4341)
Meta
(538)
RP15
(281)
RP35
(660)
RP55
(973)
RP75
(1245)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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_2034 (release 4.1)
Previous IDs: UPF0019;
Type: Domain
Author: Belitsky B, Bateman A
Number in seed: 136
Number in full: 993
Average length of the domain: 201.10 aa
Average identity of full alignment: 66 %
Average coverage of the sequence by the domain: 67.79 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.9 21.9
Trusted cut-off 21.9 22.0
Noise cut-off 21.8 21.8
Model length: 207
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Selections

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Interactions

There are 4 interactions for this family. More...

SOR_SNZ SNO ThiG ThiG

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 SOR_SNZ domain has been found. There are 98 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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