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0  structures 380  species 0  interactions 442  sequences 9  architectures

Family: HcyBio (PF01837)

Summary: Homocysteine biosynthesis enzyme, sulfur-incorporation

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Homocysteine biosynthesis enzyme, sulfur-incorporation Provide feedback

This presumed domain is about is about 360 residues long. The function of this domain is unknown. It is found in some proteins that have two C-terminal CBS PF00571 domains. There are also proteins that contain two inserted Fe4S domains near the C-terminal end of the domain. The protein O26943 has been misannotated as an inosine monophosphate dehydrogenase based on the similarity to the CBS domains. Based on genetic analyses in the methanogen Methanosarcina acetivorans, this family is a key component of the metabolic network for sulfide assimilation and trafficking in methanogens. It is essential to a novel, O-acetylhomoserine sulfhydrylase-independent pathway for homocysteine biosynthesis, and may catalyse sulfur incorporation into the side chain of an as yet unidentified amino acid precursor [1]. The DUF39-CBS and DUF39-ferredoxin architectures repeatedly occur together in the genomes of methanogenic Archaea, suggesting they may be of diverged function. This is consistent with a phylogenetic reconstruction of the DUF39 family, which clearly distinguishes the CBS-associated and ferredoxin-associated DUF39s [1].

Literature references

  1. Rauch BJ, Gustafson A, Perona JJ;, Mol Microbiol. 2014;94:1330-1342.: Novel proteins for homocysteine biosynthesis in anaerobic microorganisms. PUBMED:25315403 EPMC:25315403


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002708

This presumed domain (used to be named as DUF39) is about is about 360 residues long. The function of this domain is not clear. It is found at N terminus in some proteins that have two C-terminal cystathionine beta-synthase (CBS) domains, such as MJ0100 from Methanocaldococcus jannaschii. This domain can also be found in proteins that contain two C-terminal inserted Fe4S domains [ PUBMED:25938369 ].

In Methanocaldococcus jannaschii, MJ0100 (also known as MA1821) is involved in Hcy (homocysteine) biosynthesis. Its CBS domains bind S-adenosyl-l-methionine (SAM) and 5'-methylthioadenosine (MTA), which induce a conformational change consistent with regulatory function. Another protein in the homocysteine biosynthesis pathway, MA1822, is involved in the reduction of the disulfide formed in MA1821 during the conversion of Asa (aspartate semialdehyde) to Hcy [ PUBMED:25315403 , PUBMED:25938369 ].

The DUF39-CBS and DUF39-ferredoxin architectures repeatedly occur together in the genomes of methanogenic Archaea, suggesting they may be of diverged function. This is consistent with a phylogenetic reconstruction of the DUF39 family, which clearly distinguishes the CBS-associated and ferredoxin-associated DUF39s [ PUBMED:25315403 ].

Domain organisation

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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 and the UniProtKB 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
(87)
Full
(442)
Representative proteomes UniProt
(2448)
RP15
(90)
RP35
(270)
RP55
(457)
RP75
(699)
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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
(87)
Full
(442)
Representative proteomes UniProt
(2448)
RP15
(90)
RP35
(270)
RP55
(457)
RP75
(699)
Alignment:
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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
(87)
Full
(442)
Representative proteomes UniProt
(2448)
RP15
(90)
RP35
(270)
RP55
(457)
RP75
(699)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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_7373 (release 4.0)
Previous IDs: DUF39;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 87
Number in full: 442
Average length of the domain: 350.60 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 86.99 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.2 26.2
Trusted cut-off 26.2 30.2
Noise cut-off 23.2 26.1
Model length: 347
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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