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53  structures 702  species 1  interaction 1827  sequences 55  architectures

Family: LPMO_10 (PF03067)

Summary: Lytic polysaccharide mono-oxygenase, cellulose-degrading

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Lytic polysaccharide mono-oxygenase, cellulose-degrading Provide feedback

This domain is found associated with a wide variety of cellulose binding domains. This is a family of two very closely related proteins that together act as both a C1- and a C4-oxidising lytic polysaccharide mono-oxygenase [2] degrading cellulose. This domain is also found in baculoviral spheroidins and spindolins, protein of unknown function.

Literature references

  1. Schnellmann J, Zeltins A, Blaak H, Schrempf H; , Mol Microbiol 1994;13:807-819.: The novel lectin-like protein CHB1 is encoded by a chitin-inducible Streptomyces olivaceoviridis gene and binds specifically to crystalline alpha-chitin of fungi and other organisms. PUBMED:7815940 EPMC:7815940

  2. Forsberg Z, Mackenzie AK, Sorlie M, Rohr AK, Helland R, Arvai AS, Vaaje-Kolstad G, Eijsink VG;, Proc Natl Acad Sci U S A. 2014;111:8446-8451.: Structural and functional characterization of a conserved pair of bacterial cellulose-oxidizing lytic polysaccharide monooxygenases. PUBMED:24912171 EPMC:24912171


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004302

This domain is found associated with a wide variety of cellulose binding domains [PUBMED:7815940]. Proteins containing this domain include two very closely related proteins that together act as both a C1- and a C4-oxidising lytic polysaccharide mono-oxygenase, degrading cellulose [PUBMED:24912171]. This domain is also found in baculoviral spheroidins and spindolins [PUBMED:8376960], and in bacterial GlcNAc-binding protein A (gbpA) [PUBMED:16341015].

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...

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
(220)
Full
(1827)
Representative proteomes UniProt
(5692)
NCBI
(10088)
Meta
(30)
RP15
(409)
RP35
(889)
RP55
(1691)
RP75
(2710)
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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
(220)
Full
(1827)
Representative proteomes UniProt
(5692)
NCBI
(10088)
Meta
(30)
RP15
(409)
RP35
(889)
RP55
(1691)
RP75
(2710)
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
(220)
Full
(1827)
Representative proteomes UniProt
(5692)
NCBI
(10088)
Meta
(30)
RP15
(409)
RP35
(889)
RP55
(1691)
RP75
(2710)
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_2364 (release 6.4)
Previous IDs: Chitin_bind_3;
Type: Domain
Author: Bateman A
Number in seed: 220
Number in full: 1827
Average length of the domain: 176.20 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 52.87 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 195
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Selections

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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...

LPMO_10

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 LPMO_10 domain has been found. There are 53 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 sequence.

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