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1  structure 42  species 0  interactions 112  sequences 25  architectures

Family: BPA_C (PF18040)

Summary: beta porphyranase A C-terminal

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This is the Wikipedia entry entitled "Beta-porphyranase". More...

Beta-porphyranase Edit Wikipedia article

Beta-porphyranase
Identifiers
EC number 3.2.1.178
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum

Beta-porphyranase (EC 3.2.1.178, porphyranase, PorA, PorB, endo-beta-porphyranase) is an enzyme with systematic name porphyran beta-D-galactopyranose-(1->4)-alpha-L-galactopyranose-6-sulfate 4-glycanohydrolase.[1][2] This enzyme catalyses the following chemical reaction

Hydrolysis of beta-D-galactopyranose-(1->4)-alpha-L-galactopyranose-6-sulfate linkages in porphyran

The backbone of porphyran consists largely (~70%) of (1->3)-linked beta-D-galactopyranose followed by (1->4)-linked alpha-L-galactopyranose-6-sulfate.

References

  1. ^ Hehemann, J.H.; Correc, G.; Barbeyron, T.; Helbert, W.; Czjzek, M.; Michel, G. (2010). "Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota". Nature. 464: 908–912. PMID 20376150. doi:10.1038/nature08937. 
  2. ^ Correc, G.; Hehemann, J.H.; Czjzek, M.; Helbert, W. (2011). "Structural analysis of the degradation products of porphyran digested by Zobellia galactanivorans β-porphyranase A". Carbohydrate Polymers. 83: 277–283. doi:10.1016/j.carbpol.2010.07.060. 

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

beta porphyranase A C-terminal Provide feedback

This is the C-terminal domain found in Bacteroides plebeius of proteins such as beta-porphyranase A (BPA), a beta-galactanase that cleaves the beta-1,4 glycosidic bond . Porphyranase degrade red seaweed glycans. This domain adopts a beta sandwich shape [1].

Literature references

  1. Hehemann JH, Kelly AG, Pudlo NA, Martens EC, Boraston AB;, Proc Natl Acad Sci U S A. 2012;109:19786-19791.: Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. PUBMED:23150581 EPMC:23150581


Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 GBD (CL0202), which has the following description:

This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site [1].

The clan contains the following 70 members:

7TMR-DISMED2 Agarase_CBM Allantoicase ANAPC10 Arabino_trans_C Bac_rhamnosid_N BcsB BetaGal_dom4_5 BPA_C Calpain_III CBM-like CBM27 CBM32 CBM46 CBM60 CBM65_1 CBM_11 CBM_15 CBM_17_28 CBM_26 CBM_35 CBM_4_9 CBM_6 CE2_N CIA30 Clenterotox Cry1Ac_D5 DUF4465 DUF4627 DUF5000 DUF5010_C DUF5077 DUF5625 DUF642 Endotoxin_C Ephrin_lbd Exop_C F5_F8_type_C FBA FlhE GH101_N GH115_C Glft2_N Glyco_hydro_2_N GxDLY HA70_C Laminin_B Laminin_N Lectin_like Lipl32 Lyase_N Malectin Malectin_like Muskelin_N NPCBM P_proprotein PA-IL PAW PCMD PepX_C PINIT PITH PPC PulA_N1 Sad1_UNC SGBP_B_XBD TcA_TcB_BD Thioredoxin_10 XRCC1_N YpM

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
(15)
Full
(112)
Representative proteomes UniProt
(180)
NCBI
(355)
Meta
(3)
RP15
(35)
RP35
(75)
RP55
(116)
RP75
(142)
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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
(15)
Full
(112)
Representative proteomes UniProt
(180)
NCBI
(355)
Meta
(3)
RP15
(35)
RP35
(75)
RP55
(116)
RP75
(142)
Alignment:
Format:
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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
(15)
Full
(112)
Representative proteomes UniProt
(180)
NCBI
(355)
Meta
(3)
RP15
(35)
RP35
(75)
RP55
(116)
RP75
(142)
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

This family is new in this Pfam release.

Seed source: ECOD:EUF05287
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: El-Gebali S , Smart A
Number in seed: 15
Number in full: 112
Average length of the domain: 95.90 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 10.90 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.2 26.2
Trusted cut-off 26.2 26.2
Noise cut-off 25.8 25.3
Model length: 95
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 BPA_C domain has been found. There are 1 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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