Summary: Pectic acid lyase
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Pectic acid lyase Provide feedback
Members of this family are isozymes of pectate lyase ( EC:220.127.116.11), also called polygalacturonic transeliminase and alpha-1,4-D-endopolygalacturonic acid lyase.
Internal database links
|SCOOP:||SQHop_cyclase_C SQHop_cyclase_N Tnp_zf-ribbon_2|
|Similarity to PfamA using HHSearch:||SQHop_cyclase_C|
External database links
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This Clan includes CAZy clans GH-L, GH-M and GH-G. The members of this clan share a common structure composed of 6 helical hairpins. Most members of this superfamily are glycosyl hydrolase enzymes.
The clan contains the following 26 members:A2M_comp Bac_rhamnosid C5-epim_C Cobalamin_bind DUF1237 DUF608 GDE_C GlcNAc_2-epim Glyco_hydro_100 Glyco_hydro_127 Glyco_hydro_15 Glyco_hydro_47 Glyco_hydro_48 Glyco_hydro_63 Glyco_hydro_65m Glyco_hydro_76 Glyco_hydro_8 Glyco_hydro_88 Glyco_hydro_9 Glycoamylase LANC_like Pec_lyase Prenyltrans SQHop_cyclase_C SQHop_cyclase_N Trehalase
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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Key: available, not generated, — not available.
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Curation and family details
|Author:||TIGRFAMs, Coggill P|
|Number in seed:||11|
|Number in full:||406|
|Average length of the domain:||242.10 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||56.69 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|Download:||download the raw HMM for this family|
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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 Pec_lyase domain has been found. There are 5 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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