Summary: L,D-transpeptidase catalytic domain
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L,D-transpeptidase catalytic domain Provide feedback
This family is related to PF03734.
Internal database links
|Similarity to PfamA using HHSearch:||YkuD|
- 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
- the number of residues in the sequence
- the Pfam graphic itself.
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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 UniProtKB sequence database using the family HMM
- 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:
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||96|
|Number in full:||638|
|Average length of the domain:||167.50 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||70.05 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||5|
|Download:||download the raw HMM for this family|
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Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
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- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
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The tree shows the occurrence of this domain across different species. More...
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