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1  structure 208  species 0  interactions 228  sequences 10  architectures

Family: cpYpsA (PF12694)

Summary: Circularly permutated YpsA SLOG family

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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.

Circularly permutated YpsA SLOG family Provide feedback

The structure of proteins in this family contain central beta strands with flanking alpha helices. The structure is similar to that of a molybdenum cofactor carrier protein.This family belongs in the SLOG superfamily, circularly-permuted version of YspA famiy showing fusions to NAD utilization and ADP-ribosylation domains including NUDIX, NADAR and MACRO. Members of this family are predicted to function as sensors of nucleotide, nucleotide-derived ligands, or nucleic acids, which are potentially processed/modified by associating effectors [1].

Literature references

  1. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;, Nucleic Acids Res. 2015;43:10633-10654.: Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. PUBMED:26590262 EPMC:26590262


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024755

The structure of proteins in this family contain central beta strands with flanking alpha helices. The structure is similar to that of a molybdenum cofactor carrier protein.

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 SLOG (CL0349), which has the following description:

Members of the SLOG superfamily were shown in bacteria and plants to cleave modified AMPs to release the base as cytokinins, which function as growth-stimulating hormones in plants. Known family members such as DprA is a member of the recombination-mediator protein family, dedicated to natural bacterial transformation [1]. This clan includes members such as the classical LOG family which generates cytokinin-like molecules, the Smf/DprA family which binds single-stranded (ss)DNA and interacts with RecA during transformation and recombination and the molybdenum cofactor-binding (MoCoBD) family. The SLOG domain adopts a three-layered alpha/beta sandwich Rossmannoid fold with a characteristic substrate-binding loop rich in glycine and small residues in the standard location between strand-1 and helix-1. It is suggested that the SLOG superfamily is likely to encompass dual functions, with certain versions serving as (oligo)nucleotide sensors and others as enzymes that operate on nucleotides [2].

The clan contains the following 13 members:

cpYpsA DNA_processg_A DUF3412 LD_cluster2 LD_cluster3 LDcluster4 LSDAT_euk LSDAT_prok Lysine_decarbox STALD TPALS YAcAr YpsA

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
(40)
Full
(228)
Representative proteomes UniProt
(603)
NCBI
(717)
Meta
(17)
RP15
(97)
RP35
(184)
RP55
(246)
RP75
(288)
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HTML View  View               
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
(40)
Full
(228)
Representative proteomes UniProt
(603)
NCBI
(717)
Meta
(17)
RP15
(97)
RP35
(184)
RP55
(246)
RP75
(288)
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
(40)
Full
(228)
Representative proteomes UniProt
(603)
NCBI
(717)
Meta
(17)
RP15
(97)
RP35
(184)
RP55
(246)
RP75
(288)
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: jcsg_3imk
Previous IDs: MoCo_carrier;
Type: Family
Sequence Ontology: SO:0100021
Author: Mistry J , Iyer LM , Aravind L , Burroughs AM , El-Gebali S
Number in seed: 40
Number in full: 228
Average length of the domain: 140.90 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 53.41 %

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 26.4 29.0
Noise cut-off 25.9 26.1
Model length: 145
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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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 cpYpsA 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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