Summary: Oligogalacturonate-specific porin protein (KdgM)
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Oligogalacturonate-specific porin protein (KdgM) Provide feedback
This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM (Q934G3) from Erwinia chrysanthemi. The phytopathogenic Gram-negative bacteria Erwinia chrysanthemi secretes pectinases, which are able to degrade the pectic polymers of plant cell walls, and uses the degradation products as a carbon source for growth. KdgM is a major outer membrane protein, whose synthesis is strongly induced in the presence of pectic derivatives. KdgM behaves like a voltage-dependent porin that is slightly selective for anions and that exhibits fast block in the presence of trigalacturonate. In contrast to most porins, KdgM seems to be monomeric [1].
Literature references
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Blot N, Berrier C, Hugouvieux-Cotte-Pattat N, Ghazi A, Condemine G; , J Biol Chem 2002;277:7936-7944.: The oligogalacturonate-specific porin KdgM of Erwinia chrysanthemi belongs to a new porin family. PUBMED:11773048 EPMC:11773048
Internal database links
SCOOP: | BBP2 DUF2490 Porin_4 |
Similarity to PfamA using HHSearch: | BBP2 |
External database links
Transporter classification: | 1.B.21 1.B.35 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR009331
This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM (SWISSPROT) from Erwinia chrysanthemi. The phytopathogenic Gram-negative bacteria E. chrysanthemi secretes pectinases, which are able to degrade the pectic polymers of plant cell walls, and uses the degradation products as a carbon source for growth. KdgM is a major outer membrane protein, whose synthesis is strongly induced in the presence of pectic derivatives. KdgM behaves like a voltage-dependent porin that is slightly selective for anions and that exhibits fast block in the presence of trigalacturonate. In contrast to most porins, KdgM seems to be monomeric [PUBMED:11773048].
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 MBB (CL0193), which has the following description:
This clan gathers together a large set of beta barrel membrane proteins.Although these proteins have different numbers of beta strands in the barrel they have significant sequence similarity between families.
The clan contains the following 90 members:
Ail_Lom Alginate_exp Autotransporter Bac_surface_Ag BBP2 BBP2_2 BBP7 BCSC_C Campylo_MOMP Caps_assemb_Wzi Channel_Tsx Chlam_OMP CopB CymA DUF2219 DUF2490 DUF2715 DUF2860 DUF3078 DUF3138 DUF3187 DUF3373 DUF3573 DUF3575 DUF4421 DUF4595 DUF481 DUF5020 DUF560 Gcw_chp HP_OMP HP_OMP_2 HpuA IAT_beta KdgM LamB Legionella_OMP Lipoprot_C LptD MDM10 MipA MOSP_C MSP MtrB_PioB Omp_AT OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_like OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF PagL PagP Phenol_MetA_deg PLA1 Pom Porin_1 Porin_10 Porin_2 Porin_3 Porin_4 Porin_5 Porin_6 Porin_7 Porin_8 Porin_O_P Porin_OmpG Porin_OmpG_1_2 Porin_OmpL1 PorP_SprF ShlB Surface_Ag_2 TbpB_B_D TbpB_C Toluene_X TonB_dep_Rec TraF_2 TSA UPF0164 Usher Usher_TcfC YadA_anchor YfaZ YjbHAlignments
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...
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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 (4) |
Full (283) |
Representative proteomes | UniProt (2236) |
NCBI (3854) |
Meta (3) |
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RP15 (37) |
RP35 (119) |
RP55 (277) |
RP75 (749) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (4) |
Full (283) |
Representative proteomes | UniProt (2236) |
NCBI (3854) |
Meta (3) |
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RP15 (37) |
RP35 (119) |
RP55 (277) |
RP75 (749) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_10852 (release 9.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Moxon SJ |
Number in seed: | 4 |
Number in full: | 283 |
Average length of the domain: | 210.70 aa |
Average identity of full alignment: | 24 % |
Average coverage of the sequence by the domain: | 90.71 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 222 | ||||||||||||
Family (HMM) version: | 13 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 KdgM domain has been found. There are 4 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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