Summary: Oligogalacturonate-specific porin protein (KdgM)
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 .
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
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].
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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 59 members:Ail_Lom Autotransporter Bac_surface_Ag BBP2 BBP2_2 Campylo_MOMP Channel_Tsx CopB DUF2490 DUF2860 DUF3078 DUF3138 DUF3187 DUF3308 DUF3575 DUF481 DUF560 Gcw_chp HP_OMP HP_OMP_2 KdgM LamB Legionella_OMP MipA 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 OstA_C PagL PagP Phenol_MetA_deg Porin_1 Porin_10 Porin_2 Porin_4 Porin_7 Porin_8 Porin_O_P Porin_OmpG ShlB Surface_Ag_2 TcfC Toluene_X TonB_dep_Rec TraF_2 TSA Usher YfaZ
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Pfam-B_10852 (release 9.0)|
|Number in seed:||4|
|Number in full:||6676|
|Average length of the domain:||210.70 aa|
|Average identity of full alignment:||35 %|
|Average coverage of the sequence by the domain:||94.21 %|
|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:||9|
|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 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 seqence.
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