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Conserved domains on  [gi|1227300637|gb|ASQ80008|]
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porin [Shigella flexneri 1a]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KdgM super family cl11629
Oligogalacturonate-specific porin protein (KdgM); This family consists of several bacterial ...
 13-122 6.51e-70

Oligogalacturonate-specific porin protein (KdgM); This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM 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.


The actual alignment was detected with superfamily member PRK09980:

Pssm-ID: 416341  Cd Length: 230  Bit Score: 210.14  E-value: 6.51e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227300637  13 MKKINAIILLSSLTSASVFAGAYVENREAYNLASDQGEVMLRVGYNFDMGAGIMLTNTYTFQREDELKHGYNEIEGWYPL 92
Cdd:PRK09980    1 MKKLNTIVLLSSLTSASVFAGAYVENREAYNLASDQGEVMLRVGYNFDMGAGIMLTNTYTFQRDDELKHGYNEIEGWYPL 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1227300637  93 FKPTDKLTIQPGGLINDKSISSGGAVYLDV 122
Cdd:PRK09980   81 FKPTDKLTIQPGGLINDKSIGSGGAVYLDV 110
 
Name Accession Description Interval E-value
ompL PRK09980
porin OmpL;
13-122 6.51e-70

porin OmpL;


Pssm-ID: 182179  Cd Length: 230  Bit Score: 210.14  E-value: 6.51e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227300637  13 MKKINAIILLSSLTSASVFAGAYVENREAYNLASDQGEVMLRVGYNFDMGAGIMLTNTYTFQREDELKHGYNEIEGWYPL 92
Cdd:PRK09980    1 MKKLNTIVLLSSLTSASVFAGAYVENREAYNLASDQGEVMLRVGYNFDMGAGIMLTNTYTFQRDDELKHGYNEIEGWYPL 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1227300637  93 FKPTDKLTIQPGGLINDKSISSGGAVYLDV 122
Cdd:PRK09980   81 FKPTDKLTIQPGGLINDKSIGSGGAVYLDV 110
KdgM pfam06178
Oligogalacturonate-specific porin protein (KdgM); This family consists of several bacterial ...
 34-122 9.71e-37

Oligogalacturonate-specific porin protein (KdgM); This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM 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.


Pssm-ID: 399289  Cd Length: 215  Bit Score: 125.36  E-value: 9.71e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227300637  34 AYVENREAYNLASDQG-EVMLRVGYNFDMGAGIML--------TNTYTFQREDELKHGYNEIEgWYPLFKPTDKLTIQPG 104
Cdd:pfam06178   1 AYVDYRHEYNDASDAGnKDRLRISHRFANGAGFMLeakwksggTDTYNNKRFNELVHNGNEIE-WSYLFKPTDKFTIQPG 79

                          90
                  ....*....|....*...
gi 1227300637 105 GLINDKSISSGGAVYLDV 122
Cdd:pfam06178  80 FLLESGSIGSGYKPYLRG 97
 
Name Accession Description Interval E-value
ompL PRK09980
porin OmpL;
13-122 6.51e-70

porin OmpL;


Pssm-ID: 182179  Cd Length: 230  Bit Score: 210.14  E-value: 6.51e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227300637  13 MKKINAIILLSSLTSASVFAGAYVENREAYNLASDQGEVMLRVGYNFDMGAGIMLTNTYTFQREDELKHGYNEIEGWYPL 92
Cdd:PRK09980    1 MKKLNTIVLLSSLTSASVFAGAYVENREAYNLASDQGEVMLRVGYNFDMGAGIMLTNTYTFQRDDELKHGYNEIEGWYPL 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1227300637  93 FKPTDKLTIQPGGLINDKSISSGGAVYLDV 122
Cdd:PRK09980   81 FKPTDKLTIQPGGLINDKSIGSGGAVYLDV 110
KdgM pfam06178
Oligogalacturonate-specific porin protein (KdgM); This family consists of several bacterial ...
 34-122 9.71e-37

Oligogalacturonate-specific porin protein (KdgM); This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM 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.


Pssm-ID: 399289  Cd Length: 215  Bit Score: 125.36  E-value: 9.71e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227300637  34 AYVENREAYNLASDQG-EVMLRVGYNFDMGAGIML--------TNTYTFQREDELKHGYNEIEgWYPLFKPTDKLTIQPG 104
Cdd:pfam06178   1 AYVDYRHEYNDASDAGnKDRLRISHRFANGAGFMLeakwksggTDTYNNKRFNELVHNGNEIE-WSYLFKPTDKFTIQPG 79

                          90
                  ....*....|....*...
gi 1227300637 105 GLINDKSISSGGAVYLDV 122
Cdd:pfam06178  80 FLLESGSIGSGYKPYLRG 97
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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