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Conserved domains on  [gi|515201160|ref|WP_016809185|]
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glycosyl hydrolase family 28-related protein [Klebsiella oxytoca]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pgu1 super family cl35001
Polygalacturonase [Carbohydrate transport and metabolism];
36-94 1.84e-08

Polygalacturonase [Carbohydrate transport and metabolism];


The actual alignment was detected with superfamily member COG5434:

Pssm-ID: 444185 [Multi-domain]  Cd Length: 373  Bit Score: 55.98  E-value: 1.84e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 515201160  36 TILNVADFGAKGDGVTDDSFAFQKAFLKANEFGGAKVYFPKPRkeYLLkFPVFLFNNTE 94
Cdd:COG5434    8 KTFNITDFGAKGDGKTLNTAAIQKAIDACAAAGGGTVLVPAGT--YLT-GPIFLKSNVT 63
 
Name Accession Description Interval E-value
Pgu1 COG5434
Polygalacturonase [Carbohydrate transport and metabolism];
36-94 1.84e-08

Polygalacturonase [Carbohydrate transport and metabolism];


Pssm-ID: 444185 [Multi-domain]  Cd Length: 373  Bit Score: 55.98  E-value: 1.84e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 515201160  36 TILNVADFGAKGDGVTDDSFAFQKAFLKANEFGGAKVYFPKPRkeYLLkFPVFLFNNTE 94
Cdd:COG5434    8 KTFNITDFGAKGDGKTLNTAAIQKAIDACAAAGGGTVLVPAGT--YLT-GPIFLKSNVT 63
Pectate_lyase_3 pfam12708
Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure ...
 39-99 3.03e-08

Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure like Pectate lyase. This family is most closely related to glycosyl hydrolase family 28.


Pssm-ID: 403800 [Multi-domain]  Cd Length: 213  Bit Score: 53.86  E-value: 3.03e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 515201160   39 NVADFGAKGDGVTDDSFAFQKAFLKA-NEFGGAKVYFPKprKEYLLKFPVFLFNNTEAYGDG 99
Cdd:pfam12708   3 NVKDYGAKGDGVTDDTAAIQKAIDDGgATTTPAVVYFPP--GTYLVSSPIILYSGTVLVGDG 62
GH55_beta13glucanase-like cd23668
fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family ...
 24-98 1.52e-07

fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family includes fungal glycoside hydrolase family 55 (GH55) proteins, which contains both endo- (EC 3.2.1.39) and exo-beta-1,3-glucanases (EC 3.2.1.58), based on the hydrolysis position. These enzymes hydrolyze beta-1,3-glucan bonds via inversion of stereochemistry at the anomeric carbon. GH55 is also called laminarinase due to its ability to hydrolyze laminarin, a beta-1,3-glucan with occasional beta-1,6 branching found in brown algae such as Laminaria digitata. They have also been shown to react with the beta-1,3-glucans from fungal and plant cell walls. Trichoderma harzianum BGN13.1 and T. viride LamA1 in this family have been characterized as endo-acting enzymes while Phanerochaete chrysosporium Lam55A and Chaetomium thermophilum CtLam55 are exo-acting enzymes. The CtLam55 substrate binding cleft exhibits restricted access on one side, thus rendering the enzyme as an exo-beta-1,3-glucanase; this has been confirmed by thin layer chromatography experiments. Also, a binding pocket was identified that could explain binding of branched laminarin and accumulation of laminaritriose. A similar binding pocket has been observed in T. chrysosporium Lam55A through structural studies and site-directed mutagenesis; both support a critical glutamate as a catalytic acid and a proton relay network that activates water to serve as the catalytic base.


Pssm-ID: 467840 [Multi-domain]  Cd Length: 623  Bit Score: 53.67  E-value: 1.52e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515201160  24 GTSSRFAFASGITIL-NVADFGAKGDGVTDDSFAFQKAFLKANEFG---------GAKVYFPKPrkEYLLKFPVFLFNNT 93
Cdd:cd23668    9 NGSSPFNPNSSYKVFrNVKDYGAKGDGVTDDTAAINAAISDGNRCGggcgssttqPAVVYFPPG--TYLVSSPIIMYYYT 86


                 ....*
gi 515201160  94 EAYGD 98
Cdd:cd23668   87 QLIGD 91
PLN02218 PLN02218
polygalacturonase ADPG
 36-84 1.82e-05

polygalacturonase ADPG


Pssm-ID: 177865 [Multi-domain]  Cd Length: 431  Bit Score: 46.56  E-value: 1.82e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 515201160  36 TILNVADFGAKGDGVTDDSFAFQKAFLKANEFGGAKVYFPKPRKEYLLK 84
Cdd:PLN02218  66 TTVSVSDFGAKGDGKTDDTQAFVNAWKKACSSNGAVNLLVPKGNTYLLK 114
 
Name Accession Description Interval E-value
Pgu1 COG5434
Polygalacturonase [Carbohydrate transport and metabolism];
36-94 1.84e-08

Polygalacturonase [Carbohydrate transport and metabolism];


Pssm-ID: 444185 [Multi-domain]  Cd Length: 373  Bit Score: 55.98  E-value: 1.84e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 515201160  36 TILNVADFGAKGDGVTDDSFAFQKAFLKANEFGGAKVYFPKPRkeYLLkFPVFLFNNTE 94
Cdd:COG5434    8 KTFNITDFGAKGDGKTLNTAAIQKAIDACAAAGGGTVLVPAGT--YLT-GPIFLKSNVT 63
Pectate_lyase_3 pfam12708
Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure ...
 39-99 3.03e-08

Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure like Pectate lyase. This family is most closely related to glycosyl hydrolase family 28.


Pssm-ID: 403800 [Multi-domain]  Cd Length: 213  Bit Score: 53.86  E-value: 3.03e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 515201160   39 NVADFGAKGDGVTDDSFAFQKAFLKA-NEFGGAKVYFPKprKEYLLKFPVFLFNNTEAYGDG 99
Cdd:pfam12708   3 NVKDYGAKGDGVTDDTAAIQKAIDDGgATTTPAVVYFPP--GTYLVSSPIILYSGTVLVGDG 62
GH55_beta13glucanase-like cd23668
fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family ...
 24-98 1.52e-07

fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family includes fungal glycoside hydrolase family 55 (GH55) proteins, which contains both endo- (EC 3.2.1.39) and exo-beta-1,3-glucanases (EC 3.2.1.58), based on the hydrolysis position. These enzymes hydrolyze beta-1,3-glucan bonds via inversion of stereochemistry at the anomeric carbon. GH55 is also called laminarinase due to its ability to hydrolyze laminarin, a beta-1,3-glucan with occasional beta-1,6 branching found in brown algae such as Laminaria digitata. They have also been shown to react with the beta-1,3-glucans from fungal and plant cell walls. Trichoderma harzianum BGN13.1 and T. viride LamA1 in this family have been characterized as endo-acting enzymes while Phanerochaete chrysosporium Lam55A and Chaetomium thermophilum CtLam55 are exo-acting enzymes. The CtLam55 substrate binding cleft exhibits restricted access on one side, thus rendering the enzyme as an exo-beta-1,3-glucanase; this has been confirmed by thin layer chromatography experiments. Also, a binding pocket was identified that could explain binding of branched laminarin and accumulation of laminaritriose. A similar binding pocket has been observed in T. chrysosporium Lam55A through structural studies and site-directed mutagenesis; both support a critical glutamate as a catalytic acid and a proton relay network that activates water to serve as the catalytic base.


Pssm-ID: 467840 [Multi-domain]  Cd Length: 623  Bit Score: 53.67  E-value: 1.52e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515201160  24 GTSSRFAFASGITIL-NVADFGAKGDGVTDDSFAFQKAFLKANEFG---------GAKVYFPKPrkEYLLKFPVFLFNNT 93
Cdd:cd23668    9 NGSSPFNPNSSYKVFrNVKDYGAKGDGVTDDTAAINAAISDGNRCGggcgssttqPAVVYFPPG--TYLVSSPIIMYYYT 86


                 ....*
gi 515201160  94 EAYGD 98
Cdd:cd23668   87 QLIGD 91
GH55_beta13glucanase-like cd23668
fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family ...
 37-75 5.70e-07

fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family includes fungal glycoside hydrolase family 55 (GH55) proteins, which contains both endo- (EC 3.2.1.39) and exo-beta-1,3-glucanases (EC 3.2.1.58), based on the hydrolysis position. These enzymes hydrolyze beta-1,3-glucan bonds via inversion of stereochemistry at the anomeric carbon. GH55 is also called laminarinase due to its ability to hydrolyze laminarin, a beta-1,3-glucan with occasional beta-1,6 branching found in brown algae such as Laminaria digitata. They have also been shown to react with the beta-1,3-glucans from fungal and plant cell walls. Trichoderma harzianum BGN13.1 and T. viride LamA1 in this family have been characterized as endo-acting enzymes while Phanerochaete chrysosporium Lam55A and Chaetomium thermophilum CtLam55 are exo-acting enzymes. The CtLam55 substrate binding cleft exhibits restricted access on one side, thus rendering the enzyme as an exo-beta-1,3-glucanase; this has been confirmed by thin layer chromatography experiments. Also, a binding pocket was identified that could explain binding of branched laminarin and accumulation of laminaritriose. A similar binding pocket has been observed in T. chrysosporium Lam55A through structural studies and site-directed mutagenesis; both support a critical glutamate as a catalytic acid and a proton relay network that activates water to serve as the catalytic base.


Pssm-ID: 467840 [Multi-domain]  Cd Length: 623  Bit Score: 51.75  E-value: 5.70e-07
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 515201160  37 ILNVADFGAKGDGVTDDSFAFQKAFLKANefGGAKVYFP 75
Cdd:cd23668  303 FVNVKDYGAKGDGVTDDTAALQAILNTAA--GGKIVYFP 339
PLN02218 PLN02218
polygalacturonase ADPG
 36-84 1.82e-05

polygalacturonase ADPG


Pssm-ID: 177865 [Multi-domain]  Cd Length: 431  Bit Score: 46.56  E-value: 1.82e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 515201160  36 TILNVADFGAKGDGVTDDSFAFQKAFLKANEFGGAKVYFPKPRKEYLLK 84
Cdd:PLN02218  66 TTVSVSDFGAKGDGKTDDTQAFVNAWKKACSSNGAVNLLVPKGNTYLLK 114
PLN02793 PLN02793
Probable polygalacturonase
 37-67 2.41e-03

Probable polygalacturonase


Pssm-ID: 215426 [Multi-domain]  Cd Length: 443  Bit Score: 39.86  E-value: 2.41e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 515201160  37 ILNVADFGAKGDGVTDDSFAFQKAFLKANEF 67
Cdd:PLN02793  52 VLHVGDFGAKGDGVTDDTQAFKEAWKMACSS 82
 
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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