NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|333956877|gb|EGL74505|]
View 

hypothetical protein CSE899_00025, partial [Cronobacter sakazakii E899]

Protein Classification

polysaccharide deacetylase family protein( domain architecture ID 79029)

metal-dependent polysaccharide deacetylase family protein, belonging to the carbohydrate esterase 4 (CE4) superfamily, may catalyze the N- or O-deacetylation of a substrate such as acetylated chitin, peptidoglycan, and acetylated xylan

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
GH38-57_N_LamB_YdjC_SF super family cl49606
Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein ...
 1-93 1.84e-56

Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex. GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22). This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily.


The actual alignment was detected with superfamily member PRK05406:

Pssm-ID: 483946  Cd Length: 246  Bit Score: 174.15  E-value: 1.84e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   1 MKIDLNADLGEG-----CGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPP 75
Cdd:PRK05406   2 MKIDLNCDLGESfgawkMGDDEALLPLVTSANIACGFHAGDPAVMRRTVRLAKENGVAIGAHPGYPDLEGFGRRNMDLSP 81

                         90
                 ....*....|....*...
gi 333956877  76 ETIYAETLYQVGALAAIA 93
Cdd:PRK05406  82 EELYALVLYQIGALQAIA 99
 
Name Accession Description Interval E-value
PRK05406 PRK05406
5-oxoprolinase subunit PxpA;
1-93 1.84e-56

5-oxoprolinase subunit PxpA;


Pssm-ID: 235446  Cd Length: 246  Bit Score: 174.15  E-value: 1.84e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   1 MKIDLNADLGEG-----CGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPP 75
Cdd:PRK05406   2 MKIDLNCDLGESfgawkMGDDEALLPLVTSANIACGFHAGDPAVMRRTVRLAKENGVAIGAHPGYPDLEGFGRRNMDLSP 81

                         90
                 ....*....|....*...
gi 333956877  76 ETIYAETLYQVGALAAIA 93
Cdd:PRK05406  82 EELYALVLYQIGALQAIA 99
LamB_YcsF pfam03746
LamB/YcsF family; This family includes LamB. The lam locus of Aspergillus nidulans consists of ...
 4-93 1.30e-55

LamB/YcsF family; This family includes LamB. The lam locus of Aspergillus nidulans consists of two divergently transcribed genes, lamA and lamB, involved in the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. The exact molecular function of the proteins in this family is unknown.


Pssm-ID: 461036  Cd Length: 238  Bit Score: 171.42  E-value: 1.30e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877    4 DLNADLGEG-----CGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPPETI 78
Cdd:pfam03746   1 DLNCDLGEGfgawkMGDDEALLPLITSANIACGFHAGDPLVMRRTVRLAKEHGVAIGAHPGYPDLQGFGRREMDLSPEEL 80

                          90
                  ....*....|....*
gi 333956877   79 YAETLYQVGALAAIA 93
Cdd:pfam03746  81 YALVLYQIGALQAFA 95
PxpA COG1540
5-oxoprolinase subunit A [Amino acid transport and metabolism];
1-93 1.22e-53

5-oxoprolinase subunit A [Amino acid transport and metabolism];


Pssm-ID: 441149  Cd Length: 250  Bit Score: 166.77  E-value: 1.22e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   1 MKIDLNADLGEG-----CGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPP 75
Cdd:COG1540    1 MRIDLNSDLGESfgawtMGDDEALLPLVTSANIACGFHAGDPLVMRRTVRLAKERGVAIGAHPGYPDLAGFGRRNMDVSP 80

                         90
                 ....*....|....*...
gi 333956877  76 ETIYAETLYQVGALAAIA 93
Cdd:COG1540   81 EELYADVLYQIGALQAFA 98
LamB_YcsF_like cd10787
LamB/YcsF family of lactam utilization protein; The LamB/YbgL family includes the Aspergillus ...
 3-93 1.63e-53

LamB/YcsF family of lactam utilization protein; The LamB/YbgL family includes the Aspergillus nidulans protein LamB, and its homologs from all three kingdoms of life. The lamb gene locates at the lam locus of Aspergillus nidulans, consisting of two divergently transcribed genes, lamA and lamB, needed for the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. Although the exact molecular function of LamB is unknown, it might be required for conversion of exogenous 2-pyrrolidinone to endogenous GABA


Pssm-ID: 212099  Cd Length: 238  Bit Score: 166.07  E-value: 1.63e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   3 IDLNADLGEG-----CGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPPET 77
Cdd:cd10787    1 IDLNCDLGESfgawkMGDDEALLPLVTSANIACGFHAGDPLVMRRTVRLAKEHGVAIGAHPGYPDLQGFGRRSMDLSPDE 80

                         90
                 ....*....|....*.
gi 333956877  78 IYAETLYQVGALAAIA 93
Cdd:cd10787   81 LRALVLYQIGALQAFA 96
 
Name Accession Description Interval E-value
PRK05406 PRK05406
5-oxoprolinase subunit PxpA;
1-93 1.84e-56

5-oxoprolinase subunit PxpA;


Pssm-ID: 235446  Cd Length: 246  Bit Score: 174.15  E-value: 1.84e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   1 MKIDLNADLGEG-----CGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPP 75
Cdd:PRK05406   2 MKIDLNCDLGESfgawkMGDDEALLPLVTSANIACGFHAGDPAVMRRTVRLAKENGVAIGAHPGYPDLEGFGRRNMDLSP 81

                         90
                 ....*....|....*...
gi 333956877  76 ETIYAETLYQVGALAAIA 93
Cdd:PRK05406  82 EELYALVLYQIGALQAIA 99
LamB_YcsF pfam03746
LamB/YcsF family; This family includes LamB. The lam locus of Aspergillus nidulans consists of ...
 4-93 1.30e-55

LamB/YcsF family; This family includes LamB. The lam locus of Aspergillus nidulans consists of two divergently transcribed genes, lamA and lamB, involved in the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. The exact molecular function of the proteins in this family is unknown.


Pssm-ID: 461036  Cd Length: 238  Bit Score: 171.42  E-value: 1.30e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877    4 DLNADLGEG-----CGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPPETI 78
Cdd:pfam03746   1 DLNCDLGEGfgawkMGDDEALLPLITSANIACGFHAGDPLVMRRTVRLAKEHGVAIGAHPGYPDLQGFGRREMDLSPEEL 80

                          90
                  ....*....|....*
gi 333956877   79 YAETLYQVGALAAIA 93
Cdd:pfam03746  81 YALVLYQIGALQAFA 95
PxpA COG1540
5-oxoprolinase subunit A [Amino acid transport and metabolism];
1-93 1.22e-53

5-oxoprolinase subunit A [Amino acid transport and metabolism];


Pssm-ID: 441149  Cd Length: 250  Bit Score: 166.77  E-value: 1.22e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   1 MKIDLNADLGEG-----CGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPP 75
Cdd:COG1540    1 MRIDLNSDLGESfgawtMGDDEALLPLVTSANIACGFHAGDPLVMRRTVRLAKERGVAIGAHPGYPDLAGFGRRNMDVSP 80

                         90
                 ....*....|....*...
gi 333956877  76 ETIYAETLYQVGALAAIA 93
Cdd:COG1540   81 EELYADVLYQIGALQAFA 98
LamB_YcsF_like cd10787
LamB/YcsF family of lactam utilization protein; The LamB/YbgL family includes the Aspergillus ...
 3-93 1.63e-53

LamB/YcsF family of lactam utilization protein; The LamB/YbgL family includes the Aspergillus nidulans protein LamB, and its homologs from all three kingdoms of life. The lamb gene locates at the lam locus of Aspergillus nidulans, consisting of two divergently transcribed genes, lamA and lamB, needed for the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. Although the exact molecular function of LamB is unknown, it might be required for conversion of exogenous 2-pyrrolidinone to endogenous GABA


Pssm-ID: 212099  Cd Length: 238  Bit Score: 166.07  E-value: 1.63e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   3 IDLNADLGEG-----CGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPPET 77
Cdd:cd10787    1 IDLNCDLGESfgawkMGDDEALLPLVTSANIACGFHAGDPLVMRRTVRLAKEHGVAIGAHPGYPDLQGFGRRSMDLSPDE 80

                         90
                 ....*....|....*.
gi 333956877  78 IYAETLYQVGALAAIA 93
Cdd:cd10787   81 LRALVLYQIGALQAFA 96
LamB_YcsF_YbgL_like cd10800
Escherichia coli putative lactam utilization protein YbgL and similar proteins; This subfamily ...
 3-93 7.34e-52

Escherichia coli putative lactam utilization protein YbgL and similar proteins; This subfamily of the LamB/YbgL family is represented by the Escherichia coli putative lactam utilization protein YbgL. Although their molecular function of member of this subfamily is unknown, they show high sequence similarity to the Aspergillus nidulans lactam utilization protein LamB, which might be required for conversion of exogenous 2-pyrrolidinone to endogenous GABA.


Pssm-ID: 212111  Cd Length: 240  Bit Score: 162.16  E-value: 7.34e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   3 IDLNADLGEGCGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPPETIYAET 82
Cdd:cd10800    1 IDLNADLGEGCGNDAALLTLVSSANIACGWHAGDATTMRATVALALENGVAIGAHPGFPDRENFGRTEMELSPDELYAGL 80

                         90
                 ....*....|.
gi 333956877  83 LYQVGALAAIA 93
Cdd:cd10800   81 LYQLGALKAIV 91
LamB_YcsF_like_1 cd10801
uncharacterized proteins similar to the Aspergillus nidulans lactam utilization protein LamB; ...
 3-93 3.08e-47

uncharacterized proteins similar to the Aspergillus nidulans lactam utilization protein LamB; This mainly bacterial subfamily of the LamB/YbgL family, contains many well conserved uncharacterized proteins. Although their molecular function remains unknown, those proteins show high sequence similarity to the Aspergillus nidulans lactam utilization protein LamB, which might be required for conversion of exogenous 2-pyrrolidinone to endogenous GABA.


Pssm-ID: 212112  Cd Length: 233  Bit Score: 150.02  E-value: 3.08e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   3 IDLNADLGEGCGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPPETIYAET 82
Cdd:cd10801    1 IDLNADLGEGVGNDAALMPLISSCNIACGGHAGDEESMRKTVKLAKEYGVKIGAHPSYPDRENFGRVSMEISPQELKESL 80

                         90
                 ....*....|.
gi 333956877  83 LYQVGALAAIA 93
Cdd:cd10801   81 REQIELLKEVA 91
PRK12569 PRK12569
hypothetical protein; Provisional
 1-93 1.98e-43

hypothetical protein; Provisional


Pssm-ID: 237141  Cd Length: 245  Bit Score: 140.84  E-value: 1.98e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   1 MKIDLNADLGEGCG-------NDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQL 73
Cdd:PRK12569   3 MSIDLNSDMGEGFGpwrigdgVDEALMPLISSANIATGFHAGDPNIMRRTVELAKAHGVGIGAHPGFRDLVGFGRRHINA 82

                         90       100
                 ....*....|....*....|
gi 333956877  74 PPETIYAETLYQVGALAAIA 93
Cdd:PRK12569  83 SPQELVNDVLYQLGALREFA 102
LamB_like cd11665
Aspergillus nidulans lactam utilization protein LamB and similar proteins; This eukaryotic and ...
 3-92 3.07e-42

Aspergillus nidulans lactam utilization protein LamB and similar proteins; This eukaryotic and bacterial subfamily of the LamB/YbgL family, includes Aspergillus nidulans protein LamB. The lamb gene locates at the lam locus of Aspergillus nidulans, consisting of two divergently transcribed genes, lamA and lamB, needed for the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. Although the exact molecular function of lamb encoding protein LamB is unknown, it might be required for conversion of exogenous 2-pyrrolidinone to endogenous GABA.


Pssm-ID: 212130  Cd Length: 238  Bit Score: 137.44  E-value: 3.07e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   3 IDLNADLGEG-----CGNDAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPPET 77
Cdd:cd11665    1 VTINCDMGESfgnwkMGDDEELMPHIDVANIACGFHAGDPVVMRKTVRLAKKHGVKVGAHPSLPDLQGFGRREMALDPEE 80

                         90
                 ....*....|....*
gi 333956877  78 IYAETLYQVGALAAI 92
Cdd:cd11665   81 LAACVLYQIGALKGF 95
LamB_YcsF_like_2 cd11664
uncharacterized proteins similar to the Aspergillus nidulans lactam utilization protein LamB; ...
 3-93 1.16e-33

uncharacterized proteins similar to the Aspergillus nidulans lactam utilization protein LamB; This bacterial subfamily of the LamB/YbgL family, contains many well conserved uncharacterized proteins. Although their molecular function is unknown, those proteins show high sequence similarity to the Aspergillus nidulans lactam utilization protein LamB, which might be required for conversion of exogenous 2-pyrrolidinone to endogenous GABA.


Pssm-ID: 212129  Cd Length: 238  Bit Score: 115.63  E-value: 1.16e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333956877   3 IDLNADLGEGCGN-------DAQLMPLISSANIACGFHAGDARTMRESVRLALAHGVAIGAHPGFADRENFGRTAMQLPP 75
Cdd:cd11664    1 VDLNSDMGEGFGPwtigdgvDEEIMPLISSANIATGFHAGDPNIMDRTVQLAAEHGVGIGAHPGYRDLVGFGRRHIAATP 80

                         90
                 ....*....|....*...
gi 333956877  76 ETIYAETLYQVGALAAIA 93
Cdd:cd11664   81 EELVNDILYQLGALREFA 98
GH38-57_N_LamB_YdjC_SF cd10785
Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein ...
 24-93 4.15e-10

Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex. GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22). This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily.


Pssm-ID: 212097 [Multi-domain]  Cd Length: 203  Bit Score: 53.42  E-value: 4.15e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 333956877  24 SSANIACGFHAGDA-RTMRES-----VRLALAHGVAIGAHPGFADREnfgrTAMQLPPETIYAETLYQVGALAAIA 93
Cdd:cd10785   41 MSFNIAPISYEALFyHDLGENiklqmKSIQKNGQLEIGTHGATHPDE----SEAQSHPENVYAQITEGITWLEKHM 112
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH