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Conserved domains on  [gi|489740599|ref|WP_003644667|]
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MULTISPECIES: polysaccharide deacetylase family protein [Lactiplantibacillus]

Protein Classification

polysaccharide deacetylase family protein( domain architecture ID 10180925)

polysaccharide deacetylase family protein belonging to the carbohydrate esterase 4 (CE4) superfamily, may catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan; similar to Bacillus subtilis polysaccharide deacetylase YxkH

CATH:  3.20.20.370
CAZY:  CE4
EC:  3.-.-.-
Gene Ontology:  GO:0005975|GO:0046872|GO:0016787
PubMed:  12644381
SCOP:  3001025

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CE4_NodB_like_5s_6s cd10918
Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a ...
124-266 1.32e-45

Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, hemin storage system HmsF protein in gram-negative species, intercellular adhesion proteins IcaB, and many uncharacterized prokaryotic polysaccharide deacetylases. It also includes a putative polysaccharide deacetylase YxkH encoded by the Bacillus subtilis yxkH gene, which is one of six polysaccharide deacetylase gene homologs present in the Bacillus subtilis genome. Sequence comparison shows all family members contain a conserved domain similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, which consists of a deformed (beta/alpha)8 barrel fold with 6 or 7 strands. However, in this family, most proteins have 5 strands and some have 6 strands. Moreover, long insertions are found in many family members, whose function remains unknown.


:

Pssm-ID: 213023 [Multi-domain]  Cd Length: 157  Bit Score: 150.82  E-value: 1.32e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 124 VWITLDDSYKDNMTAAWPILKQTHQHATINFITGFT-----------HKKNHLTLADAKRMQASGnIDFQSHTVRHLDLN 192
Cdd:cd10918    2 VVLTFDDGYRDNYTYALPILKKYGLPATFFVITGYIgggnpwwapapPRPPYLTWDQLRELAASG-VEIGSHTHTHPDLT 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489740599 193 NLTYQVQLTELSSSKKWLDHNLQQNTQVICYPAGRANQQTIKADKQAGYQYALSTAPGIATSTQNPYNLTRQRV 266
Cdd:cd10918   81 TLSDEELRRELAESKERLEEELGKPVRSFAYPYGRYNPRVIAALKEAGYKAAFTTDPGLNSPGDDPYALPRINV 154
 
Name Accession Description Interval E-value
CE4_NodB_like_5s_6s cd10918
Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a ...
124-266 1.32e-45

Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, hemin storage system HmsF protein in gram-negative species, intercellular adhesion proteins IcaB, and many uncharacterized prokaryotic polysaccharide deacetylases. It also includes a putative polysaccharide deacetylase YxkH encoded by the Bacillus subtilis yxkH gene, which is one of six polysaccharide deacetylase gene homologs present in the Bacillus subtilis genome. Sequence comparison shows all family members contain a conserved domain similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, which consists of a deformed (beta/alpha)8 barrel fold with 6 or 7 strands. However, in this family, most proteins have 5 strands and some have 6 strands. Moreover, long insertions are found in many family members, whose function remains unknown.


Pssm-ID: 213023 [Multi-domain]  Cd Length: 157  Bit Score: 150.82  E-value: 1.32e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 124 VWITLDDSYKDNMTAAWPILKQTHQHATINFITGFT-----------HKKNHLTLADAKRMQASGnIDFQSHTVRHLDLN 192
Cdd:cd10918    2 VVLTFDDGYRDNYTYALPILKKYGLPATFFVITGYIgggnpwwapapPRPPYLTWDQLRELAASG-VEIGSHTHTHPDLT 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489740599 193 NLTYQVQLTELSSSKKWLDHNLQQNTQVICYPAGRANQQTIKADKQAGYQYALSTAPGIATSTQNPYNLTRQRV 266
Cdd:cd10918   81 TLSDEELRRELAESKERLEEELGKPVRSFAYPYGRYNPRVIAALKEAGYKAAFTTDPGLNSPGDDPYALPRINV 154
CDA1 COG0726
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ...
103-280 8.72e-25

Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440490 [Multi-domain]  Cd Length: 195  Bit Score: 98.19  E-value: 8.72e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 103 TLTANEAVYALKHRRIPqKKIVWITLDDSYKDNMTAAWPILKQTHQHATINFITGFTHKKNHLtladAKRMQASGnIDFQ 182
Cdd:COG0726    2 VLSLDELLPALRWGPLP-KKAVALTFDDGPREGTPRLLDLLKKYGVKATFFVVGSAVERHPEL----VREIAAAG-HEIG 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 183 SHTVRHLDLNNLTYQVQLTELSSSKKWLDHNLQQNTQVICYPAGRANQQTIKADKQAGYQYALSTA--------PGIATS 254
Cdd:COG0726   76 NHTYTHPDLTKLSEEEERAEIARAKEALEELTGKRPRGFRPPYGRYSPETLDLLAELGYRYILWDSvdsddwpyPSADAI 155
                        170       180
                 ....*....|....*....|....*.
gi 489740599 255 TQNPYNLTRQRVVPGMSLTAFQTLLT 280
Cdd:COG0726  156 VDRVLKYLKPGSIRPGTVEALPRLLD 181
Polysacc_deac_1 pfam01522
Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ...
121-244 6.49e-22

Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase. It also includes chitin deacetylase from yeast, and endoxylanases which hydrolyses glucosidic bonds in xylan.


Pssm-ID: 426305 [Multi-domain]  Cd Length: 124  Bit Score: 88.44  E-value: 6.49e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599  121 KKIVWITLDDSYKDNMTAAWPILKQTHQHATInFITGfTHKKNHLtlADAKRMQASGNiDFQSHTVRHLDLNNLTYQVQL 200
Cdd:pfam01522   6 KKVVALTFDDGPSENTPAILDVLKKYGVKATF-FVIG-GNVERYP--DLVKRMVEAGH-EIGNHTWSHPNLTGLSPEEIR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 489740599  201 TELSSSKKWLDHNLQQNTQVICYPAGRANQQTIKADKQAGYQYA 244
Cdd:pfam01522  81 KEIERAQDALEKATGKRPRLFRPPYGSYNDTVLEVAKKLGYTAV 124
 
Name Accession Description Interval E-value
CE4_NodB_like_5s_6s cd10918
Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a ...
124-266 1.32e-45

Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, hemin storage system HmsF protein in gram-negative species, intercellular adhesion proteins IcaB, and many uncharacterized prokaryotic polysaccharide deacetylases. It also includes a putative polysaccharide deacetylase YxkH encoded by the Bacillus subtilis yxkH gene, which is one of six polysaccharide deacetylase gene homologs present in the Bacillus subtilis genome. Sequence comparison shows all family members contain a conserved domain similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, which consists of a deformed (beta/alpha)8 barrel fold with 6 or 7 strands. However, in this family, most proteins have 5 strands and some have 6 strands. Moreover, long insertions are found in many family members, whose function remains unknown.


Pssm-ID: 213023 [Multi-domain]  Cd Length: 157  Bit Score: 150.82  E-value: 1.32e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 124 VWITLDDSYKDNMTAAWPILKQTHQHATINFITGFT-----------HKKNHLTLADAKRMQASGnIDFQSHTVRHLDLN 192
Cdd:cd10918    2 VVLTFDDGYRDNYTYALPILKKYGLPATFFVITGYIgggnpwwapapPRPPYLTWDQLRELAASG-VEIGSHTHTHPDLT 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489740599 193 NLTYQVQLTELSSSKKWLDHNLQQNTQVICYPAGRANQQTIKADKQAGYQYALSTAPGIATSTQNPYNLTRQRV 266
Cdd:cd10918   81 TLSDEELRRELAESKERLEEELGKPVRSFAYPYGRYNPRVIAALKEAGYKAAFTTDPGLNSPGDDPYALPRINV 154
CE4_Ecf1_like_5s cd10969
Putative catalytic NodB homology domain of a hypothetical protein Ecf1 from Escherichia coli ...
87-263 2.90e-34

Putative catalytic NodB homology domain of a hypothetical protein Ecf1 from Escherichia coli and similar proteins; This family contains a hypothetical protein Ecf1 from Escherichia coli and its prokaryotic homologs. Although their biochemical properties remain to be determined, members in this family contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily.


Pssm-ID: 213026 [Multi-domain]  Cd Length: 218  Bit Score: 123.55  E-value: 2.90e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599  87 KEFQTEMTYLKAHGYRTLTANEAVYALKHRRIPQKKIVWITLDDSYKDNMTAAWPILKQTHQHATINFITGF-------- 158
Cdd:cd10969    2 ETFEEQLKYLKKNGYRTLSLEELLAFLKGGKPLPKKSVLITFDDGYLDNYVYAYPILKKYGLKATIFVVTGFideasgvr 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 159 -------------THKKNHLTLAD--------AKRMQASGNIDFQSHTVRHLDLnnltyqvqLTELSSSKKWLDHNLQQN 217
Cdd:cd10969   82 ptlfdywsgdmpeANKIFFLKGRDevflsweeLREMEDSGVFDIQSHSHSHTRV--------EYELEESKRLLEENLGKK 153
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 489740599 218 TQVICYPAGRANQQTIKADKQAGYQYALSTAPGIATSTQNPYNLTR 263
Cdd:cd10969  154 VDHFCWPWGHYSPESLRIAKELGFKFFFTTKKGVNVPGEDPDRIKR 199
CE4_yadE_5s cd10966
Putative catalytic polysaccharide deacetylase domain of uncharacterized protein yadE and ...
121-275 2.26e-27

Putative catalytic polysaccharide deacetylase domain of uncharacterized protein yadE and similar proteins; This family contains an uncharacterized protein yadE from Escherichia coli and its bacterial homologs. Although its molecular function remains unknown, yadE shows high sequence similarity with the catalytic NodB homology domain of outer membrane lipoprotein PgaB and the surface-attached protein intercellular adhesion protein IcaB. Both PgaB and IcaB are essential in bacterial biofilm formation.


Pssm-ID: 213024 [Multi-domain]  Cd Length: 164  Bit Score: 103.90  E-value: 2.26e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 121 KKIVWITLDDSYKDNMTAAWPILKQTHQHATINFITGFT-------HKKNHLTLADAKRMQASgnIDFQSHT-------- 185
Cdd:cd10966    2 EKSVVITFDDGYKSNYEYAYPILKKYGFKATIFVIGSRIgekpqdpKILQYLSIEELKEMRDV--FEFQSHTynmhrggg 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 186 -VRHLdLNNLTYQVQLTELSSSKKWLDhnlqqNTQVICYPAGRANQQTIKADKQAGYQYALSTAPGIATSTQNPYNLTRQ 264
Cdd:cd10966   80 tGGHG-LLALSEEEILADLKKSEEILG-----SSKAFAYPYGDYNDNAIEALKEAGVKLAFTTNEGKVTPGDDPYELPRV 153
                        170
                 ....*....|.
gi 489740599 265 RVVPGMSLTAF 275
Cdd:cd10966  154 RITGGTSLEDF 164
CDA1 COG0726
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ...
103-280 8.72e-25

Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440490 [Multi-domain]  Cd Length: 195  Bit Score: 98.19  E-value: 8.72e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 103 TLTANEAVYALKHRRIPqKKIVWITLDDSYKDNMTAAWPILKQTHQHATINFITGFTHKKNHLtladAKRMQASGnIDFQ 182
Cdd:COG0726    2 VLSLDELLPALRWGPLP-KKAVALTFDDGPREGTPRLLDLLKKYGVKATFFVVGSAVERHPEL----VREIAAAG-HEIG 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 183 SHTVRHLDLNNLTYQVQLTELSSSKKWLDHNLQQNTQVICYPAGRANQQTIKADKQAGYQYALSTA--------PGIATS 254
Cdd:COG0726   76 NHTYTHPDLTKLSEEEERAEIARAKEALEELTGKRPRGFRPPYGRYSPETLDLLAELGYRYILWDSvdsddwpyPSADAI 155
                        170       180
                 ....*....|....*....|....*.
gi 489740599 255 TQNPYNLTRQRVVPGMSLTAFQTLLT 280
Cdd:COG0726  156 VDRVLKYLKPGSIRPGTVEALPRLLD 181
Polysacc_deac_1 pfam01522
Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ...
121-244 6.49e-22

Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase. It also includes chitin deacetylase from yeast, and endoxylanases which hydrolyses glucosidic bonds in xylan.


Pssm-ID: 426305 [Multi-domain]  Cd Length: 124  Bit Score: 88.44  E-value: 6.49e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599  121 KKIVWITLDDSYKDNMTAAWPILKQTHQHATInFITGfTHKKNHLtlADAKRMQASGNiDFQSHTVRHLDLNNLTYQVQL 200
Cdd:pfam01522   6 KKVVALTFDDGPSENTPAILDVLKKYGVKATF-FVIG-GNVERYP--DLVKRMVEAGH-EIGNHTWSHPNLTGLSPEEIR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 489740599  201 TELSSSKKWLDHNLQQNTQVICYPAGRANQQTIKADKQAGYQYA 244
Cdd:pfam01522  81 KEIERAQDALEKATGKRPRLFRPPYGSYNDTVLEVAKKLGYTAV 124
CE4_DAC_u4_5s cd10973
Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide ...
122-263 2.45e-19

Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; This family contains many uncharacterized bacterial polysaccharide deacetylases. Although their biological functions remain unknown, all members of the family are predicted to contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily.


Pssm-ID: 213028 [Multi-domain]  Cd Length: 157  Bit Score: 82.32  E-value: 2.45e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 122 KIVWITLDDSYKDNMTAAWPILKQTHQHATInFI-TGFTHKK--NHLTLADAKRMQASGnIDFQSHTVRHLDLNNLTYQV 198
Cdd:cd10973    1 KTVVITIDDGYKSVYTNAFPILKKYGYPFTL-FVyTEAIGRGypDYLSWDQIREMAKYG-VEIANHSYSHPHLVRLGEKM 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489740599 199 QLT-------ELSSSKKWLDHNLQQNTQVICYPAGRANQQTIKADKQAGYQYALSTAPGIATSTQNPYNLTR 263
Cdd:cd10973   79 QEQwlewirqDIEKSQQRFEKELGKKPKLFAYPYGEYNPAIIKLVKEAGFEAAFQQSGGVVSAGTDLTALPR 150
CE4_IcaB_5s cd10965
Putative catalytic polysaccharide deacetylase domain of bacterial intercellular adhesion ...
121-263 5.36e-18

Putative catalytic polysaccharide deacetylase domain of bacterial intercellular adhesion protein IcaB and similar proteins; The family is represented by the surface-attached protein intercellular adhesion protein IcaB (Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase, EC 3.5.1.-), encoded by Staphylococcus epidermidis icaB gene from the icaABC gene cluster that is involved in the synthesis of polysaccharide intercellular adhesin (PIA), which is located mainly on the cell surface. IcaB is a secreted, cell wall-associated protein that plays a crucial role in exopolysaccharide modification in bacterial biofilm formation. It catalyzes the N-deacetylation of poly-beta-1,6-N-acetyl-D-glucosamine (PNAG, also referred to as PIA), a biofilm adhesin polysaccharide. IcaB shows high homology to the N-terminal NodB homology domain of Escherichia coli PgaB. At this point, they are classified in the same family.


Pssm-ID: 200587 [Multi-domain]  Cd Length: 172  Bit Score: 79.35  E-value: 5.36e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 121 KKIVWITLDDSYKDNMTAAWPILKQTHQHATINFITGFTHKKNH----LTLADAKRMQASGNIDFQSHTvrhldlNNLTY 196
Cdd:cd10965    2 GKYVVITFDDVDQTVYDNAFPILKKLKIPFTQFVITGQVGSTNFglnlATWSQIKEMVASGLVTFGLHT------NDLHY 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 197 QVQ--------------LTELSSSKKWLDHNLQQNTQVICYPAGRANQQTIKADKQAGYQYALSTAPGIATSTQNPYNLT 262
Cdd:cd10965   76 LVKdkkklftpasysrfAEDYAKSQKCLKEKLGKKTRYFAYPYGEGNKDTQKILKKQGIQYGFTLRDKVVTNDSDNYRIP 155

                 .
gi 489740599 263 R 263
Cdd:cd10965  156 R 156
CE4_Mlr8448_like_5s cd10968
Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its ...
126-263 1.61e-17

Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its bacterial homologs; This family contains Mesorhizobium loti Mlr8448 protein and its bacterial homologs. Although their biochemical properties are yet to be determined, members in this subfamily contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily.


Pssm-ID: 213025 [Multi-domain]  Cd Length: 161  Bit Score: 77.67  E-value: 1.61e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 126 ITLDDSYKDNMTAAWPILKQTHQHATINFITGF---THKKNHLTLA-----DAKRMQASGNIDFQSHTVRHLDLNNLTYQ 197
Cdd:cd10968    5 LTFDDGYRDNLEFALPVFERHGVPFTIYVTTGFpdgTGELWWLTLEcldwdELRRLAADPLVTIGAHTITHPNLARLSDD 84
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489740599 198 VQLTELSSSKKWLDHNLQQNTQVICYPAG---RANQQTIKADKQAGYQYALSTAPGI--ATSTQNPYNLTR 263
Cdd:cd10968   85 EARREIAASRARLEAELGREVRHFAYPYGdrtAAGPREADLAREAGFATAVTTRPGVlfAEHRENLHALPR 155
CE4_DAC_u1_6s cd10970
Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide ...
123-263 1.94e-14

Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide deacetylases which consist of a 6-stranded beta/alpha barrel; This family contains uncharacterized prokaryotic polysaccharide deacetylases. Although their biological functions remain unknown, all members of the family contain a conserved domain with a 6-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily.


Pssm-ID: 213027 [Multi-domain]  Cd Length: 194  Bit Score: 70.04  E-value: 1.94e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 123 IVWITLDDSYKDNMTAAWPILKQTHQHATINFITGFTHKKNHLTLADAKRMQASGNiDFQSHTVRHLDLNNLTYQVQLTE 202
Cdd:cd10970    2 KVSLTFDDGYESQYTTAFPILQEYGIPATAAVIPDSIGSSGRLTLDQLRELQDAGW-EIASHTLTHTDLTELSADEQRAE 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489740599 203 LSSSKKWL-DHNLQQNTQVICYPAGRANQQTIKADKQAGYQYALSTAPGIATSTQNPYNLTR 263
Cdd:cd10970   81 LTESKRWLeDNGFGDGADHFAYPYGRYDDEVLELVREYYDLGRSGGGGPNGRPPLDPYRLRR 142
CE4_DAC_u2_5s cd10971
Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide ...
126-263 2.68e-11

Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; This family contains many uncharacterized prokaryotic polysaccharide deacetylases. Although their biological functions remain unknown, all members of this family are predicted to contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily.


Pssm-ID: 200593 [Multi-domain]  Cd Length: 198  Bit Score: 61.56  E-value: 2.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 126 ITLDDSYKDNMTAAWPILK---------------QTHQ----HAtINFITGFT--------------------HKKNH-- 164
Cdd:cd10971    4 LTFDDGYKDHYTYVLPELEergiqgsffvpakpvEEHKvldvNK-IHFILFIKrllqyelpeklrteildklfKKYVDis 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 165 ---------LTLADAKRMQASGNIdFQSHTVRHLDLNNLTYQVQLTELSSSKKWLDHNLQ-QNTQVICYPAGRANQQTIK 234
Cdd:cd10971   83 eeafakelyMTKDQIKQLERAGMH-IGSHGYDHYWLGRLSPEEQEAEIKKSLKFLSEVGGgHDRWTFCYPYGSFNEETLE 161
                        170       180       190
                 ....*....|....*....|....*....|
gi 489740599 235 ADKQAGYQYALSTAPGIATSTQN-PYNLTR 263
Cdd:cd10971  162 ILKENGCRLGFTTEVAIADLDDLePLELPR 191
CE4_GLA_like_6s cd10967
Putative catalytic NodB homology domain of gellan lyase and similar proteins; This family is ...
126-272 4.61e-10

Putative catalytic NodB homology domain of gellan lyase and similar proteins; This family is represented by the extracellular polysaccharide-degrading enzyme, gellan lyase (gellanase, EC 4.2.2.-), from Bacillus sp. The enzyme acts on gellan exolytically and releases a tetrasaccharide of glucuronyl-glucosyl-rhamnosyl-glucose with unsaturated glucuronic acid at the nonreducing terminus. The family also includes many uncharacterized prokaryotic polysaccharide deacetylases, which show high sequence similarity to Bacillus sp. gellan lyase. Although their biological functions remain unknown, all members of the family contain a conserved domain with a 6-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily.


Pssm-ID: 200589 [Multi-domain]  Cd Length: 202  Bit Score: 57.77  E-value: 4.61e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 126 ITLDDSYKDNMTAAwPILKQTHQHATINFITGFTHKKNHLTLADAKRMQASGNiDFQSHTVRHLDLNNLTYQVQLTELSS 205
Cdd:cd10967    5 LTFDDGYAQDLRAA-PLLAKYGLKGTFFVNSGLLGRRGYLDLEELRELAAAGH-EIGSHTVTHPDLTSLPPAELRREIAE 82
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489740599 206 SKKWLDHNLQQNTQVICYPAGRANQQTIKAdKQAGYQYALSTAPGIATSTQNPYNLTRQRVVPGMSL 272
Cdd:cd10967   83 SRAALEEIGGFPVTSFAYPFGSTNPSIVPL-LARGFIAARGVGGGGNPPNPSDPPADPADCHNADSL 148
CE4_PgaB_5s cd10964
N-terminal putative catalytic polysaccharide deacetylase domain of bacterial poly-beta-1, ...
122-263 1.14e-08

N-terminal putative catalytic polysaccharide deacetylase domain of bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, and similar proteins; This family is represented by an outer membrane lipoprotein, poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase (PgaB, EC 3.5.1.-), encoded by Escherichia coli pgaB gene from the pgaABCD (formerly ycdSRQP) operon, which affects biofilm development by promoting abiotic surface binding and intercellular adhesion. PgaB catalyzes the N-deacetylation of poly-beta-1,6-N-acetyl-D-glucosamine (PGA), a biofilm adhesin polysaccharide that stabilizes biofilms of E. coli and other bacteria. PgaB contains an N-terminal NodB homology domain with a 5-stranded beta/alpha barrel, and a C-terminal carbohydrate binding domain required for PGA N-deacetylation, which may be involved in binding to unmodified poly-beta-1,6-GlcNAc and assisting catalysis by the deacetylase domain. This family also includes several orthologs of PgaB, such as the hemin storage system HmsF protein, encoded by Yersinia pestis hmsF gene from the hmsHFRS operon, which is essential for Y. pestis biofilm formation. Like PgaB, HmsF is an outer membrane protein with an N-terminal NodB homology domain, which is likely involved in the modification of the exopolysaccharide (EPS) component of the biofilm. HmsF also has a conserved but uncharacterized C-terminal domain that is present in other HmsF-like proteins in Gram-negative bacteria. This alignment model corresponds to the N-terminal NodB homology domain.


Pssm-ID: 200586 [Multi-domain]  Cd Length: 193  Bit Score: 53.89  E-value: 1.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 122 KIVWITLDDSYKDNMTAAWPILKQ---------------THQHATINFITGFTHKKNHLTLADAKRMQASGNIDFQSHTv 186
Cdd:cd10964    4 KAVLLTFDDGYQSFYTRVYPLLKAykypavlalvgswleTPAGKKVDYGGEQLPRDRFLSWEQIREMQASGLVEIASHS- 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 187 rhldlNNLTYQVQ---------------------------------LTELSSSKKWLDHNLQQNTQVICYPAGRANQQTI 233
Cdd:cd10964   83 -----HDLHHGIPanpqgnllpaattrqydpktgryetdaeyrqriRNDLKKSSALIKKHTGRAPRVMVWPYGAYNGTLI 157
                        170       180       190
                 ....*....|....*....|....*....|
gi 489740599 234 KADKQAGYQYALSTAPGIATSTQNPYNLTR 263
Cdd:cd10964  158 EEAAKLGMQLTFTLEDGANNADQSLSSIPR 187
CE4_NodB_like_6s_7s cd10917
Catalytic NodB homology domain of rhizobial NodB-like proteins; This family belongs to the ...
122-245 9.54e-06

Catalytic NodB homology domain of rhizobial NodB-like proteins; This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes many rhizobial NodB chitooligosaccharide N-deacetylase (EC 3.5.1.-)-like proteins, mainly from bacteria and eukaryotes, such as chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan. All members of this family contain a catalytic NodB homology domain with the same overall topology and a deformed (beta/alpha)8 barrel fold with 6- or 7 strands. Their catalytic activity is dependent on the presence of a divalent cation, preferably cobalt or zinc, and they employ a conserved His-His-Asp zinc-binding triad closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. Several family members show diversity both in metal ion specificities and in the residues that coordinate the metal.


Pssm-ID: 213022 [Multi-domain]  Cd Length: 171  Bit Score: 44.92  E-value: 9.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489740599 122 KIVWITLDDSYKDNMTAAW-PILKQTHQHATInFITGfTHKKNHLTLAdaKRMQASGNIdFQSHTVRHLDLNNLTYQVQL 200
Cdd:cd10917    1 KVVALTFDDGPDPEYTPKIlDILAEYGVKATF-FVVG-ENVEKHPDLV--RRIVAEGHE-IGNHTYSHPDLTKLSPEEIR 75
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 489740599 201 TELSSSKKWLDHNLQQNTQVICYPAGRANQQTIKADKQAGYQYAL 245
Cdd:cd10917   76 AEIERTQDAIEEATGVRPRLFRPPYGAYNPEVLAAAAELGLTVVL 120
 
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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