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Conserved domains on  [gi|1081036681|gb|OFR91393|]
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intercellular adhesin biosynthesis polysaccharide N-deacetylase [Staphylococcus sp. HMSC059F04]

Protein Classification

5-oxoprolinase subunit PxpA; glycoside hydrolase family 38 protein( domain architecture ID 10024213)

5-oxoprolinase subunit PxpA catalyzes the cleavage of 5-oxoproline to form L-glutamate coupled to the hydrolysis of ATP to ADP and inorganic phosphate| glycosyl hydrolase family 38 (GH38) protein such as human core-specific lysosomal alpha 1,6-mannosidase (Epman, Man2B2) which can efficiently cleave only the alpha 1,6-linked mannose residue from (Man)3GlcNAc, but not (Man)3(GlcNAc)2 or other larger high mannose oligosaccharide

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIA_icaB TIGR03933
intercellular adhesin biosynthesis polysaccharide N-deacetylase; A common motif in bacterial ...
 40-284 1.03e-147

intercellular adhesin biosynthesis polysaccharide N-deacetylase; A common motif in bacterial biosynthesis of polysaccharide for export is modification that follows polymerization. This model describes a subfamily of polysaccharide N-deacetylases that acts on poly-beta-1,6-N-acetyl-D-glyscosamine as produced by Staphylococcus epidermidis and S. aureus. The end product in these species is designated polysaccharide intercellular adhesin (PIA), and this gene designated icaB (intercellular adhesion protein B). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Cellular processes, Pathogenesis]


:

Pssm-ID: 188448 [Multi-domain]  Cd Length: 245  Bit Score: 413.84  E-value: 1.03e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681  40 NSALALNYHRIRDDNWFKNTLFTLSNSKEIKNYSISKEAFEAEIKWLKAHGAHFLTEKEFQHYKEKGKFPPKSVWISFDD 119
Cdd:TIGR03933   1 NSALALNYHRVRKDDPLNNFISLLSSSKEIKNYSVSDSEFESQIKWLKAHDAKFLTLKEFIKYKEKGKFPKRSVWINFDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 120 MEQSVYDNANPIIEKYKIPVTGFIITGQIGNENFHNLNLSDLSTLKILNHSKYWTFSSHTDNLHSLTKDRKAIMTSTPDD 199
Cdd:TIGR03933  81 MDQTIYDNAFPILKKYKIPATGFVITGHIGDENFHNLNLIDLKQLKEMYATGLWDFESHTHDLHNLKKSNKSKFLHSSKA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 200 KLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKTVKPSENNYRIPRVLMNEDAFNKLIKK 279
Cdd:TIGR03933 161 GAKKDIDKSEKYLNKNFNKNQTSIAYPYGLINDDKIKVLKKAGIRYGFTLEEKAVTPDDNNYRIPRILVSNDAFEKLIKK 240


                  ....*
gi 1081036681 280 WDGFA 284
Cdd:TIGR03933 241 WDGFN 245
 
Name Accession Description Interval E-value
PIA_icaB TIGR03933
intercellular adhesin biosynthesis polysaccharide N-deacetylase; A common motif in bacterial ...
 40-284 1.03e-147

intercellular adhesin biosynthesis polysaccharide N-deacetylase; A common motif in bacterial biosynthesis of polysaccharide for export is modification that follows polymerization. This model describes a subfamily of polysaccharide N-deacetylases that acts on poly-beta-1,6-N-acetyl-D-glyscosamine as produced by Staphylococcus epidermidis and S. aureus. The end product in these species is designated polysaccharide intercellular adhesin (PIA), and this gene designated icaB (intercellular adhesion protein B). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Cellular processes, Pathogenesis]


Pssm-ID: 188448 [Multi-domain]  Cd Length: 245  Bit Score: 413.84  E-value: 1.03e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681  40 NSALALNYHRIRDDNWFKNTLFTLSNSKEIKNYSISKEAFEAEIKWLKAHGAHFLTEKEFQHYKEKGKFPPKSVWISFDD 119
Cdd:TIGR03933   1 NSALALNYHRVRKDDPLNNFISLLSSSKEIKNYSVSDSEFESQIKWLKAHDAKFLTLKEFIKYKEKGKFPKRSVWINFDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 120 MEQSVYDNANPIIEKYKIPVTGFIITGQIGNENFHNLNLSDLSTLKILNHSKYWTFSSHTDNLHSLTKDRKAIMTSTPDD 199
Cdd:TIGR03933  81 MDQTIYDNAFPILKKYKIPATGFVITGHIGDENFHNLNLIDLKQLKEMYATGLWDFESHTHDLHNLKKSNKSKFLHSSKA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 200 KLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKTVKPSENNYRIPRVLMNEDAFNKLIKK 279
Cdd:TIGR03933 161 GAKKDIDKSEKYLNKNFNKNQTSIAYPYGLINDDKIKVLKKAGIRYGFTLEEKAVTPDDNNYRIPRILVSNDAFEKLIKK 240


                  ....*
gi 1081036681 280 WDGFA 284
Cdd:TIGR03933 241 WDGFN 245
CE4_IcaB_5s cd10965
Putative catalytic polysaccharide deacetylase domain of bacterial intercellular adhesion ...
 109-281 2.73e-87

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: 257.70  E-value: 2.73e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 109 PPKSVWISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQIGNENFhNLNLSDLSTLKILNHSKYWTFSSHTDNLHSLTKD 188
Cdd:cd10965     1 PGKYVVITFDDVDQTVYDNAFPILKKLKIPFTQFVITGQVGSTNF-GLNLATWSQIKEMVASGLVTFGLHTNDLHYLVKD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 189 RKAIMTSTPDDKLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKTVKPSENNYRIPRVLM 268
Cdd:cd10965    80 KKKLFTPASYSRFAEDYAKSQKCLKEKLGKKTRYFAYPYGEGNKDTQKILKKQGIQYGFTLRDKVVTNDSDNYRIPRILV 159

                         170
                  ....*....|...
gi 1081036681 269 NEDAFNKLIKKWD 281
Cdd:cd10965   160 TNDSFWKLIKKWI 172
CDA1 COG0726
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ...
 93-248 9.00e-16

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: 73.93  E-value: 9.00e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681  93 FLTEKEFQHYKEKGKFPPKSVWISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQIGNenfhnlnlsDLSTLKILnHSKY 172
Cdd:COG0726     2 VLSLDELLPALRWGPLPKKAVALTFDDGPREGTPRLLDLLKKYGVKATFFVVGSAVER---------HPELVREI-AAAG 71

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1081036681 173 WTFSSHTDNLHSLTKdrkaimtsTPDDKLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYT 248
Cdd:COG0726    72 HEIGNHTYTHPDLTK--------LSEEEERAEIARAKEALEELTGKRPRGFRPPYGRYSPETLDLLAELGYRYILW 139
Polysacc_deac_1 pfam01522
Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ...
 105-246 4.73e-15

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: 69.95  E-value: 4.73e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 105 KGKFPPKSVWISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQIGNEnfhnlnlsdLSTLKILNHSKyWTFSSHTDNLHs 184
Cdd:pfam01522   1 KGPTPKKVVALTFDDGPSENTPAILDVLKKYGVKATFFVIGGNVERY---------PDLVKRMVEAG-HEIGNHTWSHP- 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1081036681 185 ltkdrkaIMTSTPDDKLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYG 246
Cdd:pfam01522  70 -------NLTGLSPEEIRKEIERAQDALEKATGKRPRLFRPPYGSYNDTVLEVAKKLGYTAV 124
pgaB PRK14582
poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB;
4-271 1.09e-11

poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB;


Pssm-ID: 184754 [Multi-domain]  Cd Length: 671  Bit Score: 64.79  E-value: 1.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681   4 FFKLCSILTLLTIL----CIFQTHTISSAKSKEKTLNV----KGNSALALNYHRIRDDnwfkntlftlsnSKEIKNYSIS 75
Cdd:PRK14582    3 RNGNKYLLMLVSILmltaCISQSRTSFIPPQDRPSLLAeqpwPHNGFVAIAYHDVEDE------------AADQRFMSVR 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681  76 KEAFEAEIKWLKAHGAHFLTEKEFQHYKEKGK-FPPKSVWISFDDMEQSVYDNANPIIEKYKI-----PVTGFIITGQIG 149
Cdd:PRK14582   71 TSALREQFAWLRENGYQPVSVAQILEAHRGGKpLPEKAVLLTFDDGYSSFYTRVFPILQAFQWpavwaPVGSWVDTPADQ 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 150 NENFHNLNL--SDLST---LKILNHSKYWTFSSHTDNLH----------------SLTKDRKAIMTSTPDD---KLKDDI 205
Cdd:PRK14582  151 PVKFGGEMVprEYFATwqqVREVARSRLVEIASHTWNSHygiqanpqgsllpaavNRAYFTDHARYETAAEyreRIRLDA 230

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1081036681 206 VKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKtVKPSENNYRIPRVLMNED 271
Cdd:PRK14582  231 VKMTEYIRTKAGKNPRVWVWPYGEANGIALEELKKLGYDMAFTLESG-LANASQLDSIPRVLIANN 295
 
Name Accession Description Interval E-value
PIA_icaB TIGR03933
intercellular adhesin biosynthesis polysaccharide N-deacetylase; A common motif in bacterial ...
 40-284 1.03e-147

intercellular adhesin biosynthesis polysaccharide N-deacetylase; A common motif in bacterial biosynthesis of polysaccharide for export is modification that follows polymerization. This model describes a subfamily of polysaccharide N-deacetylases that acts on poly-beta-1,6-N-acetyl-D-glyscosamine as produced by Staphylococcus epidermidis and S. aureus. The end product in these species is designated polysaccharide intercellular adhesin (PIA), and this gene designated icaB (intercellular adhesion protein B). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Cellular processes, Pathogenesis]


Pssm-ID: 188448 [Multi-domain]  Cd Length: 245  Bit Score: 413.84  E-value: 1.03e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681  40 NSALALNYHRIRDDNWFKNTLFTLSNSKEIKNYSISKEAFEAEIKWLKAHGAHFLTEKEFQHYKEKGKFPPKSVWISFDD 119
Cdd:TIGR03933   1 NSALALNYHRVRKDDPLNNFISLLSSSKEIKNYSVSDSEFESQIKWLKAHDAKFLTLKEFIKYKEKGKFPKRSVWINFDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 120 MEQSVYDNANPIIEKYKIPVTGFIITGQIGNENFHNLNLSDLSTLKILNHSKYWTFSSHTDNLHSLTKDRKAIMTSTPDD 199
Cdd:TIGR03933  81 MDQTIYDNAFPILKKYKIPATGFVITGHIGDENFHNLNLIDLKQLKEMYATGLWDFESHTHDLHNLKKSNKSKFLHSSKA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 200 KLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKTVKPSENNYRIPRVLMNEDAFNKLIKK 279
Cdd:TIGR03933 161 GAKKDIDKSEKYLNKNFNKNQTSIAYPYGLINDDKIKVLKKAGIRYGFTLEEKAVTPDDNNYRIPRILVSNDAFEKLIKK 240


                  ....*
gi 1081036681 280 WDGFA 284
Cdd:TIGR03933 241 WDGFN 245
CE4_IcaB_5s cd10965
Putative catalytic polysaccharide deacetylase domain of bacterial intercellular adhesion ...
 109-281 2.73e-87

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: 257.70  E-value: 2.73e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 109 PPKSVWISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQIGNENFhNLNLSDLSTLKILNHSKYWTFSSHTDNLHSLTKD 188
Cdd:cd10965     1 PGKYVVITFDDVDQTVYDNAFPILKKLKIPFTQFVITGQVGSTNF-GLNLATWSQIKEMVASGLVTFGLHTNDLHYLVKD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 189 RKAIMTSTPDDKLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKTVKPSENNYRIPRVLM 268
Cdd:cd10965    80 KKKLFTPASYSRFAEDYAKSQKCLKEKLGKKTRYFAYPYGEGNKDTQKILKKQGIQYGFTLRDKVVTNDSDNYRIPRILV 159

                         170
                  ....*....|...
gi 1081036681 269 NEDAFNKLIKKWD 281
Cdd:cd10965   160 TNDSFWKLIKKWI 172
CE4_yadE_5s cd10966
Putative catalytic polysaccharide deacetylase domain of uncharacterized protein yadE and ...
 109-272 1.45e-34

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: 122.77  E-value: 1.45e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 109 PPKSVWISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQIGNENFHNLNLSDLSTLKILNHSKYWTFSSHTDNLHSLTKD 188
Cdd:cd10966     1 PEKSVVITFDDGYKSNYEYAYPILKKYGFKATIFVIGSRIGEKPQDPKILQYLSIEELKEMRDVFEFQSHTYNMHRGGGT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 189 RKAIMTSTPDDKLKDDIVKSNlfihkQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKTVKPSENNYRIPRVLM 268
Cdd:cd10966    81 GGHGLLALSEEEILADLKKSE-----EILGSSKAFAYPYGDYNDNAIEALKEAGVKLAFTTNEGKVTPGDDPYELPRVRI 155


                  ....
gi 1081036681 269 NEDA 272
Cdd:cd10966   156 TGGT 159
CE4_NodB_like_5s_6s cd10918
Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a ...
 112-271 1.52e-29

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: 109.61  E-value: 1.52e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 112 SVWISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQIGNENFHNLNLS------DLSTLKILnHSKYWTFSSHTDNlHsl 185
Cdd:cd10918     1 PVVLTFDDGYRDNYTYALPILKKYGLPATFFVITGYIGGGNPWWAPAPprppylTWDQLREL-AASGVEIGSHTHT-H-- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 186 tkdrkAIMTSTPDDKLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKTVKPSENNYRIPR 265
Cdd:cd10918    77 -----PDLTTLSDEELRRELAESKERLEEELGKPVRSFAYPYGRYNPRVIAALKEAGYKAAFTTDPGLNSPGDDPYALPR 151


                  ....*.
gi 1081036681 266 VLMNED 271
Cdd:cd10918   152 INVSGD 157
CE4_Ecf1_like_5s cd10969
Putative catalytic NodB homology domain of a hypothetical protein Ecf1 from Escherichia coli ...
 79-279 5.05e-24

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: 96.59  E-value: 5.05e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681  79 FEAEIKWLKAHGAHFLTEKEFQHYKEKGK-FPPKSVWISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQIGNENFHNLN 157
Cdd:cd10969     4 FEEQLKYLKKNGYRTLSLEELLAFLKGGKpLPKKSVLITFDDGYLDNYVYAYPILKKYGLKATIFVVTGFIDEASGVRPT 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 158 LSDlstlkilnhskYWTFSSHTDNLHSLTKDRKAIMTSTPDDK-------------------LKDDIVKSNLFIHKQFHK 218
Cdd:cd10969    84 LFD-----------YWSGDMPEANKIFFLKGRDEVFLSWEELRemedsgvfdiqshshshtrVEYELEESKRLLEENLGK 152

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1081036681 219 NNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKTVKPSENNYRIPRVLMNEDAFNKLIKK 279
Cdd:cd10969   153 KVDHFCWPWGHYSPESLRIAKELGFKFFFTTKKGVNVPGEDPDRIKRITVKKDGGFWLKKR 213
CE4_DAC_u4_5s cd10973
Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide ...
 111-271 5.22e-22

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: 89.64  E-value: 5.22e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 111 KSVWISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQIGNENFHNLNLSDLSTLKilnhSKYWTFSSHTDNlHSLTKDRK 190
Cdd:cd10973     1 KTVVITIDDGYKSVYTNAFPILKKYGYPFTLFVYTEAIGRGYPDYLSWDQIREMA----KYGVEIANHSYS-HPHLVRLG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 191 AIMTSTPDDKLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKTVKPSENNYRIPRVLMNE 270
Cdd:cd10973    76 EKMQEQWLEWIRQDIEKSQQRFEKELGKKPKLFAYPYGEYNPAIIKLVKEAGFEAAFQQSGGVVSAGTDLTALPRFPLSG 155


                  .
gi 1081036681 271 D 271
Cdd:cd10973   156 D 156
CE4_DAC_u1_6s cd10970
Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide ...
 113-280 1.85e-16

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: 75.81  E-value: 1.85e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 113 VWISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQIGNENFhnLNLSDLSTLkilnHSKYWTFSSHTDNLHSLtkdrkai 192
Cdd:cd10970     3 VSLTFDDGYESQYTTAFPILQEYGIPATAAVIPDSIGSSGR--LTLDQLREL----QDAGWEIASHTLTHTDL------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 193 mTSTPDDKLKDDIVKSNLFIHKQ-FHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKTVKPSENNYRIPRVLMNED 271
Cdd:cd10970    70 -TELSADEQRAELTESKRWLEDNgFGDGADHFAYPYGRYDDEVLELVREYYDLGRSGGGGPNGRPPLDPYRLRRVTGEAD 148


                  ....*....
gi 1081036681 272 AFNKLIKKW 280
Cdd:cd10970   149 TTTEEVKTL 157
CDA1 COG0726
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ...
 93-248 9.00e-16

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: 73.93  E-value: 9.00e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681  93 FLTEKEFQHYKEKGKFPPKSVWISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQIGNenfhnlnlsDLSTLKILnHSKY 172
Cdd:COG0726     2 VLSLDELLPALRWGPLPKKAVALTFDDGPREGTPRLLDLLKKYGVKATFFVVGSAVER---------HPELVREI-AAAG 71

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1081036681 173 WTFSSHTDNLHSLTKdrkaimtsTPDDKLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYT 248
Cdd:COG0726    72 HEIGNHTYTHPDLTK--------LSEEEERAEIARAKEALEELTGKRPRGFRPPYGRYSPETLDLLAELGYRYILW 139
CE4_PgaB_5s cd10964
N-terminal putative catalytic polysaccharide deacetylase domain of bacterial poly-beta-1, ...
 109-271 4.41e-15

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: 71.99  E-value: 4.41e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 109 PPKSVWISFDDMEQSVYDNANPIIEKYKIP-----VTGFIIT--GQIGNENFHNLNLSDLST---LKILNHSKYWTFSSH 178
Cdd:cd10964     2 PAKAVLLTFDDGYQSFYTRVYPLLKAYKYPavlalVGSWLETpaGKKVDYGGEQLPRDRFLSweqIREMQASGLVEIASH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 179 TDNLH---------SLTkdrKAIMTSTPDDKLK-------------DDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIK 236
Cdd:cd10964    82 SHDLHhgipanpqgNLL---PAATTRQYDPKTGryetdaeyrqrirNDLKKSSALIKKHTGRAPRVMVWPYGAYNGTLIE 158

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1081036681 237 VLKKEGIRYGYTLEDK--TVKPSENNyrIPRVLMNED 271
Cdd:cd10964   159 EAAKLGMQLTFTLEDGanNADQSLSS--IPRILVENN 193
Polysacc_deac_1 pfam01522
Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ...
 105-246 4.73e-15

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: 69.95  E-value: 4.73e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 105 KGKFPPKSVWISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQIGNEnfhnlnlsdLSTLKILNHSKyWTFSSHTDNLHs 184
Cdd:pfam01522   1 KGPTPKKVVALTFDDGPSENTPAILDVLKKYGVKATFFVIGGNVERY---------PDLVKRMVEAG-HEIGNHTWSHP- 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1081036681 185 ltkdrkaIMTSTPDDKLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYG 246
Cdd:pfam01522  70 -------NLTGLSPEEIRKEIERAQDALEKATGKRPRLFRPPYGSYNDTVLEVAKKLGYTAV 124
pgaB PRK14582
poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB;
4-271 1.09e-11

poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB;


Pssm-ID: 184754 [Multi-domain]  Cd Length: 671  Bit Score: 64.79  E-value: 1.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681   4 FFKLCSILTLLTIL----CIFQTHTISSAKSKEKTLNV----KGNSALALNYHRIRDDnwfkntlftlsnSKEIKNYSIS 75
Cdd:PRK14582    3 RNGNKYLLMLVSILmltaCISQSRTSFIPPQDRPSLLAeqpwPHNGFVAIAYHDVEDE------------AADQRFMSVR 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681  76 KEAFEAEIKWLKAHGAHFLTEKEFQHYKEKGK-FPPKSVWISFDDMEQSVYDNANPIIEKYKI-----PVTGFIITGQIG 149
Cdd:PRK14582   71 TSALREQFAWLRENGYQPVSVAQILEAHRGGKpLPEKAVLLTFDDGYSSFYTRVFPILQAFQWpavwaPVGSWVDTPADQ 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 150 NENFHNLNL--SDLST---LKILNHSKYWTFSSHTDNLH----------------SLTKDRKAIMTSTPDD---KLKDDI 205
Cdd:PRK14582  151 PVKFGGEMVprEYFATwqqVREVARSRLVEIASHTWNSHygiqanpqgsllpaavNRAYFTDHARYETAAEyreRIRLDA 230

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1081036681 206 VKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYTLEDKtVKPSENNYRIPRVLMNED 271
Cdd:PRK14582  231 VKMTEYIRTKAGKNPRVWVWPYGEANGIALEELKKLGYDMAFTLESG-LANASQLDSIPRVLIANN 295
hmsF PRK14581
outer membrane N-deacetylase; Provisional
 40-271 5.20e-08

outer membrane N-deacetylase; Provisional


Pssm-ID: 184753 [Multi-domain]  Cd Length: 672  Bit Score: 53.83  E-value: 5.20e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681  40 NSALALNYHRIRDDnwfkntlftlsnSKEIKNYSISKEAFEAEIKWLKAHGAHFLTEKEFQHYKEKGK-FPPKSVWISFD 118
Cdd:PRK14581   47 NTFVVIAYHDVEDD------------SADQRYLSVRSSALNEQFVWLRDNGYHVVSVDQILAARNGGPtLPDKAVLLTFD 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 119 DMEQSVYDNANPIIEKYKI-----PVTGFIITGQIGNENFHNLN-----------LSDLSTLKILNHSKYwTFSSH---T 179
Cdd:PRK14581  115 DGYSSFYRRVYPLLKAYKWsavlaPVGTWIDTATDKKVDFGGLStdrdrfatwkqITEMSKSGLVEIGAH-TYASHygvI 193

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 180 DNLHSLTKDRKAIMTSTPDDK-----------LKDDIVKSNLFIHKQFHKNNDSIAYPYGEVSNQNIKVLKKEGIRYGYT 248
Cdd:PRK14581  194 ANPQGNTEPAAANLQYDPKTKqyetveafkqrMEKDVALITQRIVQATGKQPRVWVWPYGAPNGTVLNILRQHGYQLAMT 273

                         250       260
                  ....*....|....*....|...
gi 1081036681 249 LEDKTVKPSENNyRIPRVLMNED 271
Cdd:PRK14581  274 LDPGVANINDLM-NIPRILISNN 295
CE4_Mlr8448_like_5s cd10968
Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its ...
 115-270 2.98e-06

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: 46.47  E-value: 2.98e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 115 ISFDDMEQSVYDNANPIIEKYKIPVTGFIITGQI-GNENFHNLNLS--DLSTLKILNHSKYWTFSSHTDNLHSLTKdrka 191
Cdd:cd10968     5 LTFDDGYRDNLEFALPVFERHGVPFTIYVTTGFPdGTGELWWLTLEclDWDELRRLAADPLVTIGAHTITHPNLAR---- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 192 imtsTPDDKLKDDIVKSNLFIHKQFHKNNDSIAYPYG---EVSNQNIKVLKKEGIRYGYTLEDKTVKPS--ENNYRIPRV 266
Cdd:cd10968    81 ----LSDDEARREIAASRARLEAELGREVRHFAYPYGdrtAAGPREADLAREAGFATAVTTRPGVLFAEhrENLHALPRI 156


                  ....
gi 1081036681 267 LMNE 270
Cdd:cd10968   157 SLNG 160
CE4_GLA_like_6s cd10967
Putative catalytic NodB homology domain of gellan lyase and similar proteins; This family is ...
 115-246 3.52e-06

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: 46.60  E-value: 3.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 115 ISFDD--MEQsvyDNANPIIEKYKIPVTGFIITGQIGNENfhNLNLSDLSTL-----KILNHSKywtfsSHTDnlhsltk 187
Cdd:cd10967     5 LTFDDgyAQD---LRAAPLLAKYGLKGTFFVNSGLLGRRG--YLDLEELRELaaaghEIGSHTV-----THPD------- 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1081036681 188 drkaiMTSTPDDKLKDDIVKSNLFIHKQFHKNNDSIAYPYGEVsNQNIKVLKKEGIRYG 246
Cdd:cd10967    68 -----LTSLPPAELRREIAESRAALEEIGGFPVTSFAYPFGST-NPSIVPLLARGFIAA 120
CE4_DAC_u2_5s cd10971
Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide ...
 156-270 3.27e-04

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: 40.75  E-value: 3.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081036681 156 LNLSDLSTLKILNHSkywtFSSHTDN---LHSLTKDRKaimtstpddklKDDIVKSNLFIHKQFHK-NNDSIAYPYGEVS 231
Cdd:cd10971    92 MTKDQIKQLERAGMH----IGSHGYDhywLGRLSPEEQ-----------EAEIKKSLKFLSEVGGGhDRWTFCYPYGSFN 156

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1081036681 232 NQNIKVLKKEGIRYGYTLEDK-TVKPSENNYRIPRVLMNE 270
Cdd:cd10971   157 EETLEILKENGCRLGFTTEVAiADLDDLEPLELPRYDCND 196
 
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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