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Conserved domains on  [gi|259563529|sp|B4TBG7|]
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RecName: Full=Probable 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD

Protein Classification

4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase( domain architecture ID 11487769)

4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD catalyzes the formation of 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol from 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK15394 PRK15394
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional
 1-296 0e+00

4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional


:

Pssm-ID: 185292  Cd Length: 296  Bit Score: 601.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529   1 MTKVGLRIDVDTLRGTREGVPRLLATLHRHGVQASFFFSVGPDNMGRHLWRLIRPRFLWKMLRSNAASLYGWDILLAGTA 80
Cdd:PRK15394   1 MTKVGLRIDVDTFRGTREGVPRLLEILSKHGIQASFFFSVGPDNMGRHLWRLLKPRFLWKMLRSNAASLYGWDILLAGTA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  81 WPGKNIGNANAGIIRETATYHETGLHAWDHHAWQTHSGHWSIRQLEEDIARGITALEAIIGKPVTCSAAAGWRADGRVVR 160
Cdd:PRK15394  81 WPGKEIGKALADIIREAAKAHEVGLHAWDHHAWQAWSGVWSRQQLIEQIARGVDALEEIIGQPVTCSAAAGWRADQRVVE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529 161 AKEPFNLRYNSDCRGTTLFRPLLMPDQTGTPQIPVTLPTWDEVIGPAVQAQSFNTWIISRMLQDKGTPVYTIHAEVEGIV 240
Cdd:PRK15394 161 AKEAFGFRYNSDCRGTHPFRPLLPDGSLGTVQIPVTLPTWDEVIGRDVKAEDFNDFILDRILRDKGTPVYTIHAEVEGIA 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 259563529 241 HQPLFEDLLVRARDAGITFCPLGELLPTSPESLPLGQIVRGHIPGREGWLGCQQAA 296
Cdd:PRK15394 241 YAHNFEDLLKRAAQEGITFCPLSELLPDDLETLPLGKVVRGNIPGREGWLGCQQIA 296
 
Name Accession Description Interval E-value
PRK15394 PRK15394
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional
 1-296 0e+00

4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional


Pssm-ID: 185292  Cd Length: 296  Bit Score: 601.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529   1 MTKVGLRIDVDTLRGTREGVPRLLATLHRHGVQASFFFSVGPDNMGRHLWRLIRPRFLWKMLRSNAASLYGWDILLAGTA 80
Cdd:PRK15394   1 MTKVGLRIDVDTFRGTREGVPRLLEILSKHGIQASFFFSVGPDNMGRHLWRLLKPRFLWKMLRSNAASLYGWDILLAGTA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  81 WPGKNIGNANAGIIRETATYHETGLHAWDHHAWQTHSGHWSIRQLEEDIARGITALEAIIGKPVTCSAAAGWRADGRVVR 160
Cdd:PRK15394  81 WPGKEIGKALADIIREAAKAHEVGLHAWDHHAWQAWSGVWSRQQLIEQIARGVDALEEIIGQPVTCSAAAGWRADQRVVE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529 161 AKEPFNLRYNSDCRGTTLFRPLLMPDQTGTPQIPVTLPTWDEVIGPAVQAQSFNTWIISRMLQDKGTPVYTIHAEVEGIV 240
Cdd:PRK15394 161 AKEAFGFRYNSDCRGTHPFRPLLPDGSLGTVQIPVTLPTWDEVIGRDVKAEDFNDFILDRILRDKGTPVYTIHAEVEGIA 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 259563529 241 HQPLFEDLLVRARDAGITFCPLGELLPTSPESLPLGQIVRGHIPGREGWLGCQQAA 296
Cdd:PRK15394 241 YAHNFEDLLKRAAQEGITFCPLSELLPDDLETLPLGKVVRGNIPGREGWLGCQQIA 296
CE4_ArnD cd10939
Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol ...
 3-291 3.36e-150

Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD and other bacterial homologs; This family is represented by Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD (EC 3.5.1.n3). ArnD plays an important role in the biosynthesis of undecaprenyl phosphate alpha-4-amino-4-deoxy-L-arabinose (alpha-L-Ara4N). It catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol. The ArnD-dependent deformylation likely occurs on the inner leaflet of the inner membrane. This family also includes many uncharacterized bacterial polysaccharide deacetylases. All family members show high sequence homology to the catalytic domain of bacterial PuuE (purine utilization E) allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA), and are classified within the larger carbohydrate esterase 4 (CE4) superfamily.


Pssm-ID: 200564 [Multi-domain]  Cd Length: 290  Bit Score: 422.46  E-value: 3.36e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529   3 KVGLRIDVDTLRGTREGVPRLLATLHRHGVQASFFFSVGPDNMGRHLWRLIRPRFLWKMLRSNAASLYGWDILLAGTAWP 82
Cdd:cd10939    1 KIALKIDVDTYRGTREGVPRLLRILRRHGIKATFFFSVGPDNTGRALWRLFRPGFLKKMLRTNAPSLYGWRTLLYGTLLP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  83 GKNIGNANAGIIRETATY-HETGLHAWDHHAWQTHSGHWSIRQLEEDIARGITALEAIIGKPVTCSAAAGWRADGRVVRA 161
Cdd:cd10939   81 GPIIGRRLADIIRQVAKAgHEVGIHAWDHVKWQDRLDAMSAAEIKREFDKGVALFEKIFGRPPSTSAAPGWQANDRSLEI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529 162 KEPFNLRYNSDCRGTTLFRPLLMPDQTGTPQIPVTLPTWDEVIG-PAVQAQSFNTWIISrMLQDKGTPVYTIHAEVEGIV 240
Cdd:cd10939  161 KDEFGFRYASDCRGGHPFYPLLAGKPLGTLQIPTTLPTLDELLGrDGATADNINDYLLS-LLRPDGLNVLTIHAEVEGMK 239

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 259563529 241 HQPLFEDLLVRARDAGITFCPLGELLPTSPESLPLGQIVRGHIPGREGWLG 291
Cdd:cd10939  240 YAPIFEELLKRARARGYRFVPLGELAEELLINTPVGEVVMGEIPGRSGWLA 290
CDA1 COG0726
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ...
 4-169 7.37e-13

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: 65.84  E-value: 7.37e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529   4 VGLRIDVdtlrGTREGVPRLLATLHRHGVQASFFFsVGpDNMGRH--LWRLIrprflwkmlrsnaaslygwdillagtaw 81
Cdd:COG0726   22 VALTFDD----GPREGTPRLLDLLKKYGVKATFFV-VG-SAVERHpeLVREI---------------------------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  82 pgknignANAGiiretatyHETGLHAWDHHAWQThsghWSIRQLEEDIARGITALEAIIGKPVTCSAAAGWRADGRVVRA 161
Cdd:COG0726   68 -------AAAG--------HEIGNHTYTHPDLTK----LSEEEERAEIARAKEALEELTGKRPRGFRPPYGRYSPETLDL 128


                 ....*...
gi 259563529 162 KEPFNLRY 169
Cdd:COG0726  129 LAELGYRY 136
Polysacc_deac_1 pfam01522
Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ...
 15-145 3.30e-05

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: 42.60  E-value: 3.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529   15 GTREGVPRLLATLHRHGVQASFFFSvgpdnmgrhlwrlirprflwkmlrsnaaslygwdillagtawpGKNIGNANAGII 94
Cdd:pfam01522  16 GPSENTPAILDVLKKYGVKATFFVI-------------------------------------------GGNVERYPDLVK 52

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 259563529   95 RETATYHETGLHAWDHHAWQThsghWSIRQLEEDIARGITALEAIIGKPVT 145
Cdd:pfam01522  53 RMVEAGHEIGNHTWSHPNLTG----LSPEEIRKEIERAQDALEKATGKRPR 99
 
Name Accession Description Interval E-value
PRK15394 PRK15394
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional
 1-296 0e+00

4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional


Pssm-ID: 185292  Cd Length: 296  Bit Score: 601.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529   1 MTKVGLRIDVDTLRGTREGVPRLLATLHRHGVQASFFFSVGPDNMGRHLWRLIRPRFLWKMLRSNAASLYGWDILLAGTA 80
Cdd:PRK15394   1 MTKVGLRIDVDTFRGTREGVPRLLEILSKHGIQASFFFSVGPDNMGRHLWRLLKPRFLWKMLRSNAASLYGWDILLAGTA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  81 WPGKNIGNANAGIIRETATYHETGLHAWDHHAWQTHSGHWSIRQLEEDIARGITALEAIIGKPVTCSAAAGWRADGRVVR 160
Cdd:PRK15394  81 WPGKEIGKALADIIREAAKAHEVGLHAWDHHAWQAWSGVWSRQQLIEQIARGVDALEEIIGQPVTCSAAAGWRADQRVVE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529 161 AKEPFNLRYNSDCRGTTLFRPLLMPDQTGTPQIPVTLPTWDEVIGPAVQAQSFNTWIISRMLQDKGTPVYTIHAEVEGIV 240
Cdd:PRK15394 161 AKEAFGFRYNSDCRGTHPFRPLLPDGSLGTVQIPVTLPTWDEVIGRDVKAEDFNDFILDRILRDKGTPVYTIHAEVEGIA 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 259563529 241 HQPLFEDLLVRARDAGITFCPLGELLPTSPESLPLGQIVRGHIPGREGWLGCQQAA 296
Cdd:PRK15394 241 YAHNFEDLLKRAAQEGITFCPLSELLPDDLETLPLGKVVRGNIPGREGWLGCQQIA 296
CE4_ArnD cd10939
Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol ...
 3-291 3.36e-150

Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD and other bacterial homologs; This family is represented by Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD (EC 3.5.1.n3). ArnD plays an important role in the biosynthesis of undecaprenyl phosphate alpha-4-amino-4-deoxy-L-arabinose (alpha-L-Ara4N). It catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol. The ArnD-dependent deformylation likely occurs on the inner leaflet of the inner membrane. This family also includes many uncharacterized bacterial polysaccharide deacetylases. All family members show high sequence homology to the catalytic domain of bacterial PuuE (purine utilization E) allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA), and are classified within the larger carbohydrate esterase 4 (CE4) superfamily.


Pssm-ID: 200564 [Multi-domain]  Cd Length: 290  Bit Score: 422.46  E-value: 3.36e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529   3 KVGLRIDVDTLRGTREGVPRLLATLHRHGVQASFFFSVGPDNMGRHLWRLIRPRFLWKMLRSNAASLYGWDILLAGTAWP 82
Cdd:cd10939    1 KIALKIDVDTYRGTREGVPRLLRILRRHGIKATFFFSVGPDNTGRALWRLFRPGFLKKMLRTNAPSLYGWRTLLYGTLLP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  83 GKNIGNANAGIIRETATY-HETGLHAWDHHAWQTHSGHWSIRQLEEDIARGITALEAIIGKPVTCSAAAGWRADGRVVRA 161
Cdd:cd10939   81 GPIIGRRLADIIRQVAKAgHEVGIHAWDHVKWQDRLDAMSAAEIKREFDKGVALFEKIFGRPPSTSAAPGWQANDRSLEI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529 162 KEPFNLRYNSDCRGTTLFRPLLMPDQTGTPQIPVTLPTWDEVIG-PAVQAQSFNTWIISrMLQDKGTPVYTIHAEVEGIV 240
Cdd:cd10939  161 KDEFGFRYASDCRGGHPFYPLLAGKPLGTLQIPTTLPTLDELLGrDGATADNINDYLLS-LLRPDGLNVLTIHAEVEGMK 239

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 259563529 241 HQPLFEDLLVRARDAGITFCPLGELLPTSPESLPLGQIVRGHIPGREGWLG 291
Cdd:cd10939  240 YAPIFEELLKRARARGYRFVPLGELAEELLINTPVGEVVMGEIPGRSGWLA 290
CE4_SF cd10585
Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate ...
 3-173 5.73e-13

Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes 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, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing 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. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins.


Pssm-ID: 213020 [Multi-domain]  Cd Length: 142  Bit Score: 65.16  E-value: 5.73e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529   3 KVGLRIDVDT-LRGTREGVPRLLATLHRHGVQASFFFSVGPDNMGRhlwrlirprflwkmlrsnaaslygwdillagtaw 81
Cdd:cd10585    1 LVLLTLDDDPaFEGSPAALQRLLDLLEGYGIPATLFVIPGNANPDK---------------------------------- 46

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  82 pgKNIGNANAGIIRETATY-HETGLHAWDHHAWqtHSGHWSIRQLEEDIARGITALEAIIGKPVTCSAAAGWRADGRVVR 160
Cdd:cd10585   47 --LMKSPLNWDLLRELLAYgHEIGLHGYTHPDL--AYGNLSPEEVLEDLLRARRILEEAGGQPPKGFRAPGGNLSETVKA 122

                        170
                 ....*....|...
gi 259563529 161 AKEPFNLRYNSDC 173
Cdd:cd10585  123 LKELGDIQYDSDL 135
CDA1 COG0726
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ...
 4-169 7.37e-13

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: 65.84  E-value: 7.37e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529   4 VGLRIDVdtlrGTREGVPRLLATLHRHGVQASFFFsVGpDNMGRH--LWRLIrprflwkmlrsnaaslygwdillagtaw 81
Cdd:COG0726   22 VALTFDD----GPREGTPRLLDLLKKYGVKATFFV-VG-SAVERHpeLVREI---------------------------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  82 pgknignANAGiiretatyHETGLHAWDHHAWQThsghWSIRQLEEDIARGITALEAIIGKPVTCSAAAGWRADGRVVRA 161
Cdd:COG0726   68 -------AAAG--------HEIGNHTYTHPDLTK----LSEEEERAEIARAKEALEELTGKRPRGFRPPYGRYSPETLDL 128


                 ....*...
gi 259563529 162 KEPFNLRY 169
Cdd:COG0726  129 LAELGYRY 136
CE4_PuuE_HpPgdA_like_2 cd10941
Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar ...
 10-154 3.70e-08

Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA); This family contains many uncharacterized prokaryotic polysaccharide deacetylases (DCAs) that show high sequence similarity to the catalytic domain of bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA). PuuE allantoinase appears to be metal-independent and specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. Different from PuuE allantoinase, HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. Both PuuE allantoinase and HpPgdA function as homotetramers. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of DCA-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. In contrast to typical NodB-like DCAs, PuuE allantoinase and HpPgdA do not exhibit a solvent-accessible polysaccharide binding groove and might only bind a small molecule at the active site.


Pssm-ID: 200566 [Multi-domain]  Cd Length: 258  Bit Score: 53.45  E-value: 3.70e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  10 VDTLRGTREGVPRLLATLHRHGVQASFFFsVGpdNMGRHLWRLIRprflwkmlrsnaaslygwdillagtawpgkNIgnA 89
Cdd:cd10941   24 EDQERRLEEGLDRLLDLLDKHGVKATFFV-LG--EVAERYPDLIR------------------------------RI--A 68

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 259563529  90 NAGiiretatyHETGLHAWDHHAWQTHSghwsIRQLEEDIARGITALEAIIGKPVTcsaaaGWRA 154
Cdd:cd10941   69 EAG--------HEIASHGYAHERVDRLT----PEEFREDLRRSKKILEDITGQKVV-----GFRA 116
CE4_BsYlxY_like cd10950
Putative catalytic NodB homology domain of uncharacterized protein YlxY from Bacillus subtilis ...
 3-168 7.34e-07

Putative catalytic NodB homology domain of uncharacterized protein YlxY from Bacillus subtilis and its bacterial homologs; The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. This family is represented by Bacillus subtilis putative polysaccharide deacetylase BsYlxY, encoded by the ylxY gene, which is a member of the carbohydrate esterase 4 (CE4) superfamily. Although its biological function still remains unknown, BsYlxY shows high sequence homology to the catalytic domain of Bacillus subtilis pdaB gene encoding a putative polysaccharide deacetylase (BsPdaB), which is essential for the maintenance of spores after the late stage of sporulation and is highly conserved in spore-forming bacteria. However, disruption of the ylxY gene in B. subtilis did not cause any sporulation defect. Moreover, the Asp residue in the classical His-His-Asp zinc-binding motif of CE4 esterases is mutated to a Val residue in this family. Other catalytically relevant residues of CE4 esterases are also not conserved, which suggest that members of this family may be inactive.


Pssm-ID: 200574 [Multi-domain]  Cd Length: 188  Bit Score: 48.43  E-value: 7.34e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529   3 KVGLRIDVDTlrGTrEGVPRLLATLHRHGVQASFFFSvgpdnmGRhlWRLIRPRFLWKMlrsnaaslygwdillagtawp 82
Cdd:cd10950    7 MVALLINVAW--GE-EYLPAMLTILEKHDVKATFFLE------GR--WAKKNPDLVRKI--------------------- 54

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  83 gknignANAGiiretatyHETGLHAWDHhawqTHSGHWSIRQLEEDIARGITALEAIIGKPVTCSAAAGWRADGRVVRAK 162
Cdd:cd10950   55 ------AKDG--------HEIGNHGYSH----PDPSQLSYEQNREEIRKTNEIIEEITGEKPKLFAPPYGEFNDAVVKAA 116


                 ....*.
gi 259563529 163 EPFNLR 168
Cdd:cd10950  117 AELGMR 122
CE4_HpPgdA_like cd10938
Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar ...
 15-154 4.10e-06

Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins; This family is represented by a peptidoglycan deacetylase (HP0310, HpPgdA) from the gram-negative pathogen Helicobacter pylori. HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. It functions as a homotetramer. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of polysaccharide deacetylase (DCA)-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. In contrast to typical NodB-like DCAs, HpPgdA does not exhibit a solvent-accessible polysaccharide binding groove, suggesting that the enzyme binds a small molecule at the active site.


Pssm-ID: 200563 [Multi-domain]  Cd Length: 258  Bit Score: 47.17  E-value: 4.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  15 GTREGVPRLLATLHRHGVQASFFFSvgpdnmgrhlwrlirprflwkmlrsnaaslyGWDILlagtAWPG--KNIgnANAG 92
Cdd:cd10938   34 GARVGVPRLLDLLDRYDVKATFFVP-------------------------------GHTAE----TFPEavEAI--LAAG 76

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 259563529  93 iiretatyHETGLHAWDHHAWQTHsghwSIRQLEEDIARGITALEAIIGKPVTcsaaaGWRA 154
Cdd:cd10938   77 --------HEIGHHGYLHENPTGL----TPEEERELLERGLELLEKLTGKRPV-----GYRS 121
Polysacc_deac_1 pfam01522
Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ...
 15-145 3.30e-05

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: 42.60  E-value: 3.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529   15 GTREGVPRLLATLHRHGVQASFFFSvgpdnmgrhlwrlirprflwkmlrsnaaslygwdillagtawpGKNIGNANAGII 94
Cdd:pfam01522  16 GPSENTPAILDVLKKYGVKATFFVI-------------------------------------------GGNVERYPDLVK 52

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 259563529   95 RETATYHETGLHAWDHHAWQThsghWSIRQLEEDIARGITALEAIIGKPVT 145
Cdd:pfam01522  53 RMVEAGHEIGNHTWSHPNLTG----LSPEEIRKEIERAQDALEKATGKRPR 99
CE4_NodB_like_3 cd10959
Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases; This ...
 18-146 2.64e-04

Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases; This family includes many uncharacterized bacterial polysaccharide deacetylases. Although their biological function still remains unknown, members in this family show high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an extracellular metal-dependent polysaccharide deacetylase with de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. Like SpPgdA, this family is a member of the carbohydrate esterase 4 (CE4) superfamily.


Pssm-ID: 200582 [Multi-domain]  Cd Length: 187  Bit Score: 41.05  E-value: 2.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  18 EGVPRLLATLHRHGVQASFFFsVGpDNMGRHlwrlirPRFLWKMlrsnaaslygwdillagtawpgknignANAGiiret 97
Cdd:cd10959   14 EYTPALLDLLARHGAKATFFV-VG-ERAERH------PDLIRRI---------------------------VDEG----- 53

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 259563529  98 atyHETGLHAWDH-HAWqthsgHWSIRQLEEDIARGITALEAIIGKPVTC 146
Cdd:cd10959   54 ---HEIGNHGYRHrHPW-----LRSPWKAIRDLRRAARIIEQLTGRPPRY 95
CE4_NodB_like_5s_6s cd10918
Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a ...
 27-145 3.11e-04

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: 40.27  E-value: 3.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  27 LHRHGVQASFFFSVGPDNMGRHLWRLI--RPRFL-WKMLRSNAASlyGWDIllagtawpgknignanagiiretatyhet 103
Cdd:cd10918   21 LKKYGLPATFFVITGYIGGGNPWWAPAppRPPYLtWDQLRELAAS--GVEI----------------------------- 69

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 259563529 104 GLHAWDHHAWQTHSghwsIRQLEEDIARGITALEAIIGKPVT 145
Cdd:cd10918   70 GSHTHTHPDLTTLS----DEELRRELAESKERLEEELGKPVR 107
CE4_PuuE_HpPgdA_like cd10916
Catalytic domain of bacterial PuuE allantoinases, Helicobacter pylori peptidoglycan ...
 15-157 9.15e-04

Catalytic domain of bacterial PuuE allantoinases, Helicobacter pylori peptidoglycan deacetylase (HpPgdA), and similar proteins; This family is a member of the very large and functionally diverse carbohydrate esterase 4 (CE4) superfamily. It contains bacterial PuuE (purine utilization E) allantoinases, a peptidoglycan deacetylase from Helicobacter pylori (HpPgdA), Escherichia coli ArnD, and many uncharacterized homologs from all three kingdoms of life. PuuE allantoinase appears to be metal-independent and specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. Different from PuuE allantoinase, HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. Both PuuE allantoinase and HpPgdA function as a homotetramer. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of polysaccharide deacetylase (DCA)-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. However, in contrast with the typical DCAs, PuuE allantoinase and HpPgdA might not exhibit a solvent-accessible polysaccharide binding groove and only recognize a small substrate molecule. ArnD catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol.


Pssm-ID: 213021 [Multi-domain]  Cd Length: 247  Bit Score: 39.99  E-value: 9.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  15 GTREGVPRLLATLHRHGVQASFFfsvgpdnmgrhlwrlirprflwkmlrsnaaslygwdillagtaWPGKnIGNANAGII 94
Cdd:cd10916   33 GLRVGIPRLLDLLDRHGVRATFF-------------------------------------------VPGR-VAERFPDAV 68

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 259563529  95 RETATY-HETGLHAWDHHAWQTHSGhwsiRQLEEDIARGITALEAIIGKPVTcsaaaGWRADGR 157
Cdd:cd10916   69 RAIVAAgHEIAAHGYAHEDVLALSR----EQEREVLLRSLELLEELTGQRPT-----GWRSPGL 123
CE4_NodB_like_6s_7s cd10917
Catalytic NodB homology domain of rhizobial NodB-like proteins; This family belongs to the ...
 17-161 9.36e-04

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: 39.14  E-value: 9.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  17 REGVPRLLATLHRHGVQASFFFSvgpdnmgrhlwrlirprflwkmlrsnaaslygwdillagtawpGKNIgNANAGIIRE 96
Cdd:cd10917   13 PEYTPKILDILAEYGVKATFFVV-------------------------------------------GENV-EKHPDLVRR 48

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 259563529  97 TATY-HETGLHAWDHhawqTHSGHWSIRQLEEDIARGITALEAIIGKPVTCSAAAGWRADGRVVRA 161
Cdd:cd10917   49 IVAEgHEIGNHTYSH----PDLTKLSPEEIRAEIERTQDAIEEATGVRPRLFRPPYGAYNPEVLAA 110
CE4_GLA_like_6s cd10967
Putative catalytic NodB homology domain of gellan lyase and similar proteins; This family is ...
 22-145 8.42e-03

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: 36.59  E-value: 8.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 259563529  22 RLLATLHRHGVQASFFFSVGpdnmgrhlWRLIRPRFLWKMLRsnaaslygwDILLAGtawpgknignanagiiretatyH 101
Cdd:cd10967   16 RAAPLLAKYGLKGTFFVNSG--------LLGRRGYLDLEELR---------ELAAAG----------------------H 56

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 259563529 102 ETGLHAWDHhawqTHSGHWSIRQLEEDIARGITALEAIIGKPVT 145
Cdd:cd10967   57 EIGSHTVTH----PDLTSLPPAELRREIAESRAALEEIGGFPVT 96
 
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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