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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 213 PVLITLDDGYKNNL-NAYYILNKlndasYQAKATIFMIGNKIDKKTG-----------LSTEEIREMSDSGIiSFQAHTE 280
Cdd:cd10918     1 PVVLTFDDGYRDNYtYALPILKK-----YGLPATFFVITGYIGGGNPwwapapprppyLTWDQLRELAASGV-EIGSHTH 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 281 HHPSLTTITD--FQSELGGNKERLEKLTGKRVTALAYPSGHYNEQVVEETK-SYFDYAVTTNAGIATADSSPYELERIRI 357
Cdd:cd10918    75 THPDLTTLSDeeLRRELAESKERLEEELGKPVRSFAYPYGRYNPRVIAALKeAGYKAAFTTDPGLNSPGDDPYALPRINV 154

                  ...
gi 2085999356 358 SYS 360
Cdd:cd10918   155 SGD 157

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 213 PVLITLDDGYKNNL-NAYYILNKlndasYQAKATIFMIGNKIDKKTG-----------LSTEEIREMSDSGIiSFQAHTE 280
Cdd:cd10918     1 PVVLTFDDGYRDNYtYALPILKK-----YGLPATFFVITGYIGGGNPwwapapprppyLTWDQLRELAASGV-EIGSHTH 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 281 HHPSLTTITD--FQSELGGNKERLEKLTGKRVTALAYPSGHYNEQVVEETK-SYFDYAVTTNAGIATADSSPYELERIRI 357
Cdd:cd10918    75 THPDLTTLSDeeLRRELAESKERLEEELGKPVRSFAYPYGRYNPRVIAALKeAGYKAAFTTDPGLNSPGDDPYALPRINV 154

                  ...
gi 2085999356 358 SYS 360
Cdd:cd10918   155 SGD 157

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 211 EKPVLITLDDGYKNNLNAYY-ILNKlndasYQAKATIFMIGNKIDKktglSTEEIREMSDSGIiSFQAHTEHHPSLTTIT 289
Cdd:pfam01522   6 KKVVALTFDDGPSENTPAILdVLKK-----YGVKATFFVIGGNVER----YPDLVKRMVEAGH-EIGNHTWSHPNLTGLS 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2085999356 290 D--FQSELGGNKERLEKLTGKRVTALAYPSGHYNEQVVEETKSY 331
Cdd:pfam01522  76 PeeIRKEIERAQDALEKATGKRPRLFRPPYGSYNDTVLEVAKKL 119

Bacterial SH3 domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2085999356  76 ENLNLREGPSSQEPLLFTIPKGEEVTVLSE-AGSWYKV-NYQTYTGYVDSSYLS 127
Cdd:pfam08239   1 SGLNVRSGPSTSSEVVGTLPKGEKVEVLEEqGGGWYKVrTYDGYEGWVSSSYLS 54

Bacterial SH3 domain homologues;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2085999356   74 TDENLNLREGPSSQEPLLFTIPKGEEVTVLSEAGS-WYKVNYQT-YTGYV 121
Cdd:smart00287   7 TGDGLNVRTGPGTSSPIIGTLKKGDKVKVLGVDGQdWAKITYGSgQRGYV 56

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 213 PVLITLDDGYKNNL-NAYYILNKlndasYQAKATIFMIGNKIDKKTG-----------LSTEEIREMSDSGIiSFQAHTE 280
Cdd:cd10918     1 PVVLTFDDGYRDNYtYALPILKK-----YGLPATFFVITGYIGGGNPwwapapprppyLTWDQLRELAASGV-EIGSHTH 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 281 HHPSLTTITD--FQSELGGNKERLEKLTGKRVTALAYPSGHYNEQVVEETK-SYFDYAVTTNAGIATADSSPYELERIRI 357
Cdd:cd10918    75 THPDLTTLSDeeLRRELAESKERLEEELGKPVRSFAYPYGRYNPRVIAALKeAGYKAAFTTDPGLNSPGDDPYALPRINV 154

                  ...
gi 2085999356 358 SYS 360
Cdd:cd10918   155 SGD 157

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 211 EKPVLITLDDGYKNNL-NAYYILNKlndasYQAKATIFMIGNKIDKKTG-------LSTEEIREMSDsgIISFQAHTEH- 281
Cdd:cd10966     2 EKSVVITFDDGYKSNYeYAYPILKK-----YGFKATIFVIGSRIGEKPQdpkilqyLSIEELKEMRD--VFEFQSHTYNm 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 282 HPSLTT----ITDFQSELGGNKERLEKLTGKRVTALAYPSGHYNEQVVEETKSY-FDYAVTTNAGIATADSSPYELERIR 356
Cdd:cd10966    75 HRGGGTgghgLLALSEEEILADLKKSEEILGSSKAFAYPYGDYNDNAIEALKEAgVKLAFTTNEGKVTPGDDPYELPRVR 154

                         170
                  ....*....|
gi 2085999356 357 ISYSTTLEAF 366
Cdd:cd10966   155 ITGGTSLEDF 164

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 211 EKPVLITLDDGYKNNLNAYY-ILNKlndasYQAKATIFMIGNKIDKktglSTEEIREMSDSGIiSFQAHTEHHPSLTTIT 289
Cdd:pfam01522   6 KKVVALTFDDGPSENTPAILdVLKK-----YGVKATFFVIGGNVER----YPDLVKRMVEAGH-EIGNHTWSHPNLTGLS 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2085999356 290 D--FQSELGGNKERLEKLTGKRVTALAYPSGHYNEQVVEETKSY 331
Cdd:pfam01522  76 PeeIRKEIERAQDALEKATGKRPRLFRPPYGSYNDTVLEVAKKL 119

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 214 VLITLDDGYKNNLNAYYILNKlndasYQAKATIFMIGNKIDKKTGLSTEEIREMSDSG--IISfqaHTEHHPSLTTITDF 291
Cdd:cd10967     3 VSLTFDDGYAQDLRAAPLLAK-----YGLKGTFFVNSGLLGRRGYLDLEELRELAAAGheIGS---HTVTHPDLTSLPPA 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2085999356 292 Q--SELGGNKERLEKLTGKRVTALAYPSGHYNEQVVEETKSYFDYAVTTNAGIAT 344
Cdd:cd10967    75 ElrREIAESRAALEEIGGFPVTSFAYPFGSTNPSIVPLLARGFIAARGVGGGGNP 129

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 214 VLITLDDGYKNNLN-AYYILNKlndasYQAKATIFmIGNKIDKKTG---------LSTEEIREMSDSGIISFQAHTEHHP 283
Cdd:cd10968     3 AVLTFDDGYRDNLEfALPVFER-----HGVPFTIY-VTTGFPDGTGelwwltlecLDWDELRRLAADPLVTIGAHTITHP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 284 SLTTITD--FQSELGGNKERLEKLTGKRVTALAYP------SGHYNEQVVEEtkSYFDYAVTTNAGIATADS--SPYELE 353
Cdd:cd10968    77 NLARLSDdeARREIAASRARLEAELGREVRHFAYPygdrtaAGPREADLARE--AGFATAVTTRPGVLFAEHreNLHALP 154

                  ....*.
gi 2085999356 354 RIRISY 359
Cdd:cd10968   155 RISLNG 160

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 212 KPVLITLDDGYkNNLNAYYILNKLndASYQAKATIFMIGNKIDKktglSTEEIREMSDSGIIsFQAHTEHHPSLTTITD- 290
Cdd:cd10917     1 KVVALTFDDGP-DPEYTPKILDIL--AEYGVKATFFVVGENVEK----HPDLVRRIVAEGHE-IGNHTYSHPDLTKLSPe 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2085999356 291 -FQSELGGNKERLEKLTGKRVTALAYPSGHYNEQVVEETKSYFDYAVTTNagIATADSSPYELERI 355
Cdd:cd10917    73 eIRAEIERTQDAIEEATGVRPRLFRPPYGAYNPEVLAAAAELGLTVVLWS--VDSLDWKDPSPDQI 136

Bacterial SH3 domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2085999356  76 ENLNLREGPSSQEPLLFTIPKGEEVTVLSE-AGSWYKV-NYQTYTGYVDSSYLS 127
Cdd:pfam08239   1 SGLNVRSGPSTSSEVVGTLPKGEKVEVLEEqGGGWYKVrTYDGYEGWVSSSYLS 54

Catalytic NodB homology domain of Bacillus subtilis polysaccharide deacetylase PdaA, 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 pdaA gene encoding polysaccharide deacetylase BsPdaA, which is a member of the carbohydrate esterase 4 (CE4) superfamily. BsPdaA deacetylates peptidoglycan N-acetylmuramic acid (MurNAc) residues to facilitate the formation of muramic delta-lactam, which is required for recognition of germination lytic enzymes. BsPdaA deficiency leads to the absence of muramic delta-lactam residues in the spore cortex. Like other CE4 esterases, BsPdaA consists of a single catalytic NodB homology domain that appears to adopt a deformed (beta/alpha)8 barrel fold with a putative substrate binding groove harboring the majority of the conserved residues. It utilizes a general acid/base catalytic mechanism involving a tetrahedral transition intermediate, where a water molecule functions as the nucleophile tightly associated to the zinc cofactor.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 211 EKPVLITLDDGYkNNLNAYYILNKLNDasYQAKATIFMIGNKIDKKTGLsteeIREMSDSG-IISfqAHTEHHPSLTTIT 289
Cdd:cd10948    39 EKVIYLTFDEGY-ENGYTPKILDVLKK--NDVKATFFVTGHYVKSNPDL----IKRMVDEGhIIG--NHTVHHPDMTTLS 109

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2085999356 290 D--FQSELGGNKERLEKLTGKR-VTALAYPSGHYNEQVVEETKS-----------YFDYAV 336
Cdd:cd10948   110 DekFKKEITGVEEEYKEVTGKEmMKYFRPPRGEFSERSLKITKDlgyttvfwsfaYRDWEV 170

outer membrane N-deacetylase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 160 ILMYHAIDEyQGNGSQELYVTPENFEIQMQYLKTEGFTPITFDEIKEIDEIEKP-----VLITLDDGYKNNLNAYYILNK 234
Cdd:PRK14581   51 VIAYHDVED-DSADQRYLSVRSSALNEQFVWLRDNGYHVVSVDQILAARNGGPTlpdkaVLLTFDDGYSSFYRRVYPLLK 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 235 lndaSYQAKATIFMIGNKIDKKT-------GLST--------EEIREMSDSGIISFQAHT-EHH------PSLTT----- 287
Cdd:PRK14581  130 ----AYKWSAVLAPVGTWIDTATdkkvdfgGLSTdrdrfatwKQITEMSKSGLVEIGAHTyASHygvianPQGNTepaaa 205

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 288 -------ITDFQSElGGNKERLEK-----------LTGKRVTALAYPSGHYNEQVVEETKSY-FDYAVTTNAGIATAdSS 348
Cdd:PRK14581  206 nlqydpkTKQYETV-EAFKQRMEKdvalitqrivqATGKQPRVWVWPYGAPNGTVLNILRQHgYQLAMTLDPGVANI-ND 283

                         250       260
                  ....*....|....*....|....
gi 2085999356 349 PYELERIRISYSTTLEAFDYLLNQ 372
Cdd:PRK14581  284 LMNIPRILISNNPSLKDFALTVTS 307

Catalytic NodB homology domain of Streptococcus pneumoniae peptidoglycan deacetylase PgdA, Bacillus subtilis BsYjeA protein, and their bacterial homologs; This family is represented by Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA), a member of the carbohydrate esterase 4 (CE4) superfamily. SpPgdA protects gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan N-acetylglucosamine (GlcNAc) residues. It consists of three separate domains: N-terminal, middle and C-terminal (catalytic) domains. The catalytic NodB homology domain is similar to the deformed (beta/alpha)8 barrel fold adopted by other CE4 esterases, which harbors a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad closely associated with conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The enzyme is able to accept GlcNAc3 as a substrate, with the N-acetyl of the middle sugar being removed by the enzyme. This family also includes Bacillus subtilis BsYjeA protein encoded by the yjeA gene, which is one of the six polysaccharide deacetylase gene homologs (pdaA, pdaB/ybaN, yheN, yjeA, yxkH and ylxY) in the Bacillus subtilis genome. Although homology comparison shows that the BsYjeA protein contains a polysaccharide deacetylase domain, and was predicted to be a membrane-bound xylanase or a membrane-bound chitooligosaccharide deacetylase, more recent research indicates BsYjeA might be a novel non-specific secretory endonuclease which creates random nicks progressively on the two strands of dsDNA, resulting in highly distinguishable intermediates/products very different in chemical and physical compositions over time. In addition, BsYjeA shares several enzymatic properties with the well-understood DNase I endonuclease. Both enzymes are active on ssDNA and dsDNA, both generate random nicks, and both require Mg2+ or Mn2+ for hydrolytic activity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 212 KPVLITLDDGyKNNLNAYYILNKLndASYQAKATIFMIGNKIDKktglSTEEIREMSDSGiISFQAHTEHHPSLTTITD- 290
Cdd:cd10947     1 KVVALTFDDG-PDPTTTPQVLKTL--KKYKAPATFFMLGSNVKT----YPELVRRVLDAG-HEIGNHSWSHPQLTKLSVa 72

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2085999356 291 -FQSELGGNKERLEKLTGKRVTALAYPSGHYNEQV 324
Cdd:cd10947    73 eAEKQINDTDDAIEKATGNRPTLLRPPYGATNRSI 107

Uncharacterized conserved protein YgiM, contains N-terminal SH3 domain, DUF1202 family [General function prediction only];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2085999356  62 DERVGHVSKTF---------QTDENLNLREGPSSQEPLLFTIPKGEEVTVLSEAGSWYKVNYQTyTGYV 121
Cdd:COG3103    52 NGKTGWVSSRYltvtpsareRLPDELNLRAGPSTSSEVLGLLPKGETVTVLKKSGGWFKVGYRG-TGWV 119

Bacterial SH3 domain homologues;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2085999356   74 TDENLNLREGPSSQEPLLFTIPKGEEVTVLSEAGS-WYKVNYQT-YTGYV 121
Cdd:smart00287   7 TGDGLNVRTGPGTSSPIIGTLKKGDKVKVLGVDGQdWAKITYGSgQRGYV 56

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 212 KPVLITLDDGyKNNLNAYYILNKLndASYQAKATIFMIGNKIDKKTGLsteeIREMSDSG-IISFQAHTEHHPSLTTITD 290
Cdd:cd10959     1 KEVALTFDDG-PDPEYTPALLDLL--ARHGAKATFFVVGERAERHPDL----IRRIVDEGhEIGNHGYRHRHPWLRSPWK 73

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2085999356 291 FQSELGGNKERLEKLTGKRVTALAYPSGHYN 321
Cdd:cd10959    74 AIRDLRRAARIIEQLTGRPPRYYRPPWGHLN 104

Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins; This family is represented by a putative polysaccharide deacetylase PgdA from the oral pathogen Streptococcus mutans (SmPgdA) and Bacillus subtilis YheN (BsYheN), which are members of the carbohydrate esterase 4 (CE4) superfamily. SmPgdA is an extracellular metal-dependent polysaccharide deacetylase with a typical CE4 fold, with metal bound to a His-His-Asp triad. It possesses de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. SmPgdA plays a role in tuning cell surface properties and in interactions with (salivary) agglutinin, an essential component of the innate immune system, most likely through deacetylation of an as-yet-unidentified polysaccharide. SmPgdA shows significant homology to the catalytic domains of peptidoglycan deacetylases from Streptococcus pneumoniae (SpPgdA) and Listeria monocytogenes (LmPgdA), both of which are involved in the bacterial defense mechanism against human mucosal lysozyme. The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. The biological function of BsYheN is still unknown. This family also includes many uncharacterized polysaccharide deacetylases mainly found in bacteria.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 212 KPVLITLDDGYKNNLNAyyILNKLNDasYQAKATIFMIGNKIDKKTGLsteeIREMSDSG--IISfqaHTEHH------P 283
Cdd:cd10944     1 KVVYLTFDDGPSKNTPK--ILDILKK--YNVKATFFVIGSNVEKYPEL----VKRIVKEGhaIGL---HSYTHdykklyS 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2085999356 284 SLTTitdFQSELGGNKERLEKLTGKRVTALAYPSGHYNEQVVEETKSYF 332
Cdd:cd10944    70 SPEA---FIKDLNKTQDLIKKITGVKTKLIRFPGGSSNTGLMKALRKAL 115

Catalytic NodB homology domain of uncharacterized bacterial glycosyl transferase, group 2-like family proteins; This family includes many uncharacterized bacterial proteins containing an N-terminal GH18 (glycosyl hydrolase, family 18) domain, a middle NodB-like homology domain, and a C-terminal GT2-like (glycosyl transferase group 2) domain. Although their biological function is unknown, members in this family contain a middle NodB homology domain that is similar to the catalytic domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), 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. The presence of three domains suggests that members of this family may be multifunctional.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 212 KPVLITLDDG----YKNNlnayyILNKLNDasYQAKATIFMIGNKIDKKTGLSTEEIREMSDSGiisfqAHTEHHPSLTT 287
Cdd:cd10962     1 KKIALTFDDGpdpeWTPQ-----ILDILKE--YQIPATFFVIGENAVNNPELVKRIIDEGHEIG-----NHTFTHPDLDL 68

                          90       100
                  ....*....|....*....|....
gi 2085999356 288 ITDFQS--ELGGNKERLEKLTGKR 309
Cdd:cd10962    69 LSEKRTrlELNATQRLIEAATGHS 92

Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; This family contains 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 213 PVLITLDDGYKNNLNayYILNKLNDA------------------SYQAKATIFM-IGNKIDKKTGLSTEEIREMSDSGiI 273
Cdd:cd10972     6 PVVLTFDDGSPGQFR--YIEKNGQLVidpdtavgiledfkeehpDFPPTGTFYVnPGPFGFGQPEYAEQKLRWLVELG-Y 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085999356 274 SFQAHTEHHPSLTTITD--FQSELGGNKERLEKLT-GKRVTALAYPSG---HYNEQVVE----ETKSYfDYAVTTNAGiA 343
Cdd:cd10972    83 EIGNHTYTHVNLNKLDAeeIQEELARVNKMIEEAIpGYEVESLALPFGmkpKENRALVLsgeyEGVSY-KHQAVLLVG-A 160

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2085999356 344 TADSSPYE-------LERIRISYSTTLEAFDYLLNQ 372
Cdd:cd10972   161 EPAPSPYSkdfdpaaIPRIRASGTQGDDWYLYMKKF 196

Bacterial SH3 domain; SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues. They are found in a great variety of intracellular or membrane-associated proteins, in a variety of proteins with enzymatic activity, in adaptor proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteriztic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region. Family members include probable invasion-associated protein p60 that are conceptually translated from iap genes. The iap gene, which is regarded as a virulence-associated gene in L. monocytogenes, codes for a gene product that has murein-lytic activity and is involved in cell division.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2085999356  75 DENLNLREGPSSQEPLLFTIPKGEEVTVLSEAGSWYKVN-YQTYTGYVDSSYLSE 128
Cdd:pfam06347   2 KDEVNLRRGPSDKAAVAAYLEAGVPVRVVACKDNWCRVRdADGAEGWIYKSLLWG 56