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Conserved domains on  [gi|1378107607|gb|PTY00719|]
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hypothetical protein DB345_00125 [Spartobacteria bacterium LR76]

Protein Classification

right-handed parallel beta-helix repeat-containing protein( domain architecture ID 11677118)

right-handed parallel beta-helix repeat-containing protein that may share some similarity with pectate lyases, similar to Bacteroides thetaiotaomicron alpha-1,3-galactosidase B that removes both branched alpha-1,3-linked galactose residues of blood group B antigens and linear alpha-1,3-linked galactose structures

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CBM6-CBM35-CBM36_like super family cl14880
Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module ...
 427-597 1.62e-37

Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules. This alignment model also contains the C-terminal domains of bacterial insecticidal toxins, where they may be involved in determining insect specificity through carbohydrate binding functionality.


The actual alignment was detected with superfamily member cd14490:

Pssm-ID: 449372  Cd Length: 156  Bit Score: 137.77  E-value: 1.62e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  427 GAELPFETCEAEDTAHPGLVRRlEDPTVSSPAREASGRSYAHLGTVGDYIDIPVSSPANTAVFRVCVPDAPSGSSVTYTL 506
Cdd:cd14490      1 GATVPFTEYEAENATTNGTAIG-PDRTYGTIASEASGRRAVRLDATGQYVEFTLTAPANAIVVRYSIPDSPAGGGITATL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  507 TLqkVVNGVEQslqaGPVVISPTHAWLYANASTPNDyeglsndsSPDRKPCVFWDEVRVRLGEELPTGTKLRLKKSQGDT 586
Cdd:cd14490     80 SL--YVNGVKV----QTLNLTSKYSWLYGGYPWSND--------PSGGKPHHFYDEARLLLDQTYPAGTKIKLQKDSGDT 145

                          170
                   ....*....|.
gi 1378107607  587 AEYYLVDLVDL 597
Cdd:cd14490    146 ASYYTIDFVDF 156
Pgu1 super family cl35001
Polygalacturonase [Carbohydrate transport and metabolism];
600-815 7.56e-08

Polygalacturonase [Carbohydrate transport and metabolism];


The actual alignment was detected with superfamily member COG5434:

Pssm-ID: 444185 [Multi-domain]  Cd Length: 373  Bit Score: 55.60  E-value: 7.56e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  600 ATPIAPPAEpfLSVADFGASGSDSADDTAAIQQCLNAASAyEPKKVVWIPSGRYYqQQPFTVPAGVKVR---GAgpwftE 676
Cdd:COG5434      1 AEPSFPAKT--FNITDFGAKGDGKTLNTAAIQKAIDACAA-AGGGTVLVPAGTYL-TGPIFLKSNVTLHlekGA-----T 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  677 ILGSqvDPPDDWSGTMGFKLDSDVEV-SDLF----VESLARTGRSI----GSNAFDGGKGKTG----------------- 730
Cdd:COG5434     72 LLGS--TDPADYPLVETRWEGGELKGySALIyaenAENIAITGEGTidgnGDAWWPWKKEARQsgwvpvgaydylrprli 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  731 --WKVNNVWISH-TLT--GFWVQGTGQVRNCRVR------FTYA---DGITIAHSANgVLIENNHVRgCGDDGTAILSHR 796
Cdd:COG5434    150 qlKNCKNVLLEGvTLRnsPFWTIHPLGCENVTVDgvtidnPADApntDGIDPDSCRN-VLIENCYID-TGDDAIAIKSGR 227

                          250       260
                   ....*....|....*....|.
gi 1378107607  797 THTGDTR--TENCTLRRNTVS 815
Cdd:COG5434    228 DADGRRNrpTENIVIRNCTFR 248
Beta_helix pfam13229
Right handed beta helix region; This region contains a parallel beta helix region that shares ...
 743-949 1.34e-06

Right handed beta helix region; This region contains a parallel beta helix region that shares some similarity with Pectate lyases.


:

Pssm-ID: 463811 [Multi-domain]  Cd Length: 158  Bit Score: 49.33  E-value: 1.34e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  743 TGFWVQGTG--QVRNCRVRFTYADGITIAHSANgVLIENNHVRGCGDDGTAILShrthTGDTRTENCTLRRNTVSAIWwg 820
Cdd:pfam13229    1 SGILLNGSSnaTIKNNTISNNGGYGIYLRGSSN-ATIENNTITNNGGDGIEISG----SSNNTISNNTISNNGGGGIA-- 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  821 mngdLGGGKGHLVEYNYLVDNAlfpGLGINqpvsedfgMFALENSIVRRNLVlrsggfargtplngqwgsalwilagnSN 900
Cdd:pfam13229   74 ----LRGSSNNLIENNTISNNG---GAGIY--------LSDSSNNTIENNII--------------------------HN 112

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1378107607  901 NGLFGSEAIHAAiNNVTIADNRILDATYKGLQIQGGAPQyaVSFLRNII 949
Cdd:pfam13229  113 NGGSGIVIEDSS-NNVTISNNTVTNNKGAGILIVGGSSN--NTVENNTF 158
 
Name Accession Description Interval E-value
CBM6-CBM35-CBM36_like_1 cd14490
uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily; ...
 427-597 1.62e-37

uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules.


Pssm-ID: 271156  Cd Length: 156  Bit Score: 137.77  E-value: 1.62e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  427 GAELPFETCEAEDTAHPGLVRRlEDPTVSSPAREASGRSYAHLGTVGDYIDIPVSSPANTAVFRVCVPDAPSGSSVTYTL 506
Cdd:cd14490      1 GATVPFTEYEAENATTNGTAIG-PDRTYGTIASEASGRRAVRLDATGQYVEFTLTAPANAIVVRYSIPDSPAGGGITATL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  507 TLqkVVNGVEQslqaGPVVISPTHAWLYANASTPNDyeglsndsSPDRKPCVFWDEVRVRLGEELPTGTKLRLKKSQGDT 586
Cdd:cd14490     80 SL--YVNGVKV----QTLNLTSKYSWLYGGYPWSND--------PSGGKPHHFYDEARLLLDQTYPAGTKIKLQKDSGDT 145

                          170
                   ....*....|.
gi 1378107607  587 AEYYLVDLVDL 597
Cdd:cd14490    146 ASYYTIDFVDF 156
Pgu1 COG5434
Polygalacturonase [Carbohydrate transport and metabolism];
600-815 7.56e-08

Polygalacturonase [Carbohydrate transport and metabolism];


Pssm-ID: 444185 [Multi-domain]  Cd Length: 373  Bit Score: 55.60  E-value: 7.56e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  600 ATPIAPPAEpfLSVADFGASGSDSADDTAAIQQCLNAASAyEPKKVVWIPSGRYYqQQPFTVPAGVKVR---GAgpwftE 676
Cdd:COG5434      1 AEPSFPAKT--FNITDFGAKGDGKTLNTAAIQKAIDACAA-AGGGTVLVPAGTYL-TGPIFLKSNVTLHlekGA-----T 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  677 ILGSqvDPPDDWSGTMGFKLDSDVEV-SDLF----VESLARTGRSI----GSNAFDGGKGKTG----------------- 730
Cdd:COG5434     72 LLGS--TDPADYPLVETRWEGGELKGySALIyaenAENIAITGEGTidgnGDAWWPWKKEARQsgwvpvgaydylrprli 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  731 --WKVNNVWISH-TLT--GFWVQGTGQVRNCRVR------FTYA---DGITIAHSANgVLIENNHVRgCGDDGTAILSHR 796
Cdd:COG5434    150 qlKNCKNVLLEGvTLRnsPFWTIHPLGCENVTVDgvtidnPADApntDGIDPDSCRN-VLIENCYID-TGDDAIAIKSGR 227

                          250       260
                   ....*....|....*....|.
gi 1378107607  797 THTGDTR--TENCTLRRNTVS 815
Cdd:COG5434    228 DADGRRNrpTENIVIRNCTFR 248
GH55_beta13glucanase-like cd23668
fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family ...
 606-674 4.83e-07

fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family includes fungal glycoside hydrolase family 55 (GH55) proteins, which contains both endo- (EC 3.2.1.39) and exo-beta-1,3-glucanases (EC 3.2.1.58), based on the hydrolysis position. These enzymes hydrolyze beta-1,3-glucan bonds via inversion of stereochemistry at the anomeric carbon. GH55 is also called laminarinase due to its ability to hydrolyze laminarin, a beta-1,3-glucan with occasional beta-1,6 branching found in brown algae such as Laminaria digitata. They have also been shown to react with the beta-1,3-glucans from fungal and plant cell walls. Trichoderma harzianum BGN13.1 and T. viride LamA1 in this family have been characterized as endo-acting enzymes while Phanerochaete chrysosporium Lam55A and Chaetomium thermophilum CtLam55 are exo-acting enzymes. The CtLam55 substrate binding cleft exhibits restricted access on one side, thus rendering the enzyme as an exo-beta-1,3-glucanase; this has been confirmed by thin layer chromatography experiments. Also, a binding pocket was identified that could explain binding of branched laminarin and accumulation of laminaritriose. A similar binding pocket has been observed in T. chrysosporium Lam55A through structural studies and site-directed mutagenesis; both support a critical glutamate as a catalytic acid and a proton relay network that activates water to serve as the catalytic base.


Pssm-ID: 467840 [Multi-domain]  Cd Length: 623  Bit Score: 53.67  E-value: 4.83e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1378107607  606 PAEPFLSVADFGASGSDSADDTAAIQQCLNAASAyepKKVVWIPSGRYYQQQPFTVPAGVKVRG--------AGPWF 674
Cdd:cd23668    299 PASQFVNVKDYGAKGDGVTDDTAALQAILNTAAG---GKIVYFPAGTYIVTDTLFIPPGSRIVGeawsqimaSGSKF 372
Beta_helix pfam13229
Right handed beta helix region; This region contains a parallel beta helix region that shares ...
 743-949 1.34e-06

Right handed beta helix region; This region contains a parallel beta helix region that shares some similarity with Pectate lyases.


Pssm-ID: 463811 [Multi-domain]  Cd Length: 158  Bit Score: 49.33  E-value: 1.34e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  743 TGFWVQGTG--QVRNCRVRFTYADGITIAHSANgVLIENNHVRGCGDDGTAILShrthTGDTRTENCTLRRNTVSAIWwg 820
Cdd:pfam13229    1 SGILLNGSSnaTIKNNTISNNGGYGIYLRGSSN-ATIENNTITNNGGDGIEISG----SSNNTISNNTISNNGGGGIA-- 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  821 mngdLGGGKGHLVEYNYLVDNAlfpGLGINqpvsedfgMFALENSIVRRNLVlrsggfargtplngqwgsalwilagnSN 900
Cdd:pfam13229   74 ----LRGSSNNLIENNTISNNG---GAGIY--------LSDSSNNTIENNII--------------------------HN 112

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1378107607  901 NGLFGSEAIHAAiNNVTIADNRILDATYKGLQIQGGAPQyaVSFLRNII 949
Cdd:pfam13229  113 NGGSGIVIEDSS-NNVTISNNTVTNNKGAGILIVGGSSN--NTVENNTF 158
Beta_helix pfam13229
Right handed beta helix region; This region contains a parallel beta helix region that shares ...
 734-814 4.36e-05

Right handed beta helix region; This region contains a parallel beta helix region that shares some similarity with Pectate lyases.


Pssm-ID: 463811 [Multi-domain]  Cd Length: 158  Bit Score: 44.71  E-value: 4.36e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  734 NNVWISHTLTGFWVQGT--GQVRNCRVRFTYADGITIAHSANGVLIENNHVRGCGDDGTAILSHRThtgdtrteNCTLRR 811
Cdd:pfam13229   84 NNTISNNGGAGIYLSDSsnNTIENNIIHNNGGSGIVIEDSSNNVTISNNTVTNNKGAGILIVGGSS--------NNTVEN 155


                   ...
gi 1378107607  812 NTV 814
Cdd:pfam13229  156 NTF 158
NosD COG3420
Nitrous oxide reductase accessory protein NosD, contains tandem CASH domains [Inorganic ion ...
 741-1003 1.20e-03

Nitrous oxide reductase accessory protein NosD, contains tandem CASH domains [Inorganic ion transport and metabolism];


Pssm-ID: 442646 [Multi-domain]  Cd Length: 343  Bit Score: 42.21  E-value: 1.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  741 TLTGFWVQGTGQvrncrvRFTYAD-GITIaHSANGVLIENNHVRGCGDdgtAILSHrthtgdtRTENCTLRRNTVS--AI 817
Cdd:COG3420     81 TVRGLTITGSGD------SLTDDDaGIYV-RGADNAVIENNRIENNLF---GIYLE-------GSDNNVIRNNTISgnRD 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  818 WWGMNGD---LGGGKGHLVEYN---------YL--VDNALFPGlgiNQPVSEDFG---MFAlENSIVRRNLVLRSGG--- 877
Cdd:COG3420    144 LRADRGNgihLWNSPGNVIEGNtisggrdgiYLefSDNNVIRN---NTIRNLRYGihyMYS-NDNLVEGNTFRDNGAgia 219

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  878 --FARGTPLNGQwgsalwILAGNSNNGLFGSEaihaaINNVTIADNRILDATyKGLQIQGGApqyavsflRNIIRKT--- 952
Cdd:COG3420    220 lmYSKGNTVRGN------TILGNSGYGILLKE-----SSDSVIEGNTISGNG-KGIFIYNSN--------RNTIRGNlfa 279

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1378107607  953 -GDFGVLIEPGSvgqsilfERNTVTcvpegKSVFVNASPTTYTAESYNNSWN 1003
Cdd:COG3420    280 gNGIGIHLTAGS-------EGNRIY-----GNNFIGNRTQVKYVGGRDNEWS 319
 
Name Accession Description Interval E-value
CBM6-CBM35-CBM36_like_1 cd14490
uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily; ...
 427-597 1.62e-37

uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules.


Pssm-ID: 271156  Cd Length: 156  Bit Score: 137.77  E-value: 1.62e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  427 GAELPFETCEAEDTAHPGLVRRlEDPTVSSPAREASGRSYAHLGTVGDYIDIPVSSPANTAVFRVCVPDAPSGSSVTYTL 506
Cdd:cd14490      1 GATVPFTEYEAENATTNGTAIG-PDRTYGTIASEASGRRAVRLDATGQYVEFTLTAPANAIVVRYSIPDSPAGGGITATL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  507 TLqkVVNGVEQslqaGPVVISPTHAWLYANASTPNDyeglsndsSPDRKPCVFWDEVRVRLGEELPTGTKLRLKKSQGDT 586
Cdd:cd14490     80 SL--YVNGVKV----QTLNLTSKYSWLYGGYPWSND--------PSGGKPHHFYDEARLLLDQTYPAGTKIKLQKDSGDT 145

                          170
                   ....*....|.
gi 1378107607  587 AEYYLVDLVDL 597
Cdd:cd14490    146 ASYYTIDFVDF 156
Pgu1 COG5434
Polygalacturonase [Carbohydrate transport and metabolism];
600-815 7.56e-08

Polygalacturonase [Carbohydrate transport and metabolism];


Pssm-ID: 444185 [Multi-domain]  Cd Length: 373  Bit Score: 55.60  E-value: 7.56e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  600 ATPIAPPAEpfLSVADFGASGSDSADDTAAIQQCLNAASAyEPKKVVWIPSGRYYqQQPFTVPAGVKVR---GAgpwftE 676
Cdd:COG5434      1 AEPSFPAKT--FNITDFGAKGDGKTLNTAAIQKAIDACAA-AGGGTVLVPAGTYL-TGPIFLKSNVTLHlekGA-----T 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  677 ILGSqvDPPDDWSGTMGFKLDSDVEV-SDLF----VESLARTGRSI----GSNAFDGGKGKTG----------------- 730
Cdd:COG5434     72 LLGS--TDPADYPLVETRWEGGELKGySALIyaenAENIAITGEGTidgnGDAWWPWKKEARQsgwvpvgaydylrprli 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  731 --WKVNNVWISH-TLT--GFWVQGTGQVRNCRVR------FTYA---DGITIAHSANgVLIENNHVRgCGDDGTAILSHR 796
Cdd:COG5434    150 qlKNCKNVLLEGvTLRnsPFWTIHPLGCENVTVDgvtidnPADApntDGIDPDSCRN-VLIENCYID-TGDDAIAIKSGR 227

                          250       260
                   ....*....|....*....|.
gi 1378107607  797 THTGDTR--TENCTLRRNTVS 815
Cdd:COG5434    228 DADGRRNrpTENIVIRNCTFR 248
GH55_beta13glucanase-like cd23668
fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family ...
 606-674 4.83e-07

fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family includes fungal glycoside hydrolase family 55 (GH55) proteins, which contains both endo- (EC 3.2.1.39) and exo-beta-1,3-glucanases (EC 3.2.1.58), based on the hydrolysis position. These enzymes hydrolyze beta-1,3-glucan bonds via inversion of stereochemistry at the anomeric carbon. GH55 is also called laminarinase due to its ability to hydrolyze laminarin, a beta-1,3-glucan with occasional beta-1,6 branching found in brown algae such as Laminaria digitata. They have also been shown to react with the beta-1,3-glucans from fungal and plant cell walls. Trichoderma harzianum BGN13.1 and T. viride LamA1 in this family have been characterized as endo-acting enzymes while Phanerochaete chrysosporium Lam55A and Chaetomium thermophilum CtLam55 are exo-acting enzymes. The CtLam55 substrate binding cleft exhibits restricted access on one side, thus rendering the enzyme as an exo-beta-1,3-glucanase; this has been confirmed by thin layer chromatography experiments. Also, a binding pocket was identified that could explain binding of branched laminarin and accumulation of laminaritriose. A similar binding pocket has been observed in T. chrysosporium Lam55A through structural studies and site-directed mutagenesis; both support a critical glutamate as a catalytic acid and a proton relay network that activates water to serve as the catalytic base.


Pssm-ID: 467840 [Multi-domain]  Cd Length: 623  Bit Score: 53.67  E-value: 4.83e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1378107607  606 PAEPFLSVADFGASGSDSADDTAAIQQCLNAASAyepKKVVWIPSGRYYQQQPFTVPAGVKVRG--------AGPWF 674
Cdd:cd23668    299 PASQFVNVKDYGAKGDGVTDDTAALQAILNTAAG---GKIVYFPAGTYIVTDTLFIPPGSRIVGeawsqimaSGSKF 372
Beta_helix pfam13229
Right handed beta helix region; This region contains a parallel beta helix region that shares ...
 743-949 1.34e-06

Right handed beta helix region; This region contains a parallel beta helix region that shares some similarity with Pectate lyases.


Pssm-ID: 463811 [Multi-domain]  Cd Length: 158  Bit Score: 49.33  E-value: 1.34e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  743 TGFWVQGTG--QVRNCRVRFTYADGITIAHSANgVLIENNHVRGCGDDGTAILShrthTGDTRTENCTLRRNTVSAIWwg 820
Cdd:pfam13229    1 SGILLNGSSnaTIKNNTISNNGGYGIYLRGSSN-ATIENNTITNNGGDGIEISG----SSNNTISNNTISNNGGGGIA-- 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  821 mngdLGGGKGHLVEYNYLVDNAlfpGLGINqpvsedfgMFALENSIVRRNLVlrsggfargtplngqwgsalwilagnSN 900
Cdd:pfam13229   74 ----LRGSSNNLIENNTISNNG---GAGIY--------LSDSSNNTIENNII--------------------------HN 112

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1378107607  901 NGLFGSEAIHAAiNNVTIADNRILDATYKGLQIQGGAPQyaVSFLRNII 949
Cdd:pfam13229  113 NGGSGIVIEDSS-NNVTISNNTVTNNKGAGILIVGGSSN--NTVENNTF 158
Beta_helix pfam13229
Right handed beta helix region; This region contains a parallel beta helix region that shares ...
 734-814 4.36e-05

Right handed beta helix region; This region contains a parallel beta helix region that shares some similarity with Pectate lyases.


Pssm-ID: 463811 [Multi-domain]  Cd Length: 158  Bit Score: 44.71  E-value: 4.36e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  734 NNVWISHTLTGFWVQGT--GQVRNCRVRFTYADGITIAHSANGVLIENNHVRGCGDDGTAILSHRThtgdtrteNCTLRR 811
Cdd:pfam13229   84 NNTISNNGGAGIYLSDSsnNTIENNIIHNNGGSGIVIEDSSNNVTISNNTVTNNKGAGILIVGGSS--------NNTVEN 155


                   ...
gi 1378107607  812 NTV 814
Cdd:pfam13229  156 NTF 158
Pectate_lyase_3 pfam12708
Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure ...
 610-653 5.20e-05

Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure like Pectate lyase. This family is most closely related to glycosyl hydrolase family 28.


Pssm-ID: 403800 [Multi-domain]  Cd Length: 213  Bit Score: 45.39  E-value: 5.20e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1378107607  610 FLSVADFGASGSDSADDTAAIQQCLNAASAYEPKKVVWIPSGRY 653
Cdd:pfam12708    1 FRNVKDYGAKGDGVTDDTAAIQKAIDDGGATTTPAVVYFPPGTY 44
GH55-like cd23271
glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family includes ...
 606-756 6.19e-04

glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family includes glycoside hydrolase family 55 (GH55) domains, which contains both endo- (EC 3.2.1.39) and exo-beta-1,3-glucanases (EC 3.2.1.58), based on the hydrolysis position. These enzymes hydrolyze beta-1,3-glucan bonds via inversion of stereochemistry at the anomeric carbon. GH55 is also called laminarinase due to its ability to hydrolyze laminarin, a beta-1,3-glucan with occasional beta-1,6 branching, found in brown algae such as Laminaria digitata. They have also been shown to react with the beta-1,3-glucans from fungal and plant cell walls. Also included in this family is SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E, a secreted protein encoded by SACTE_4363. Structural studies reveal an extended substrate-binding cleft with six or more subsites for sugar binding formed at the interface of two right handed beta-helical domains. Mutation studies support a critical glutamate as a catalytic acid and a proton relay network that activates water to serve as the catalytic base. Trichoderma harzianum and T. viride LamA1 have been characterized as endo-acting enzymes while Phanerochaete chrysosporium Lam55A, Chaetomium thermophilum CtLam55, as well as SacteLam55A, are exo-acting enzymes.


Pssm-ID: 467839 [Multi-domain]  Cd Length: 564  Bit Score: 43.52  E-value: 6.19e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  606 PAEPFLSVADFGASGSDSADDTAAIQqclNAASAYEPKKVVWIPSGRYYQQQPFTVPAGVKVRGAGpwFTEILGSQVDPP 685
Cdd:cd23271    248 PLSQFVSVKPGGAKGDGHTDDTEAIN---AAFDQGAGCLILLFDPGVYIVTQTIEIPRATVILGEG--LATIIPDGGKFT 322

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  686 DDWSGTMGFKL-----DSDVEVSDLFVESLARTGRSI----GSNAFDGGKGKTGwkvnnVWISHTLTGFWVQGTGQVRNC 756
Cdd:cd23271    323 DYNNPVPVLQVgdpgsSGGVEVADLIFDTGGPVNGAIlvewNVDGADHAANAAG-----LWDVHVRIGGAAQSGLQVGQC 397
NosD COG3420
Nitrous oxide reductase accessory protein NosD, contains tandem CASH domains [Inorganic ion ...
 741-1003 1.20e-03

Nitrous oxide reductase accessory protein NosD, contains tandem CASH domains [Inorganic ion transport and metabolism];


Pssm-ID: 442646 [Multi-domain]  Cd Length: 343  Bit Score: 42.21  E-value: 1.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  741 TLTGFWVQGTGQvrncrvRFTYAD-GITIaHSANGVLIENNHVRGCGDdgtAILSHrthtgdtRTENCTLRRNTVS--AI 817
Cdd:COG3420     81 TVRGLTITGSGD------SLTDDDaGIYV-RGADNAVIENNRIENNLF---GIYLE-------GSDNNVIRNNTISgnRD 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  818 WWGMNGD---LGGGKGHLVEYN---------YL--VDNALFPGlgiNQPVSEDFG---MFAlENSIVRRNLVLRSGG--- 877
Cdd:COG3420    144 LRADRGNgihLWNSPGNVIEGNtisggrdgiYLefSDNNVIRN---NTIRNLRYGihyMYS-NDNLVEGNTFRDNGAgia 219

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  878 --FARGTPLNGQwgsalwILAGNSNNGLFGSEaihaaINNVTIADNRILDATyKGLQIQGGApqyavsflRNIIRKT--- 952
Cdd:COG3420    220 lmYSKGNTVRGN------TILGNSGYGILLKE-----SSDSVIEGNTISGNG-KGIFIYNSN--------RNTIRGNlfa 279

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1378107607  953 -GDFGVLIEPGSvgqsilfERNTVTcvpegKSVFVNASPTTYTAESYNNSWN 1003
Cdd:COG3420    280 gNGIGIHLTAGS-------EGNRIY-----GNNFIGNRTQVKYVGGRDNEWS 319
Beta_helix pfam13229
Right handed beta helix region; This region contains a parallel beta helix region that shares ...
 802-976 4.85e-03

Right handed beta helix region; This region contains a parallel beta helix region that shares some similarity with Pectate lyases.


Pssm-ID: 463811 [Multi-domain]  Cd Length: 158  Bit Score: 38.93  E-value: 4.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  802 TRTENCTLRRNTVSAIWWgmNG-DLGGGKGHLVEYNYLVDNAlFPGLGINQPVsedfgmfaleNSIVRRNLVlrsggfar 880
Cdd:pfam13229    6 NGSSNATIKNNTISNNGG--YGiYLRGSSNATIENNTITNNG-GDGIEISGSS----------NNTISNNTI-------- 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1378107607  881 gtplngqwgsalwilagnSNNGLFGSEAIHAaiNNVTIADNRILDATYKGLQIQGgapQYAVSFLRNIIRKTGDFGVLIE 960
Cdd:pfam13229   65 ------------------SNNGGGGIALRGS--SNNLIENNTISNNGGAGIYLSD---SSNNTIENNIIHNNGGSGIVIE 121

                          170
                   ....*....|....*.
gi 1378107607  961 PGSvgQSILFERNTVT 976
Cdd:pfam13229  122 DSS--NNVTISNNTVT 135
 
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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