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Conserved domains on  [gi|1512457664|gb|AYV64444|]
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agarase [Cloning vector pAgaL1]

Protein Classification

glycoside hydrolase family 16 protein( domain architecture ID 10115007)

glycoside hydrolase family 16 protein similar to endo-beta-1,3-glucanase (also called laminarinase), which hydrolyzes 1,3-beta-D-glucosidic linkages in 1,3-beta-D-glucans such as laminarins, curdlans, paramylons, lichenans, and pachymans

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
GH16_beta_agarase cd02178
Beta-agarase, member of glycosyl hydrolase family 16; Beta-agarase is a glycosyl hydrolase ...
 18-290 1.45e-97

Beta-agarase, member of glycosyl hydrolase family 16; Beta-agarase is a glycosyl hydrolase family 16 (GH16) member that hydrolyzes the internal beta-1,4-linkage of agarose, a hydrophilic polysaccharide found in the cell wall of Rhodophyceaea, marine red algae. Agarose is a linear chain of galactose units linked by alternating L-alpha-1,3- and D-beta-1,4-linkages that are additionally modified by a 3,6-anhydro-bridge. Agarose forms thermo-reversible gels that are widely used in the food industry or as a laboratory medium. While beta-agarases are also found in two other families derived from the sequence-based classification of glycosyl hydrolases (GH50, and GH86) the GH16 members are most abundant. This domain adopts a curved beta-sandwich conformation, with a tunnel-shaped active site cavity, referred to as a jellyroll fold.


:

Pssm-ID: 185687  Cd Length: 258  Bit Score: 298.49  E-value: 1.45e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  18 TAADWDGIPVPADPGEGNvWELHP-LSDDFNYeapaagkSTAFYERWKEGFINPWTGPGLTEWRPEYSLVSNGRLQIKSG 96
Cdd:cd02178     1 AAADWDPIPLPDQPGGGE-WELNEsVSDEFNG-------TSLDTSKWNPNNPNGWTGRGPTEFSADNVSVEDGNLVLSAT 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  97 RKPG-----TNQVYLGSITSKTTLTYpLYMEARAKLSNMVLASDFWLLSA--DSTEEIDVIEAYGSDRpgQEWFAERLHL 169
Cdd:cd02178    73 RHPGtelgnGYKVTTGSITSKEKVKY-GYFEARAKASNLPMSSAFWLLSDtkDSTTEIDILEHYGGDR--EEWFATRMNS 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 170 SHHVFIREPFQDYQPTDAGTWYadGNGTRWADGYHRVGVYWRDPWHLEYYVDGQLVRTASGPDIidpngfTNGTGLSKPM 249
Cdd:cd02178   150 NTHVFIRDPEQDYQPKDDGSWY--YNPTELADDFHVYGVYWKDPDTIRFYIDGVLVRTVENSEI------TDGTGFDQPM 221

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1512457664 250 HAIINMEDQSWRSDngitPTDAELADPNRNTYNVDWVRFYK 290
Cdd:cd02178   222 YIIIDTETYDWRGE----PTDEELADDSKNTFYVDYVRVYK 258
CBM6_agarase-like cd04079
Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 ...
 460-593 2.90e-43

Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 alpha- and beta agarases; This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family 16 agarases. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the activity of alpha- and beta-agarase catalytic modules which are involved in the hydrolysis of 1,4-beta-D-galactosidic linkages. These CBM6s bind specifically to the non-reducing end of agarose chains, recognizing only the first repeat of the disaccharide, and directing the appended catalytic modules to areas of the plant cell wall attacked by beta-agarases. 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. This family includes three tandem CBM6s from the Saccharophagus degradans agarase Aga86E, and three tandem CBM6s from Vibrio sp. strain PO-303 AgaA; in both these proteins these are appended to a GH16 domain. Vibrio AgaA also contains a Big-2-like protein-protein interaction domain. This family also includes two tandem CBM6s from an endo-type beta-agarase from a deep-sea Microbulbifer-like isolate, which are appended to a GH16 domain, and two of three CBM6s of Alteromonas agarilytica AgaA alpha-agarase, which are appended to a GH96 domain.


:

Pssm-ID: 271145  Cd Length: 134  Bit Score: 151.26  E-value: 2.90e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 460 AESITLELSDFVTTGKVGAaVAGDTVMGFNPNG-SNINYNTSGDWAEYQLDVTTTGSYVITLATATPISGdVNAQISING 538
Cdd:cd04079     1 GGTIVIEAESFTATGGTFD-DGPDGVSGYSVNGgTAINYVNTGDYADYTVNVPEAGTYSVEYLIGTPVSG-AAIELLVDG 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1512457664 539 QTVGTLAISNTGDWESYVDFVLPSPVTLSAGTHTLRVQSSGNSAWQWNGDKVTLT 593
Cdd:cd04079    79 NSVATTAVPNTGGWDNFQALTLASTVNLTAGTHTIRLTAAGSNDWQWNLDKFTLT 133
CBM6_agarase-like cd04079
Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 ...
 319-453 5.98e-38

Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 alpha- and beta agarases; This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family 16 agarases. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the activity of alpha- and beta-agarase catalytic modules which are involved in the hydrolysis of 1,4-beta-D-galactosidic linkages. These CBM6s bind specifically to the non-reducing end of agarose chains, recognizing only the first repeat of the disaccharide, and directing the appended catalytic modules to areas of the plant cell wall attacked by beta-agarases. 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. This family includes three tandem CBM6s from the Saccharophagus degradans agarase Aga86E, and three tandem CBM6s from Vibrio sp. strain PO-303 AgaA; in both these proteins these are appended to a GH16 domain. Vibrio AgaA also contains a Big-2-like protein-protein interaction domain. This family also includes two tandem CBM6s from an endo-type beta-agarase from a deep-sea Microbulbifer-like isolate, which are appended to a GH16 domain, and two of three CBM6s of Alteromonas agarilytica AgaA alpha-agarase, which are appended to a GH96 domain.


:

Pssm-ID: 271145  Cd Length: 134  Bit Score: 136.62  E-value: 5.98e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 319 GDVTTVELGDFYSTGKDGASVsGDTVPGFNRNG-SNINYNTSGDWGDYTVTLPEAGDYRVELVTASPMTGeLGAELQFNG 397
Cdd:cd04079     1 GGTIVIEAESFTATGGTFDDG-PDGVSGYSVNGgTAINYVNTGDYADYTVNVPEAGTYSVEYLIGTPVSG-AAIELLVDG 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1512457664 398 -STLVTALGNTGGWESYQAFQFAQTVSVsAAGDYGFRVKSIGTSAWQWNGDAIRFVK 453
Cdd:cd04079    79 nSVATTAVPNTGGWDNFQALTLASTVNL-TAGTHTIRLTAAGSNDWQWNLDKFTLTK 134
 
Name Accession Description Interval E-value
GH16_beta_agarase cd02178
Beta-agarase, member of glycosyl hydrolase family 16; Beta-agarase is a glycosyl hydrolase ...
 18-290 1.45e-97

Beta-agarase, member of glycosyl hydrolase family 16; Beta-agarase is a glycosyl hydrolase family 16 (GH16) member that hydrolyzes the internal beta-1,4-linkage of agarose, a hydrophilic polysaccharide found in the cell wall of Rhodophyceaea, marine red algae. Agarose is a linear chain of galactose units linked by alternating L-alpha-1,3- and D-beta-1,4-linkages that are additionally modified by a 3,6-anhydro-bridge. Agarose forms thermo-reversible gels that are widely used in the food industry or as a laboratory medium. While beta-agarases are also found in two other families derived from the sequence-based classification of glycosyl hydrolases (GH50, and GH86) the GH16 members are most abundant. This domain adopts a curved beta-sandwich conformation, with a tunnel-shaped active site cavity, referred to as a jellyroll fold.


Pssm-ID: 185687  Cd Length: 258  Bit Score: 298.49  E-value: 1.45e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  18 TAADWDGIPVPADPGEGNvWELHP-LSDDFNYeapaagkSTAFYERWKEGFINPWTGPGLTEWRPEYSLVSNGRLQIKSG 96
Cdd:cd02178     1 AAADWDPIPLPDQPGGGE-WELNEsVSDEFNG-------TSLDTSKWNPNNPNGWTGRGPTEFSADNVSVEDGNLVLSAT 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  97 RKPG-----TNQVYLGSITSKTTLTYpLYMEARAKLSNMVLASDFWLLSA--DSTEEIDVIEAYGSDRpgQEWFAERLHL 169
Cdd:cd02178    73 RHPGtelgnGYKVTTGSITSKEKVKY-GYFEARAKASNLPMSSAFWLLSDtkDSTTEIDILEHYGGDR--EEWFATRMNS 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 170 SHHVFIREPFQDYQPTDAGTWYadGNGTRWADGYHRVGVYWRDPWHLEYYVDGQLVRTASGPDIidpngfTNGTGLSKPM 249
Cdd:cd02178   150 NTHVFIRDPEQDYQPKDDGSWY--YNPTELADDFHVYGVYWKDPDTIRFYIDGVLVRTVENSEI------TDGTGFDQPM 221

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1512457664 250 HAIINMEDQSWRSDngitPTDAELADPNRNTYNVDWVRFYK 290
Cdd:cd02178   222 YIIIDTETYDWRGE----PTDEELADDSKNTFYVDYVRVYK 258
CBM6_agarase-like cd04079
Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 ...
 460-593 2.90e-43

Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 alpha- and beta agarases; This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family 16 agarases. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the activity of alpha- and beta-agarase catalytic modules which are involved in the hydrolysis of 1,4-beta-D-galactosidic linkages. These CBM6s bind specifically to the non-reducing end of agarose chains, recognizing only the first repeat of the disaccharide, and directing the appended catalytic modules to areas of the plant cell wall attacked by beta-agarases. 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. This family includes three tandem CBM6s from the Saccharophagus degradans agarase Aga86E, and three tandem CBM6s from Vibrio sp. strain PO-303 AgaA; in both these proteins these are appended to a GH16 domain. Vibrio AgaA also contains a Big-2-like protein-protein interaction domain. This family also includes two tandem CBM6s from an endo-type beta-agarase from a deep-sea Microbulbifer-like isolate, which are appended to a GH16 domain, and two of three CBM6s of Alteromonas agarilytica AgaA alpha-agarase, which are appended to a GH96 domain.


Pssm-ID: 271145  Cd Length: 134  Bit Score: 151.26  E-value: 2.90e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 460 AESITLELSDFVTTGKVGAaVAGDTVMGFNPNG-SNINYNTSGDWAEYQLDVTTTGSYVITLATATPISGdVNAQISING 538
Cdd:cd04079     1 GGTIVIEAESFTATGGTFD-DGPDGVSGYSVNGgTAINYVNTGDYADYTVNVPEAGTYSVEYLIGTPVSG-AAIELLVDG 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1512457664 539 QTVGTLAISNTGDWESYVDFVLPSPVTLSAGTHTLRVQSSGNSAWQWNGDKVTLT 593
Cdd:cd04079    79 NSVATTAVPNTGGWDNFQALTLASTVNLTAGTHTIRLTAAGSNDWQWNLDKFTLT 133
CBM6_agarase-like cd04079
Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 ...
 319-453 5.98e-38

Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 alpha- and beta agarases; This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family 16 agarases. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the activity of alpha- and beta-agarase catalytic modules which are involved in the hydrolysis of 1,4-beta-D-galactosidic linkages. These CBM6s bind specifically to the non-reducing end of agarose chains, recognizing only the first repeat of the disaccharide, and directing the appended catalytic modules to areas of the plant cell wall attacked by beta-agarases. 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. This family includes three tandem CBM6s from the Saccharophagus degradans agarase Aga86E, and three tandem CBM6s from Vibrio sp. strain PO-303 AgaA; in both these proteins these are appended to a GH16 domain. Vibrio AgaA also contains a Big-2-like protein-protein interaction domain. This family also includes two tandem CBM6s from an endo-type beta-agarase from a deep-sea Microbulbifer-like isolate, which are appended to a GH16 domain, and two of three CBM6s of Alteromonas agarilytica AgaA alpha-agarase, which are appended to a GH96 domain.


Pssm-ID: 271145  Cd Length: 134  Bit Score: 136.62  E-value: 5.98e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 319 GDVTTVELGDFYSTGKDGASVsGDTVPGFNRNG-SNINYNTSGDWGDYTVTLPEAGDYRVELVTASPMTGeLGAELQFNG 397
Cdd:cd04079     1 GGTIVIEAESFTATGGTFDDG-PDGVSGYSVNGgTAINYVNTGDYADYTVNVPEAGTYSVEYLIGTPVSG-AAIELLVDG 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1512457664 398 -STLVTALGNTGGWESYQAFQFAQTVSVsAAGDYGFRVKSIGTSAWQWNGDAIRFVK 453
Cdd:cd04079    79 nSVATTAVPNTGGWDNFQALTLASTVNL-TAGTHTIRLTAAGSNDWQWNLDKFTLTK 134
BglS COG2273
Beta-glucanase, GH16 family [Carbohydrate transport and metabolism];
6-290 9.03e-23

Beta-glucanase, GH16 family [Carbohydrate transport and metabolism];


Pssm-ID: 441874 [Multi-domain]  Cd Length: 259  Bit Score: 98.14  E-value: 9.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664   6 ITLLASLLGTGATAAdwdgiPVPADPGEGNVWELhPLSDDFNYEAPAAGKstafyerWkegfiNPWTGPG------LTEW 79
Cdd:COG2273     3 LLLLLALLLAALAAA-----GAASSAPAAAGWTL-VFSDEFDGTSLDTSK-------W-----TYDTGGPgwgngeLQYY 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  80 RPEYSLVSNGRLQIKSGRKPGTNQVYL---GSITSKTTLTYPL-YMEARAKLSN---MVLAsdFWLLSADSTE------E 146
Cdd:COG2273    65 TDENVSVENGNLVITARKEPYGGGGRPytsGRITTKGKFSFTYgRFEARAKLPKgqgLWPA--FWMLGGDIDGgwpasgE 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 147 IDVIEAYGSDrpgqewfAERLHLSHHVfirepfqDYQPTDAGTWYADGNGTRWADGYHRVGVYWrDPWHLEYYVDGQLVR 226
Cdd:COG2273   143 IDIMEFVGKD-------PNKVHGNVHY-------GGYNGGEGIGASYDLPFDASDDFHTYAVEW-TPDSIRWYVDGVLVH 207

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1512457664 227 TASGPDIIDPNGFTngtglsKPMHAIINMEdqsWRSDNGITPTDAELADpnrnTYNVDWVRFYK 290
Cdd:COG2273   208 TVTPADVGGPWPFD------QPFYLILNLA---VGGNWPGAPDTTGFPA----TMEVDYVRVYQ 258
CBM_6 pfam03422
Carbohydrate binding module (family 6);
491-594 5.17e-13

Carbohydrate binding module (family 6);


Pssm-ID: 397476  Cd Length: 125  Bit Score: 66.22  E-value: 5.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 491 NGSNINYNTSGDWAEY-QLDVTTTGSYVITlATATPISGDVNAQISINGQT---VGTLAISNTGDWESYVDfvLPSPVTL 566
Cdd:pfam03422  21 GGVNVGYIDNGDWIAYkDVDFGSGGAYTFT-ARVASGAGGGSIELRLDSPTgtlIGTVSVPSTGGWQTYVT--VSANVTL 97

                          90       100
                  ....*....|....*....|....*...
gi 1512457664 567 SAGTHTLRVQSSGNSAWQWNGDKVTLTA 594
Cdd:pfam03422  98 PTGVHDLYLVFTGGGGYLFNIDWFQFTK 125
CBD_IV smart00606
Cellulose Binding Domain Type IV;
491-584 2.15e-10

Cellulose Binding Domain Type IV;


Pssm-ID: 128869 [Multi-domain]  Cd Length: 129  Bit Score: 58.50  E-value: 2.15e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  491 NGSNINYNTSGDWAEY-QLDVTTTGSYVITLATATpISGDVNAQISIN---GQTVGTLAISNTGDWESYVDfvLPSPVTL 566
Cdd:smart00606  29 GGKNVGYIDDGDWIAYkDVDFGSSGAYTFTARVAS-GNAGGSIELRLDsptGTLVGTVDVPSTGGWQTYQT--VSATVTL 105

                           90
                   ....*....|....*...
gi 1512457664  567 SAGTHTLRVQSSGNSAWQ 584
Cdd:smart00606 106 PAGVHDVYLVFKGGNYFN 123
CBM_6 pfam03422
Carbohydrate binding module (family 6);
336-453 2.29e-05

Carbohydrate binding module (family 6);


Pssm-ID: 397476  Cd Length: 125  Bit Score: 44.27  E-value: 2.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 336 GASVSGDTVPGfnrNGSNINYNTSGDWGDYT-VTLPEAGDYRVELVTASPMTGELgAELQFNGSTL----VTALGNTGGW 410
Cdd:pfam03422  10 GVSTEKTTDYG---GGVNVGYIDNGDWIAYKdVDFGSGGAYTFTARVASGAGGGS-IELRLDSPTGtligTVSVPSTGGW 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1512457664 411 ESYQAFQFAQTvsvSAAGDYGFRVKSIGTSAWQWNGDAIRFVK 453
Cdd:pfam03422  86 QTYVTVSANVT---LPTGVHDLYLVFTGGGGYLFNIDWFQFTK 125
CBD_IV smart00606
Cellulose Binding Domain Type IV;
350-451 2.42e-05

Cellulose Binding Domain Type IV;


Pssm-ID: 128869 [Multi-domain]  Cd Length: 129  Bit Score: 44.25  E-value: 2.42e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  350 NGSNINYNTSGDWGDYT-VTLPEAGDYRVEL-VTASPMTGELGAELQFNGSTLV--TALGNTGGWESYqafqfaQTVSVS 425
Cdd:smart00606  29 GGKNVGYIDDGDWIAYKdVDFGSSGAYTFTArVASGNAGGSIELRLDSPTGTLVgtVDVPSTGGWQTY------QTVSAT 102

                           90       100
                   ....*....|....*....|....*....
gi 1512457664  426 ---AAGDYGFRVKSIGTSAwqWNGDAIRF 451
Cdd:smart00606 103 vtlPAGVHDVYLVFKGGNY--FNIDWFRF 129
Glyco_hydro_16 pfam00722
Glycosyl hydrolases family 16;
79-227 2.31e-04

Glycosyl hydrolases family 16;


Pssm-ID: 395585 [Multi-domain]  Cd Length: 168  Bit Score: 42.19  E-value: 2.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  79 WRPEYSLVSNGRLQIKSGRKPGtnqvylGSITSKTTLTYPlYMEARAKLSNMV-LASDFWLLSADSTE--EIDVieaygs 155
Cdd:pfam00722   1 WGGDNVSVSNGGLTLTLDKYTG------SGFQSKFYYLYG-KVEARIKAARGAgVVTAFYLSSEDWDDhdEIDF------ 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 156 drpgqEWFAERLHlshhvfirepfqDYQptdaGTWYADGNGTRWA----------DGYHRVGVYWrDPWHLEYYVDGQLV 225
Cdd:pfam00722  68 -----EFLGNDTG------------QVQ----TNVYGNGKGNRGEqrfslwfdptADFHTYSILW-NPDKITWYVDGVPV 125


                  ..
gi 1512457664 226 RT 227
Cdd:pfam00722 126 RT 127
 
Name Accession Description Interval E-value
GH16_beta_agarase cd02178
Beta-agarase, member of glycosyl hydrolase family 16; Beta-agarase is a glycosyl hydrolase ...
 18-290 1.45e-97

Beta-agarase, member of glycosyl hydrolase family 16; Beta-agarase is a glycosyl hydrolase family 16 (GH16) member that hydrolyzes the internal beta-1,4-linkage of agarose, a hydrophilic polysaccharide found in the cell wall of Rhodophyceaea, marine red algae. Agarose is a linear chain of galactose units linked by alternating L-alpha-1,3- and D-beta-1,4-linkages that are additionally modified by a 3,6-anhydro-bridge. Agarose forms thermo-reversible gels that are widely used in the food industry or as a laboratory medium. While beta-agarases are also found in two other families derived from the sequence-based classification of glycosyl hydrolases (GH50, and GH86) the GH16 members are most abundant. This domain adopts a curved beta-sandwich conformation, with a tunnel-shaped active site cavity, referred to as a jellyroll fold.


Pssm-ID: 185687  Cd Length: 258  Bit Score: 298.49  E-value: 1.45e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  18 TAADWDGIPVPADPGEGNvWELHP-LSDDFNYeapaagkSTAFYERWKEGFINPWTGPGLTEWRPEYSLVSNGRLQIKSG 96
Cdd:cd02178     1 AAADWDPIPLPDQPGGGE-WELNEsVSDEFNG-------TSLDTSKWNPNNPNGWTGRGPTEFSADNVSVEDGNLVLSAT 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  97 RKPG-----TNQVYLGSITSKTTLTYpLYMEARAKLSNMVLASDFWLLSA--DSTEEIDVIEAYGSDRpgQEWFAERLHL 169
Cdd:cd02178    73 RHPGtelgnGYKVTTGSITSKEKVKY-GYFEARAKASNLPMSSAFWLLSDtkDSTTEIDILEHYGGDR--EEWFATRMNS 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 170 SHHVFIREPFQDYQPTDAGTWYadGNGTRWADGYHRVGVYWRDPWHLEYYVDGQLVRTASGPDIidpngfTNGTGLSKPM 249
Cdd:cd02178   150 NTHVFIRDPEQDYQPKDDGSWY--YNPTELADDFHVYGVYWKDPDTIRFYIDGVLVRTVENSEI------TDGTGFDQPM 221

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1512457664 250 HAIINMEDQSWRSDngitPTDAELADPNRNTYNVDWVRFYK 290
Cdd:cd02178   222 YIIIDTETYDWRGE----PTDEELADDSKNTFYVDYVRVYK 258
CBM6_agarase-like cd04079
Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 ...
 460-593 2.90e-43

Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 alpha- and beta agarases; This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family 16 agarases. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the activity of alpha- and beta-agarase catalytic modules which are involved in the hydrolysis of 1,4-beta-D-galactosidic linkages. These CBM6s bind specifically to the non-reducing end of agarose chains, recognizing only the first repeat of the disaccharide, and directing the appended catalytic modules to areas of the plant cell wall attacked by beta-agarases. 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. This family includes three tandem CBM6s from the Saccharophagus degradans agarase Aga86E, and three tandem CBM6s from Vibrio sp. strain PO-303 AgaA; in both these proteins these are appended to a GH16 domain. Vibrio AgaA also contains a Big-2-like protein-protein interaction domain. This family also includes two tandem CBM6s from an endo-type beta-agarase from a deep-sea Microbulbifer-like isolate, which are appended to a GH16 domain, and two of three CBM6s of Alteromonas agarilytica AgaA alpha-agarase, which are appended to a GH96 domain.


Pssm-ID: 271145  Cd Length: 134  Bit Score: 151.26  E-value: 2.90e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 460 AESITLELSDFVTTGKVGAaVAGDTVMGFNPNG-SNINYNTSGDWAEYQLDVTTTGSYVITLATATPISGdVNAQISING 538
Cdd:cd04079     1 GGTIVIEAESFTATGGTFD-DGPDGVSGYSVNGgTAINYVNTGDYADYTVNVPEAGTYSVEYLIGTPVSG-AAIELLVDG 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1512457664 539 QTVGTLAISNTGDWESYVDFVLPSPVTLSAGTHTLRVQSSGNSAWQWNGDKVTLT 593
Cdd:cd04079    79 NSVATTAVPNTGGWDNFQALTLASTVNLTAGTHTIRLTAAGSNDWQWNLDKFTLT 133
CBM6_agarase-like cd04079
Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 ...
 319-453 5.98e-38

Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 alpha- and beta agarases; This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family 16 agarases. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the activity of alpha- and beta-agarase catalytic modules which are involved in the hydrolysis of 1,4-beta-D-galactosidic linkages. These CBM6s bind specifically to the non-reducing end of agarose chains, recognizing only the first repeat of the disaccharide, and directing the appended catalytic modules to areas of the plant cell wall attacked by beta-agarases. 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. This family includes three tandem CBM6s from the Saccharophagus degradans agarase Aga86E, and three tandem CBM6s from Vibrio sp. strain PO-303 AgaA; in both these proteins these are appended to a GH16 domain. Vibrio AgaA also contains a Big-2-like protein-protein interaction domain. This family also includes two tandem CBM6s from an endo-type beta-agarase from a deep-sea Microbulbifer-like isolate, which are appended to a GH16 domain, and two of three CBM6s of Alteromonas agarilytica AgaA alpha-agarase, which are appended to a GH96 domain.


Pssm-ID: 271145  Cd Length: 134  Bit Score: 136.62  E-value: 5.98e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 319 GDVTTVELGDFYSTGKDGASVsGDTVPGFNRNG-SNINYNTSGDWGDYTVTLPEAGDYRVELVTASPMTGeLGAELQFNG 397
Cdd:cd04079     1 GGTIVIEAESFTATGGTFDDG-PDGVSGYSVNGgTAINYVNTGDYADYTVNVPEAGTYSVEYLIGTPVSG-AAIELLVDG 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1512457664 398 -STLVTALGNTGGWESYQAFQFAQTVSVsAAGDYGFRVKSIGTSAWQWNGDAIRFVK 453
Cdd:cd04079    79 nSVATTAVPNTGGWDNFQALTLASTVNL-TAGTHTIRLTAAGSNDWQWNLDKFTLTK 134
BglS COG2273
Beta-glucanase, GH16 family [Carbohydrate transport and metabolism];
6-290 9.03e-23

Beta-glucanase, GH16 family [Carbohydrate transport and metabolism];


Pssm-ID: 441874 [Multi-domain]  Cd Length: 259  Bit Score: 98.14  E-value: 9.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664   6 ITLLASLLGTGATAAdwdgiPVPADPGEGNVWELhPLSDDFNYEAPAAGKstafyerWkegfiNPWTGPG------LTEW 79
Cdd:COG2273     3 LLLLLALLLAALAAA-----GAASSAPAAAGWTL-VFSDEFDGTSLDTSK-------W-----TYDTGGPgwgngeLQYY 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  80 RPEYSLVSNGRLQIKSGRKPGTNQVYL---GSITSKTTLTYPL-YMEARAKLSN---MVLAsdFWLLSADSTE------E 146
Cdd:COG2273    65 TDENVSVENGNLVITARKEPYGGGGRPytsGRITTKGKFSFTYgRFEARAKLPKgqgLWPA--FWMLGGDIDGgwpasgE 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 147 IDVIEAYGSDrpgqewfAERLHLSHHVfirepfqDYQPTDAGTWYADGNGTRWADGYHRVGVYWrDPWHLEYYVDGQLVR 226
Cdd:COG2273   143 IDIMEFVGKD-------PNKVHGNVHY-------GGYNGGEGIGASYDLPFDASDDFHTYAVEW-TPDSIRWYVDGVLVH 207

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1512457664 227 TASGPDIIDPNGFTngtglsKPMHAIINMEdqsWRSDNGITPTDAELADpnrnTYNVDWVRFYK 290
Cdd:COG2273   208 TVTPADVGGPWPFD------QPFYLILNLA---VGGNWPGAPDTTGFPA----TMEVDYVRVYQ 258
Glyco_hydrolase_16 cd00413
glycosyl hydrolase family 16; The O-Glycosyl hydrolases are a widespread group of enzymes that ...
 44-289 1.41e-20

glycosyl hydrolase family 16; The O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycosyl hydrolase family 16. Family 16 includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues.


Pssm-ID: 185683 [Multi-domain]  Cd Length: 210  Bit Score: 90.19  E-value: 1.41e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  44 DDFNYEAPAAGKSTAFYERWkegfinpwtGPGLTEWRPE-YSLVSNGRLQIKSGRKPGTNQVYLGSITSKTTLTYPLYME 122
Cdd:cd00413     1 DDFDGLALDTSKWTIQDGPS---------WGGNMTNSPNnVYVENDGGLTLRTDRDQTDGPYSSAEIDSQKNNYTYGYYE 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 123 ARAKLSNMV-LASDFWLLSAD----STEEIDvIEAYGSDRPGQEWFaerlhlsHHVFIREPFqdyQPTDAGTWYADGNGt 197
Cdd:cd00413    72 ARAKLAGGPgAVSAFWTYSDDddppDGGEID-IEFLGRDPTTVQTN-------VHWPGYGAG---ATTGEEKSVHLPFD- 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 198 rWADGYHRVGVYWrDPWHLEYYVDGQLVRTasgpdiidpngfTNGTGLSKPMHAIINMEDQ-SWRSDNGITPTDAELAdp 276
Cdd:cd00413   140 -PADDFHTYRVDW-TPGEITFYVDGVLVAT------------ITNQVPDDPMNIILNLWSDgGWWWGGPPPGAPAYME-- 203

                         250
                  ....*....|...
gi 1512457664 277 nrntynVDWVRFY 289
Cdd:cd00413   204 ------IDWVRVY 210
CBM6_cellulase-like cd04080
Carbohydrate Binding Module 6 (CBM6); appended to glycoside hydrolase (GH) domains, including ...
 491-593 5.47e-17

Carbohydrate Binding Module 6 (CBM6); appended to glycoside hydrolase (GH) domains, including GH5 (cellulase); This family includes carbohydrate binding module 6 (CBM6) domains that are appended to several glycoside hydrolase (GH) domains, including GH5 (cellulase) and GH16, as well as to coagulation factor 5/8 carbohydrate-binding domains. CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. The CBM6s are appended to GHs that display a diversity of substrate specificities. For some members of this family information is available about the specific substrates of the appended GH domains. It includes the CBM domains of various enzymes involved in cell wall degradation including, an extracellular beta-1,3-glucanase from Lysobacter enzymogenes encoded by the gluC gene (its catalytic domain belongs to the GH16 family), the tandem CBM domains of Pseudomonas sp. PE2 beta-1,3(4)-glucanase A (its catalytic domain also belongs to GH16), and a family 6 CBM from Cellvibrio mixtus Endoglucanase 5A (CmCBM6) which binds to the beta1,4-beta1,3-mixed linked glucans lichenan, and barley beta-glucan, cello-oligosaccharides, insoluble forms of cellulose, the beta1,3-glucan laminarin, and xylooligosaccharides, and the CBM6 of Fibrobacter succinogenes S85 XynD xylanase, appended to a GH10 domain, and Cellvibrio japonicas Cel5G appended to a GH5 (cellulase) domain. GH5 (cellulase) family includes enzymes with several known activities such as endoglucanase, beta-mannanase, and xylanase, which are involved in the degradation of cellulose and xylans. GH16 family includes enzymes with lichenase, xyloglucan endotransglycosylase (XET), and beta-agarase activities. 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. For CmCBM6 it has been shown that these two binding sites have different ligand specificities.


Pssm-ID: 271146  Cd Length: 144  Bit Score: 78.04  E-value: 5.47e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 491 NGSNINYNTSGDWAEYQLDVTTTGSYVITLATATPiSGDVNAQISINGQTV-GTLAISNTGDWESYVDFVLPSpVTLSAG 569
Cdd:cd04080    46 GGYNVGWIDAGEWLEYTVNVPEAGTYTVSFRVASP-SGGGSLSLEVDGGTVlGTVDVPNTGGWQTWQTVTTTV-VLLPAG 123

                          90       100
                  ....*....|....*....|....
gi 1512457664 570 THTLRVQSSGNSawqWNGDKVTLT 593
Cdd:cd04080   124 THTLRLVFVGGG---FNLNWFEFT 144
GH16_laminarinase_like cd08023
Laminarinase, member of the glycosyl hydrolase family 16; Laminarinase, also known as glucan ...
 43-289 1.49e-14

Laminarinase, member of the glycosyl hydrolase family 16; Laminarinase, also known as glucan endo-1,3-beta-D-glucosidase, is a glycosyl hydrolase family 16 member that hydrolyzes 1,3-beta-D-glucosidic linkages in 1,3-beta-D-glucans such as laminarins, curdlans, paramylons, and pachymans, with very limited action on mixed-link (1,3-1,4-)-beta-D-glucans.


Pssm-ID: 185693 [Multi-domain]  Cd Length: 235  Bit Score: 73.43  E-value: 1.49e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  43 SDDFNYEAPAAGKstafyeRWKegFINPWTGPGLTEW-----RPEYSLVSNGRLQIKsGRKPGTNQVYLGSITS------ 111
Cdd:cd08023     2 SDEFDGDGLPDPS------KWT--YETGGGGNGNNELqyytyRPENAYVEDGNLVIT-ARKEPDKGGDGYPYTSgrittk 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 112 -KTTLTYpLYMEARAKLSNMV-LASDFWLLSADSTE-------EIDVIEAYGSDrpgQEWFAERLHLshhvfirePFQDY 182
Cdd:cd08023    73 gKFSFTY-GRVEARAKLPKGQgTWPAFWMLGENIKYvgwpasgEIDIMEYVGNE---PNTVYGTLHG--------GATND 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 183 QPTDAGTWYADGNGTrWADGYHRVGVYWrDPWHLEYYVDGQLVRTASGPDIIDPNGFTngtgLSKPMHAIINMedqSWRS 262
Cdd:cd08023   141 GNNGSGGSYTLPTDD-LSDDFHTYAVEW-TPDKITFYVDGKLYFTYTNPNTDNGGQWP----FDQPFYLILNL---AVGG 211

                         250       260
                  ....*....|....*....|....*..
gi 1512457664 263 DNGItPTDAELADPNrnTYNVDWVRFY 289
Cdd:cd08023   212 NWPG-PPDDDTPFPA--TMEVDYVRVY 235
CBM_6 pfam03422
Carbohydrate binding module (family 6);
491-594 5.17e-13

Carbohydrate binding module (family 6);


Pssm-ID: 397476  Cd Length: 125  Bit Score: 66.22  E-value: 5.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 491 NGSNINYNTSGDWAEY-QLDVTTTGSYVITlATATPISGDVNAQISINGQT---VGTLAISNTGDWESYVDfvLPSPVTL 566
Cdd:pfam03422  21 GGVNVGYIDNGDWIAYkDVDFGSGGAYTFT-ARVASGAGGGSIELRLDSPTgtlIGTVSVPSTGGWQTYVT--VSANVTL 97

                          90       100
                  ....*....|....*....|....*...
gi 1512457664 567 SAGTHTLRVQSSGNSAWQWNGDKVTLTA 594
Cdd:pfam03422  98 PTGVHDLYLVFTGGGGYLFNIDWFQFTK 125
CBM6_cellulase-like cd04080
Carbohydrate Binding Module 6 (CBM6); appended to glycoside hydrolase (GH) domains, including ...
 319-452 8.96e-13

Carbohydrate Binding Module 6 (CBM6); appended to glycoside hydrolase (GH) domains, including GH5 (cellulase); This family includes carbohydrate binding module 6 (CBM6) domains that are appended to several glycoside hydrolase (GH) domains, including GH5 (cellulase) and GH16, as well as to coagulation factor 5/8 carbohydrate-binding domains. CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. The CBM6s are appended to GHs that display a diversity of substrate specificities. For some members of this family information is available about the specific substrates of the appended GH domains. It includes the CBM domains of various enzymes involved in cell wall degradation including, an extracellular beta-1,3-glucanase from Lysobacter enzymogenes encoded by the gluC gene (its catalytic domain belongs to the GH16 family), the tandem CBM domains of Pseudomonas sp. PE2 beta-1,3(4)-glucanase A (its catalytic domain also belongs to GH16), and a family 6 CBM from Cellvibrio mixtus Endoglucanase 5A (CmCBM6) which binds to the beta1,4-beta1,3-mixed linked glucans lichenan, and barley beta-glucan, cello-oligosaccharides, insoluble forms of cellulose, the beta1,3-glucan laminarin, and xylooligosaccharides, and the CBM6 of Fibrobacter succinogenes S85 XynD xylanase, appended to a GH10 domain, and Cellvibrio japonicas Cel5G appended to a GH5 (cellulase) domain. GH5 (cellulase) family includes enzymes with several known activities such as endoglucanase, beta-mannanase, and xylanase, which are involved in the degradation of cellulose and xylans. GH16 family includes enzymes with lichenase, xyloglucan endotransglycosylase (XET), and beta-agarase activities. 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. For CmCBM6 it has been shown that these two binding sites have different ligand specificities.


Pssm-ID: 271146  Cd Length: 144  Bit Score: 66.10  E-value: 8.96e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 319 GDVTTVELGDFYSTGKDGASVSGDTvpgfnRNGSNINYNTSGDWGDYTVTLPEAGDYRVELVTASPMTGelGA-ELQFNG 397
Cdd:cd04080    20 HDTTPGNEGGYYRNDGVDIETTSDT-----GGGYNVGWIDAGEWLEYTVNVPEAGTYTVSFRVASPSGG--GSlSLEVDG 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1512457664 398 STLVT--ALGNTGGWESYQAFQfaQTVSVSAAGDYGFRVKSIGTSawqWNGDAIRFV 452
Cdd:cd04080    93 GTVLGtvDVPNTGGWQTWQTVT--TTVVLLPAGTHTLRLVFVGGG---FNLNWFEFT 144
CBD_IV smart00606
Cellulose Binding Domain Type IV;
491-584 2.15e-10

Cellulose Binding Domain Type IV;


Pssm-ID: 128869 [Multi-domain]  Cd Length: 129  Bit Score: 58.50  E-value: 2.15e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  491 NGSNINYNTSGDWAEY-QLDVTTTGSYVITLATATpISGDVNAQISIN---GQTVGTLAISNTGDWESYVDfvLPSPVTL 566
Cdd:smart00606  29 GGKNVGYIDDGDWIAYkDVDFGSSGAYTFTARVAS-GNAGGSIELRLDsptGTLVGTVDVPSTGGWQTYQT--VSATVTL 105

                           90
                   ....*....|....*...
gi 1512457664  567 SAGTHTLRVQSSGNSAWQ 584
Cdd:smart00606 106 PAGVHDVYLVFKGGNYFN 123
CBM35_pectate_lyase-like cd04082
Carbohydrate Binding Module family 35 (CBM35), pectate lyase-like; appended mainly to enzymes ...
 495-581 6.96e-09

Carbohydrate Binding Module family 35 (CBM35), pectate lyase-like; appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans; This family includes carbohydrate binding module family 35 (CBM35) domains that are non-catalytic carbohydrate binding domains that are appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans. Included in this family are CBM35s of pectate lyases, including pectate lyase 10A from Cellvibrio japonicas, these enzymes release delta-4,5-anhydrogalaturonic acid (delta4,5-GalA) from pectin, thus identifying a signature molecule for plant cell wall degradation. CBM35s are unique in that they display conserved specificity through extensive sequence similarity but divergent function through their appended catalytic modules. They are known to bind alpha-D-galactose (Gal), mannan (Man), xylan, glucuronic acid (GlcA), a beta-polymer of mannose, and possibly glucans, forming four subfamilies based on general ligand specificities (galacto, urono, manno, and gluco configurations). In contrast to most CBMs that are generally rigid proteins, CBM35 undergoes significant conformational change upon ligand binding. Some CBM35s bind their ligands in a calcium-dependent manner, especially those binding uronic acids.


Pssm-ID: 271148  Cd Length: 124  Bit Score: 54.10  E-value: 6.96e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 495 INY-NTSGDWAEYQLDVTTTGSYVITLATATPISGDVNAQISINGQTV-GTLAISNTGDWESYVDFVLPspVTLSAGTHT 572
Cdd:cd04082    28 VNTdNAVGSYIEWTVNAPTAGTYTLTFRYANGSTSNRPADISVNGNTVaATLSFPSTGAWTTWATSSVT--VPLNAGTNT 105


                  ....*....
gi 1512457664 573 LRVQSSGNS 581
Cdd:cd04082   106 IRLTATTAE 114
CBM6-CBM35-CBM36_like cd02795
Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module ...
 478-592 3.08e-07

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.


Pssm-ID: 271143  Cd Length: 124  Bit Score: 49.49  E-value: 3.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 478 AAVAGDTVMGFNPNGSNINYNTSGDWAEYQLDVTTTGSYVITLATATPIS-GDVNAQISINGQTVGTLAISNTGDWESYV 556
Cdd:cd02795    11 GGTAVSTAAGASGGGYVIGFSSGGDSVTFTVTVPKAGTYRLAVRYASPNGnGSRSVSLDGNGKLVGTITVPSTGGWDTWG 90

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1512457664 557 DFVLPSPVTlSAGTHTLRVQSSGNSaWQWNGDKVTL 592
Cdd:cd02795    91 TASVSVNLP-DAGGHTLKIVGTGDN-GGANIDYVVV 124
CBM_6 pfam03422
Carbohydrate binding module (family 6);
336-453 2.29e-05

Carbohydrate binding module (family 6);


Pssm-ID: 397476  Cd Length: 125  Bit Score: 44.27  E-value: 2.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 336 GASVSGDTVPGfnrNGSNINYNTSGDWGDYT-VTLPEAGDYRVELVTASPMTGELgAELQFNGSTL----VTALGNTGGW 410
Cdd:pfam03422  10 GVSTEKTTDYG---GGVNVGYIDNGDWIAYKdVDFGSGGAYTFTARVASGAGGGS-IELRLDSPTGtligTVSVPSTGGW 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1512457664 411 ESYQAFQFAQTvsvSAAGDYGFRVKSIGTSAWQWNGDAIRFVK 453
Cdd:pfam03422  86 QTYVTVSANVT---LPTGVHDLYLVFTGGGGYLFNIDWFQFTK 125
CBD_IV smart00606
Cellulose Binding Domain Type IV;
350-451 2.42e-05

Cellulose Binding Domain Type IV;


Pssm-ID: 128869 [Multi-domain]  Cd Length: 129  Bit Score: 44.25  E-value: 2.42e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  350 NGSNINYNTSGDWGDYT-VTLPEAGDYRVEL-VTASPMTGELGAELQFNGSTLV--TALGNTGGWESYqafqfaQTVSVS 425
Cdd:smart00606  29 GGKNVGYIDDGDWIAYKdVDFGSSGAYTFTArVASGNAGGSIELRLDSPTGTLVgtVDVPSTGGWQTY------QTVSAT 102

                           90       100
                   ....*....|....*....|....*....
gi 1512457664  426 ---AAGDYGFRVKSIGTSAwqWNGDAIRF 451
Cdd:smart00606 103 vtlPAGVHDVYLVFKGGNY--FNIDWFRF 129
CBM6_xylanase-like cd04084
Carbohydrate Binding Module 6 (CBM6); many are appended to glycoside hydrolase (GH) family 11 ...
 478-573 2.52e-05

Carbohydrate Binding Module 6 (CBM6); many are appended to glycoside hydrolase (GH) family 11 and GH43 xylanase domains; This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family domains, including GH3, GH11, and GH43 domains. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. Examples of proteins having CMB6s belonging to this family are Microbispora bispora GghA, a 1,4-beta-D-glucan glucohydrolase (GH3); Clostridium thermocellum xylanase U (GH11), and Penicillium purpurogenum ABF3, a bifunctional alpha-L-arabinofuranosidase/xylobiohydrolase (GH43). GH3 comprises enzymes with activities including beta-glucosidase (hydrolyzes beta-galactosidase) and beta-xylosidase (hydrolyzes 1,4-beta-D-xylosidase). GH11 family comprises enzymes with xylanase (endo-1,4-beta-xylanase) activity which catalyze the hydrolysis of beta-1,4 bonds of xylan, the major component of hemicelluloses, to generate xylooligosaccharides and xylose. GH43 includes beta-xylosidases and beta-xylanases, using aryl-glycosides as substrates. 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.


Pssm-ID: 271150  Cd Length: 123  Bit Score: 43.77  E-value: 2.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 478 AAVAGDTVMGFNPNGSNINYNTSGDWAEY-QLDVTT-TGSYVITLATATPiSGDVNAQI-SINGQTVGTLAISNTGDWES 554
Cdd:cd04084     9 ADSSGVKTEATGDGGVYVGAIDNGDWIAFkNVDFGSgATSFTARVASAGA-GGTIEVRLdSPDGPLIGTLEVPNTGGWQT 87

                          90
                  ....*....|....*....
gi 1512457664 555 YVDFvlPSPVTLSAGTHTL 573
Cdd:cd04084    88 WTTV--SAPVTGVTGVHDL 104
CBM35_galactosidase-like cd04081
Carbohydrate Binding Module family 35 (CBM35); appended mainly to enzymes that bind ...
 459-580 4.34e-05

Carbohydrate Binding Module family 35 (CBM35); appended mainly to enzymes that bind alpha-D-galactose (CBM35-Gal), including glycoside hydrolase (GH) families GH27 and GH43; This family includes carbohydrate binding module family 35 (CBM35); these are non-catalytic carbohydrate binding domains that are appended mainly to enzymes that bind alpha-D-galactose (CBM35-Gal), including glycoside hydrolase (GH) families GH27 and GH43. Examples of proteins which contain CBM35s belonging to this family includes the CBM35 of an exo-beta-1,3-galactanase from Phanerochaete chrysosporium 9 (Pc1,3Gal43A) which is appended to a GH43 domain, and the CBM35 domain of two bifunctional proteins with beta-L-arabinopyranosidase/alpha-D-galactopyranosidase activities from Fusarium oxysporum 12S, Foap1 and Foap2 (Fo/AP1 and Fo/AP2), that are appended to GH27 domains. CBM35s are unique in that they display conserved specificity through extensive sequence similarity but divergent function through their appended catalytic modules. They are known to bind alpha-D-galactose (Gal), mannan (Man), xylan, glucuronic acid (GlcA), a beta-polymer of mannose, and possibly glucans, forming four subfamilies based on general ligand specificities (galacto, urono, manno, and gluco configurations). Some CBM35s bind their ligands in a calcium-dependent manner. In contrast to most CBMs that are generally rigid proteins, CBM35 undergoes significant conformational change upon ligand binding. GH43 includes beta-xylosidases and beta-xylanases, using aryl-glycosides as substrates, while family GH27 includes alpha-galactosidases, alpha-N-acetylgalactosaminidases, and isomaltodextranases.


Pssm-ID: 271147  Cd Length: 125  Bit Score: 43.44  E-value: 4.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 459 PAESITLELSDFVTTGKVGAAVAGDTVMGFNPNGSNINYNTsgdwaeyqLDVTTTGSYVITLATATPISGDVNAQISING 538
Cdd:cd04081     4 EAEAATLTGSAAAVSCSCGCSGGGAVGVGGGGNGGTVTFNN--------VTASAAGTYTLTIDYINGDVNDRNATVSVNG 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1512457664 539 QTVGTLAISNTGDWESYVDFVLpsPVTLSAGTHTLRVQSSGN 580
Cdd:cd04081    76 GAAQRVAFPPTGGWNTPGSVTV--LVDLKAGSNTITFSNSGG 115
CBM_35 pfam16990
Carbohydrate binding module (family 35); This is a mannan-specific carbohydrate binding domain, ...
 477-585 4.87e-05

Carbohydrate binding module (family 35); This is a mannan-specific carbohydrate binding domain, previously known as the X4 module. Unlike other carbohydrate binding modules, binding to substrate causes a conformational change.


Pssm-ID: 293595  Cd Length: 119  Bit Score: 42.90  E-value: 4.87e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 477 GAAVAGDTvMGFNPNGSNINYNTSGDWAEYQLDVTTTGSYVITLATATPISGDVNAQIsINGQTVGTLAISNTgdweSYV 556
Cdd:pfam16990  11 GTSVDTTA-PGVSGTGYVGEFQGAGDAVSWNVNVPVAGEYNLNVTHSAPYGSKENTLV-VNGTAVATNAFAES----TEV 84

                          90       100
                  ....*....|....*....|....*....
gi 1512457664 557 DFVLPSPVTLSAGTHTLRVQSSgnsaWQW 585
Cdd:pfam16990  85 PQTTVITVTLKAGANTIGIDRD----WGW 109
CBM35_Lmo2446-like cd04083
Carbohydrate Binding Module 35 (CBM35) domains similar to Lmo2446; This family includes ...
 497-582 1.27e-04

Carbohydrate Binding Module 35 (CBM35) domains similar to Lmo2446; This family includes carbohydrate binding module 35 (CBM35) domains that are appended to several carbohydrate binding enzymes. Some CBM35 domains belonging to this family are appended to glycoside hydrolase (GH) family domains, including glycoside hydrolase family 31 (GH31), for example the CBM35 domain of Lmo2446, an uncharacterized protein from Listeria monocytogenes EGD-e. These CBM35s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. GH31 has a wide range of hydrolytic activities such as alpha-glucosidase, alpha-xylosidase, 6-alpha-glucosyltransferase, or alpha-1,4-glucan lyase, cleaving a terminal carbohydrate moiety from a substrate that may be a starch or a glycoprotein. Most characterized GH31 enzymes are alpha-glucosidases.


Pssm-ID: 271149  Cd Length: 125  Bit Score: 41.86  E-value: 1.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 497 YNTSGDWAEYQLDVTTTGSYVITLATATPISGDVNAQISINGQTVGTLAISNTGDWESYVDFVLpsPVTLSAGTHTLRVQ 576
Cdd:cd04083    32 FATAGASVTFTVNVPAAGTYTLTLRYANGTGSAKTLSLYVNGTKVKQVSLPSTGSWDTWGTATE--TVTLRAGTNTIELR 109


                  ....*..
gi 1512457664 577 S-SGNSA 582
Cdd:cd04083   110 YdAGDSG 116
CBM35_mannanase-like cd04086
Carbohydrate Binding Module 35 (CBM35); appended to several carbohydrate binding enzymes, ...
 463-593 1.57e-04

Carbohydrate Binding Module 35 (CBM35); appended to several carbohydrate binding enzymes, including several glycoside hydrolase (GH) family 26 mannanase domains; This family includes carbohydrate binding module 35 (CBM35) domains that are appended to several carbohydrate binding enzymes, including periplasmic component of ABC-type sugar transport system involved in carbohydrate transport and metabolism, and several glycoside hydrolase (GH) domains, including GH26. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. Examples of proteins having CMB35s belonging to this family are mannanase A from Clostridium thermocellum (GH26), Man26B from Paenibacillus sp. BME-14 (GH26), and the multifunctional Cel44C-Man26A from Paenibacillus polymyxa GS01 (which has two GH domains, GH44 and GH26). GH26 mainly includes mannan endo-1,4-beta-mannosidase which hydrolyzes 1,4-beta-D-linkages in mannans, galacto-mannans, glucomannans, and galactoglucomannans, but displays little activity towards other plant cell wall polysaccharides. A few proteins belonging to this family have additional CBM3 domains; these CBM3s are not found in the CBM6-CBM35-CBM36_like superfamily.


Pssm-ID: 271152  Cd Length: 119  Bit Score: 41.43  E-value: 1.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 463 ITLELSDFVTTG-KVGAAVAGDT----VMGFNPNGSNInyntsgdwaEYQLDVTTTGSYVITLATATPiSGDVNAQISIN 537
Cdd:cd04086     1 ITYEAEDGTLTGvTVATSRSGYSgtgyVTGFDDDGDSL---------TFTVNVPEAGLYDLVIRYAAP-YGDKENNLYVN 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1512457664 538 GQTVGTLAISNTGDW-ESYVDFVLpspvtLSAGTHTLRVQSSgnsaWQW-NGDKVTLT 593
Cdd:cd04086    71 GTSVGEISFPATTKFtEVSAGKVL-----LNAGENTITIENS----WGWyDIDYITVT 119
Glyco_hydro_16 pfam00722
Glycosyl hydrolases family 16;
79-227 2.31e-04

Glycosyl hydrolases family 16;


Pssm-ID: 395585 [Multi-domain]  Cd Length: 168  Bit Score: 42.19  E-value: 2.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664  79 WRPEYSLVSNGRLQIKSGRKPGtnqvylGSITSKTTLTYPlYMEARAKLSNMV-LASDFWLLSADSTE--EIDVieaygs 155
Cdd:pfam00722   1 WGGDNVSVSNGGLTLTLDKYTG------SGFQSKFYYLYG-KVEARIKAARGAgVVTAFYLSSEDWDDhdEIDF------ 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 156 drpgqEWFAERLHlshhvfirepfqDYQptdaGTWYADGNGTRWA----------DGYHRVGVYWrDPWHLEYYVDGQLV 225
Cdd:pfam00722  68 -----EFLGNDTG------------QVQ----TNVYGNGKGNRGEqrfslwfdptADFHTYSILW-NPDKITWYVDGVPV 125


                  ..
gi 1512457664 226 RT 227
Cdd:pfam00722 126 RT 127
CBM6-CBM35-CBM36_like cd02795
Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module ...
 323-451 8.76e-03

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.


Pssm-ID: 271143  Cd Length: 124  Bit Score: 36.78  E-value: 8.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1512457664 323 TVELGDFYSTGKDGASVSGDTVPGfnrnGSNINYNTSGDWGDYTVTLPEAGDYRVELVTASPmTGELGAELQFNG---ST 399
Cdd:cd02795     1 RIEAEDATLTGGTAVSTAAGASGG----GYVIGFSSGGDSVTFTVTVPKAGTYRLAVRYASP-NGNGSRSVSLDGngkLV 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1512457664 400 LVTALGNTGGWESYQAFQFaqTVSVSAAGDYGFRVKSiGTSAWQWNGDAIRF 451
Cdd:cd02795    76 GTITVPSTGGWDTWGTASV--SVNLPDAGGHTLKIVG-TGDNGGANIDYVVV 124
 
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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