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Conserved domains on  [gi|746271081|ref|WP_039318889|]
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polysaccharide lyase family protein [Pectobacterium brasiliense]

Protein Classification

similar to rhamnogalacturonate lyase( domain architecture ID 10179202)

protein similar to rhamnogalacturonate lyase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RGL4_N cd10320
N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 25-291 7.24e-87

N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold; the middle and C-terminal domains are both putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.


:

Pssm-ID: 199907 [Multi-domain]  Cd Length: 265  Bit Score: 270.03  E-value: 7.24e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081  25 VSLSVSGLNTVLDNGLLKVAFGEDGSAVSMVTGGKnivtnlsGAARDPSKTRSAYLDYYINDAhakGVKDFVPERVEVLR 104
Cdd:cd10320    1 FGLTDSGSAVVVDNGLLGLVFSVDGGIVTGILYGG-------LLENDNGKGDRGYLDLVSIVY---GGTEQTPGKLSHIE 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 105 NDREMAHVAYIDDRDG------LLRLEYHLIMRRGVSGLYSYVVAENSgNQDVKVSELRNVYRFDPARLDHLYNGDRQGK 178
Cdd:cd10320   71 SGLGATVSATQSGDYIqisfsrTFETELHYVVRKGEPGIYMYTVATHP-APEPSLGELRTVFRLNPDLFPNGAISDDRGD 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 179 PLLYSQLEASPkVQDETWRLPDDSIYSKYDFAGYMRAAPFWGVFGNGVGAWLIHGNREYFSGDALKQDLLVHQDAIILNY 258
Cdd:cd10320  150 PPPGTALEGKE-VQDDTFPLPDGEYDSKYYYSGYNRDNKVHGVYGDGVGAWMIMPSREYSSGGPLKQDLTVHGGPILLNY 228

                        250       260       270
                 ....*....|....*....|....*....|...
gi 746271081 259 MTGSHFGTPDMVAPPGWKKFYGPWLLYINQGDT 291
Cdd:cd10320  229 FNSGHYGGKDLNATEGWRKLFGPYLLYFNSGGA 261
RGL4_C cd10317
C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 419-573 8.14e-46

C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.


:

Pssm-ID: 199905  Cd Length: 161  Bit Score: 158.59  E-value: 8.14e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 419 WAIGQANRQASEFRFGNEARNT---RWQHEVPANLTFDIGRSDYQRDWYYAQTKPGKWDIRFALQPE--KKTYFLNIALA 493
Cdd:cd10317    1 WQIGTPDRTAAEFRNGDLLPNYhpsDWRLAPPGDLTYTVGSSDSDFDWYYAQSVNGPWTIRFDLTAVqaTGGATLRIALA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 494 AASNSGmseptMPQLAVAVNGTTLETLTYAND-KTIYRGALQsGRYHIARIPVSSRFLKNGNNTITLQLKGGS-----VM 567
Cdd:cd10317   81 GASAGG-----RPQVRVNDNGPLLPTAPTGNDsRGIYRGAYR-GNYHLYEFDIPASLLVAGTNTITLTVVSGSslspgVM 154


                 ....*.
gi 746271081 568 YDVVTL 573
Cdd:cd10317  155 YDAIRL 160
RGL4_M cd10316
Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 322-403 2.73e-18

Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle domain represented by this model and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.


:

Pssm-ID: 199904  Cd Length: 92  Bit Score: 79.99  E-value: 2.73e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 322 ERTQVSGRV-----ASQQSVTVVLSSSLDEPFDVQTRGYSYQATTDTQGNFAIPHVRPGNYHLAVYANSGtqPGIVAEQT 396
Cdd:cd10316    1 GRGTVSGRLllpdgASAAIAVVGLANPGEQGSQFETKGYQYWTEADSDGRFTIPNVRPGTYRLTAYADGI--FGYVAQDT 78


                 ....*..
gi 746271081 397 LSVSGDK 403
Cdd:cd10316   79 VTVTAGG 85
 
Name Accession Description Interval E-value
RGL4_N cd10320
N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 25-291 7.24e-87

N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold; the middle and C-terminal domains are both putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.


Pssm-ID: 199907 [Multi-domain]  Cd Length: 265  Bit Score: 270.03  E-value: 7.24e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081  25 VSLSVSGLNTVLDNGLLKVAFGEDGSAVSMVTGGKnivtnlsGAARDPSKTRSAYLDYYINDAhakGVKDFVPERVEVLR 104
Cdd:cd10320    1 FGLTDSGSAVVVDNGLLGLVFSVDGGIVTGILYGG-------LLENDNGKGDRGYLDLVSIVY---GGTEQTPGKLSHIE 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 105 NDREMAHVAYIDDRDG------LLRLEYHLIMRRGVSGLYSYVVAENSgNQDVKVSELRNVYRFDPARLDHLYNGDRQGK 178
Cdd:cd10320   71 SGLGATVSATQSGDYIqisfsrTFETELHYVVRKGEPGIYMYTVATHP-APEPSLGELRTVFRLNPDLFPNGAISDDRGD 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 179 PLLYSQLEASPkVQDETWRLPDDSIYSKYDFAGYMRAAPFWGVFGNGVGAWLIHGNREYFSGDALKQDLLVHQDAIILNY 258
Cdd:cd10320  150 PPPGTALEGKE-VQDDTFPLPDGEYDSKYYYSGYNRDNKVHGVYGDGVGAWMIMPSREYSSGGPLKQDLTVHGGPILLNY 228

                        250       260       270
                 ....*....|....*....|....*....|...
gi 746271081 259 MTGSHFGTPDMVAPPGWKKFYGPWLLYINQGDT 291
Cdd:cd10320  229 FNSGHYGGKDLNATEGWRKLFGPYLLYFNSGGA 261
RGL4_C cd10317
C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 419-573 8.14e-46

C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.


Pssm-ID: 199905  Cd Length: 161  Bit Score: 158.59  E-value: 8.14e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 419 WAIGQANRQASEFRFGNEARNT---RWQHEVPANLTFDIGRSDYQRDWYYAQTKPGKWDIRFALQPE--KKTYFLNIALA 493
Cdd:cd10317    1 WQIGTPDRTAAEFRNGDLLPNYhpsDWRLAPPGDLTYTVGSSDSDFDWYYAQSVNGPWTIRFDLTAVqaTGGATLRIALA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 494 AASNSGmseptMPQLAVAVNGTTLETLTYAND-KTIYRGALQsGRYHIARIPVSSRFLKNGNNTITLQLKGGS-----VM 567
Cdd:cd10317   81 GASAGG-----RPQVRVNDNGPLLPTAPTGNDsRGIYRGAYR-GNYHLYEFDIPASLLVAGTNTITLTVVSGSslspgVM 154


                 ....*.
gi 746271081 568 YDVVTL 573
Cdd:cd10317  155 YDAIRL 160
CBM-like pfam14683
Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase ...
 417-573 4.10e-26

Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll beta-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion.


Pssm-ID: 464260  Cd Length: 158  Bit Score: 104.59  E-value: 4.10e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081  417 VVWAIGQANRQASEFRFGNEARNTRWQHevPA-NLTFDIGRSDYqRDWYYAQTKPGKWDIRFAL--QPEKKTYFLNIALA 493
Cdd:pfam14683   1 TLWQIGDPDRTAAGFLNADPNYKNYRMH--PSdDLTYTVGTSDY-SDWFFAQVNRGTWTIKFTLdsVQAAGAATLRIALA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081  494 AASNSGmseptmpQLAVAVNGTTLETL---TYANDKTIYRGALQSGRYHIARIPVSSRFLKNGNNTITL-QLKGGS---- 565
Cdd:pfam14683  78 GAFAGG-------RLQVRVNGWTGNLPaapTIGDSRGITRGGIYRGLYRLYEFDIPASLLVAGENTITLtVIRFLSpfrg 150


                  ....*...
gi 746271081  566 VMYDVVTL 573
Cdd:pfam14683 151 VMYDYIRL 158
RGL4_M cd10316
Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 322-403 2.73e-18

Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle domain represented by this model and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.


Pssm-ID: 199904  Cd Length: 92  Bit Score: 79.99  E-value: 2.73e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 322 ERTQVSGRV-----ASQQSVTVVLSSSLDEPFDVQTRGYSYQATTDTQGNFAIPHVRPGNYHLAVYANSGtqPGIVAEQT 396
Cdd:cd10316    1 GRGTVSGRLllpdgASAAIAVVGLANPGEQGSQFETKGYQYWTEADSDGRFTIPNVRPGTYRLTAYADGI--FGYVAQDT 78


                 ....*..
gi 746271081 397 LSVSGDK 403
Cdd:cd10316   79 VTVTAGG 85
fn3_3 pfam14686
Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase ...
 351-400 3.39e-08

Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits.


Pssm-ID: 464261  Cd Length: 74  Bit Score: 50.66  E-value: 3.39e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 746271081  351 QTRGYSYQATTDTQGNFAIPHVRPGNYHLAVYANSGtqPGIVAEQTLSVS 400
Cdd:pfam14686  21 ESKGYQYWTRADSSGSFTIPNVRPGTYRLTAYADGL--FGDYKQDDVTVS 68
Rhamnogal_lyase pfam06045
Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the ...
 14-176 1.18e-06

Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the rhamnogalacturonan I (RG-I) backbone of pectin. This family contains mainly members from plants, but also contains the plant pathogen Erwinia chrysanthemi.


Pssm-ID: 283658  Cd Length: 211  Bit Score: 49.48  E-value: 1.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081   14 APYSYSAQDNAVSLSVSGLNTVLDNGLLKVAFGE-DGsavsMVTGGK-NIVTNLSgAARDPSKTRsAYLDYYINDAHAKG 91
Cdd:pfam06045   5 PATSPAGGQAGVSLKVQLRYVVVDNGIVEVTFSNpDG----LVTGIKyNGVDNLL-EILNKIDNR-GYWDLVWSKPGERT 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081   92 VKD--FVPERVEVLRNDREMAHVAYIDDRDGLLR-------LEYHLIMRRGVSGLYSYVVAEN-SGNQDVKVSELRNVYR 161
Cdd:pfam06045  79 GKTdvIKGTKFEIVYQNEEQIEISFSRTWDPSLRgsavplnVDKRFIIRRGVSGFYMYAILEHlEGWPDFDLDQTRIVFK 158

                         170
                  ....*....|....*.
gi 746271081  162 FDPARLDHL-YNGDRQ 176
Cdd:pfam06045 159 LRKDKFDYMaIADNRQ 174
 
Name Accession Description Interval E-value
RGL4_N cd10320
N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 25-291 7.24e-87

N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold; the middle and C-terminal domains are both putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.


Pssm-ID: 199907 [Multi-domain]  Cd Length: 265  Bit Score: 270.03  E-value: 7.24e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081  25 VSLSVSGLNTVLDNGLLKVAFGEDGSAVSMVTGGKnivtnlsGAARDPSKTRSAYLDYYINDAhakGVKDFVPERVEVLR 104
Cdd:cd10320    1 FGLTDSGSAVVVDNGLLGLVFSVDGGIVTGILYGG-------LLENDNGKGDRGYLDLVSIVY---GGTEQTPGKLSHIE 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 105 NDREMAHVAYIDDRDG------LLRLEYHLIMRRGVSGLYSYVVAENSgNQDVKVSELRNVYRFDPARLDHLYNGDRQGK 178
Cdd:cd10320   71 SGLGATVSATQSGDYIqisfsrTFETELHYVVRKGEPGIYMYTVATHP-APEPSLGELRTVFRLNPDLFPNGAISDDRGD 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 179 PLLYSQLEASPkVQDETWRLPDDSIYSKYDFAGYMRAAPFWGVFGNGVGAWLIHGNREYFSGDALKQDLLVHQDAIILNY 258
Cdd:cd10320  150 PPPGTALEGKE-VQDDTFPLPDGEYDSKYYYSGYNRDNKVHGVYGDGVGAWMIMPSREYSSGGPLKQDLTVHGGPILLNY 228

                        250       260       270
                 ....*....|....*....|....*....|...
gi 746271081 259 MTGSHFGTPDMVAPPGWKKFYGPWLLYINQGDT 291
Cdd:cd10320  229 FNSGHYGGKDLNATEGWRKLFGPYLLYFNSGGA 261
RGL4_C cd10317
C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 419-573 8.14e-46

C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.


Pssm-ID: 199905  Cd Length: 161  Bit Score: 158.59  E-value: 8.14e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 419 WAIGQANRQASEFRFGNEARNT---RWQHEVPANLTFDIGRSDYQRDWYYAQTKPGKWDIRFALQPE--KKTYFLNIALA 493
Cdd:cd10317    1 WQIGTPDRTAAEFRNGDLLPNYhpsDWRLAPPGDLTYTVGSSDSDFDWYYAQSVNGPWTIRFDLTAVqaTGGATLRIALA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 494 AASNSGmseptMPQLAVAVNGTTLETLTYAND-KTIYRGALQsGRYHIARIPVSSRFLKNGNNTITLQLKGGS-----VM 567
Cdd:cd10317   81 GASAGG-----RPQVRVNDNGPLLPTAPTGNDsRGIYRGAYR-GNYHLYEFDIPASLLVAGTNTITLTVVSGSslspgVM 154


                 ....*.
gi 746271081 568 YDVVTL 573
Cdd:cd10317  155 YDAIRL 160
CBM-like pfam14683
Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase ...
 417-573 4.10e-26

Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll beta-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion.


Pssm-ID: 464260  Cd Length: 158  Bit Score: 104.59  E-value: 4.10e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081  417 VVWAIGQANRQASEFRFGNEARNTRWQHevPA-NLTFDIGRSDYqRDWYYAQTKPGKWDIRFAL--QPEKKTYFLNIALA 493
Cdd:pfam14683   1 TLWQIGDPDRTAAGFLNADPNYKNYRMH--PSdDLTYTVGTSDY-SDWFFAQVNRGTWTIKFTLdsVQAAGAATLRIALA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081  494 AASNSGmseptmpQLAVAVNGTTLETL---TYANDKTIYRGALQSGRYHIARIPVSSRFLKNGNNTITL-QLKGGS---- 565
Cdd:pfam14683  78 GAFAGG-------RLQVRVNGWTGNLPaapTIGDSRGITRGGIYRGLYRLYEFDIPASLLVAGENTITLtVIRFLSpfrg 150


                  ....*...
gi 746271081  566 VMYDVVTL 573
Cdd:pfam14683 151 VMYDYIRL 158
RGL4_M cd10316
Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 322-403 2.73e-18

Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle domain represented by this model and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.


Pssm-ID: 199904  Cd Length: 92  Bit Score: 79.99  E-value: 2.73e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081 322 ERTQVSGRV-----ASQQSVTVVLSSSLDEPFDVQTRGYSYQATTDTQGNFAIPHVRPGNYHLAVYANSGtqPGIVAEQT 396
Cdd:cd10316    1 GRGTVSGRLllpdgASAAIAVVGLANPGEQGSQFETKGYQYWTEADSDGRFTIPNVRPGTYRLTAYADGI--FGYVAQDT 78


                 ....*..
gi 746271081 397 LSVSGDK 403
Cdd:cd10316   79 VTVTAGG 85
fn3_3 pfam14686
Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase ...
 351-400 3.39e-08

Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits.


Pssm-ID: 464261  Cd Length: 74  Bit Score: 50.66  E-value: 3.39e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 746271081  351 QTRGYSYQATTDTQGNFAIPHVRPGNYHLAVYANSGtqPGIVAEQTLSVS 400
Cdd:pfam14686  21 ESKGYQYWTRADSSGSFTIPNVRPGTYRLTAYADGL--FGDYKQDDVTVS 68
Rhamnogal_lyase pfam06045
Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the ...
 14-176 1.18e-06

Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the rhamnogalacturonan I (RG-I) backbone of pectin. This family contains mainly members from plants, but also contains the plant pathogen Erwinia chrysanthemi.


Pssm-ID: 283658  Cd Length: 211  Bit Score: 49.48  E-value: 1.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081   14 APYSYSAQDNAVSLSVSGLNTVLDNGLLKVAFGE-DGsavsMVTGGK-NIVTNLSgAARDPSKTRsAYLDYYINDAHAKG 91
Cdd:pfam06045   5 PATSPAGGQAGVSLKVQLRYVVVDNGIVEVTFSNpDG----LVTGIKyNGVDNLL-EILNKIDNR-GYWDLVWSKPGERT 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081   92 VKD--FVPERVEVLRNDREMAHVAYIDDRDGLLR-------LEYHLIMRRGVSGLYSYVVAEN-SGNQDVKVSELRNVYR 161
Cdd:pfam06045  79 GKTdvIKGTKFEIVYQNEEQIEISFSRTWDPSLRgsavplnVDKRFIIRRGVSGFYMYAILEHlEGWPDFDLDQTRIVFK 158

                         170
                  ....*....|....*.
gi 746271081  162 FDPARLDHL-YNGDRQ 176
Cdd:pfam06045 159 LRKDKFDYMaIADNRQ 174
CarboxypepD_reg pfam13620
Carboxypeptidase regulatory-like domain;
325-405 8.66e-05

Carboxypeptidase regulatory-like domain;


Pssm-ID: 433354 [Multi-domain]  Cd Length: 81  Bit Score: 41.11  E-value: 8.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746271081  325 QVSGRVASQQS-----VTVVLSSsldepfdvQTRGYSYQATTDTQGNFAIPHVRPGNYHLAVYAnSGTQPGIVAEQTLSV 399
Cdd:pfam13620   1 TISGTVTDPSGapvpgATVTVTN--------TDTGTVRTTTTDADGRYRFPGLPPGTYTVTVSA-PGFKTATRTGVTVTA 71


                  ....*.
gi 746271081  400 SGDKQV 405
Cdd:pfam13620  72 GQTTTL 77
 
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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