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Conserved domains on  [gi|334184375|ref|NP_001189578|]
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Rhamnogalacturonate lyase family protein [Arabidopsis thaliana]

Protein Classification

peptidase associated/transthyretin-like domain-containing protein; TonB-dependent receptor( domain architecture ID 10179217)

peptidase associated/transthyretin-like domain-containing protein| TonB dependent receptor having a carboxypeptidase regulatory-like domain, may act as a channel to allow import of extracellular nutrients, such as iron-siderophore complexes or non-Fe compounds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CBM-like pfam14683
Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase ...
 403-591 3.94e-63

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: 204.74  E-value: 3.94e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375  403 TLWEIGVPDRTAGEFYIPDPYPtlmnKLYVNplqdrfrqyglwdryadlYPQNDLVYTIGVSDYrSDWFFAHVARNvgnd 482
Cdd:pfam14683   1 TLWQIGDPDRTAAGFLNADPNY----KNYRM------------------HPSDDLTYTVGTSDY-SDWFFAQVNRG---- 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375  483 tyqptTWQIIFNLKNVNRIGRYTLRIALASA-ADSELQIRINDPKSDaIFTTGFIGKDNAIARHGIH-GLYRLYSIDVAG 560
Cdd:pfam14683  54 -----TWTIKFTLDSVQAAGAATLRIALAGAfAGGRLQVRVNGWTGN-LPAAPTIGDSRGITRGGIYrGLYRLYEFDIPA 127

                         170       180       190
                  ....*....|....*....|....*....|.
gi 334184375  561 NLLSVGDNTIFLTQTRSRTPFQGIMYDYIRL 591
Cdd:pfam14683 128 SLLVAGENTITLTVIRFLSPFRGVMYDYIRL 158
RGL4_N cd10320
N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 61-261 8.25e-56

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: 189.52  E-value: 8.25e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375  61 TVVVDNGIVQVTFSNPEGLITGIKYHGiDNVLDDKIDDRGYWDVVWYEPEKKQKT------------------------- 115
Cdd:cd10320    9 AVVVDNGLLGLVFSVDGGIVTGILYGG-LLENDNGKGDRGYLDLVSIVYGGTEQTpgklshiesglgatvsatqsgdyiq 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 116 ------------------------------------------------DKFDFMAISDDRqrsmpsmADRENSKSLAYKE 147
Cdd:cd10320   88 isfsrtfetelhyvvrkgepgiymytvathpapepslgelrtvfrlnpDLFPNGAISDDR-------GDPPPGTALEGKE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 148 AVLLTNPSNPmfkGEVDDKYMYSMEDKDNNVHGWISSDppVGFWMITPSDEFRLGGPIKQDLTSHAGPITLSMFTSTHYA 227
Cdd:cd10320  161 VQDDTFPLPD---GEYDSKYYYSGYNRDNKVHGVYGDG--VGAWMIMPSREYSSGGPLKQDLTVHGGPILLNYFNSGHYG 235

                        250       260       270
                 ....*....|....*....|....*....|....
gi 334184375 228 GKemrmDYRNGEPWKKVFGPVLAYLNSVSPKDST 261
Cdd:cd10320  236 GK----DLNATEGWRKLFGPYLLYFNSGGAPSTL 265
RGL4_M cd10316
Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 294-393 3.48e-31

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: 116.58  E-value: 3.48e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 294 QRGTLEGQFLIKDsyvsrlKIYGKFAFVGLAPIGEAGSwQTESKGYQFWTKADRRGRFIIENVRAGNYSLYAWGSGfIGD 373
Cdd:cd10316    1 GRGTVSGRLLLPD------GASAAIAVVGLANPGEQGS-QFETKGYQYWTEADSDGRFTIPNVRPGTYRLTAYADG-IFG 72

                         90       100
                 ....*....|....*....|
gi 334184375 374 YKYEQNITITPGSEMNVGPL 393
Cdd:cd10316   73 YVAQDTVTVTAGGTTALGDL 92
 
Name Accession Description Interval E-value
CBM-like pfam14683
Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase ...
 403-591 3.94e-63

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: 204.74  E-value: 3.94e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375  403 TLWEIGVPDRTAGEFYIPDPYPtlmnKLYVNplqdrfrqyglwdryadlYPQNDLVYTIGVSDYrSDWFFAHVARNvgnd 482
Cdd:pfam14683   1 TLWQIGDPDRTAAGFLNADPNY----KNYRM------------------HPSDDLTYTVGTSDY-SDWFFAQVNRG---- 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375  483 tyqptTWQIIFNLKNVNRIGRYTLRIALASA-ADSELQIRINDPKSDaIFTTGFIGKDNAIARHGIH-GLYRLYSIDVAG 560
Cdd:pfam14683  54 -----TWTIKFTLDSVQAAGAATLRIALAGAfAGGRLQVRVNGWTGN-LPAAPTIGDSRGITRGGIYrGLYRLYEFDIPA 127

                         170       180       190
                  ....*....|....*....|....*....|.
gi 334184375  561 NLLSVGDNTIFLTQTRSRTPFQGIMYDYIRL 591
Cdd:pfam14683 128 SLLVAGENTITLTVIRFLSPFRGVMYDYIRL 158
RGL4_N cd10320
N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 61-261 8.25e-56

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: 189.52  E-value: 8.25e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375  61 TVVVDNGIVQVTFSNPEGLITGIKYHGiDNVLDDKIDDRGYWDVVWYEPEKKQKT------------------------- 115
Cdd:cd10320    9 AVVVDNGLLGLVFSVDGGIVTGILYGG-LLENDNGKGDRGYLDLVSIVYGGTEQTpgklshiesglgatvsatqsgdyiq 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 116 ------------------------------------------------DKFDFMAISDDRqrsmpsmADRENSKSLAYKE 147
Cdd:cd10320   88 isfsrtfetelhyvvrkgepgiymytvathpapepslgelrtvfrlnpDLFPNGAISDDR-------GDPPPGTALEGKE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 148 AVLLTNPSNPmfkGEVDDKYMYSMEDKDNNVHGWISSDppVGFWMITPSDEFRLGGPIKQDLTSHAGPITLSMFTSTHYA 227
Cdd:cd10320  161 VQDDTFPLPD---GEYDSKYYYSGYNRDNKVHGVYGDG--VGAWMIMPSREYSSGGPLKQDLTVHGGPILLNYFNSGHYG 235

                        250       260       270
                 ....*....|....*....|....*....|....
gi 334184375 228 GKemrmDYRNGEPWKKVFGPVLAYLNSVSPKDST 261
Cdd:cd10320  236 GK----DLNATEGWRKLFGPYLLYFNSGGAPSTL 265
RGL4_C cd10317
C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 405-592 2.15e-53

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: 179.39  E-value: 2.15e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 405 WEIGVPDRTAGEFYIPDPYPTLMNKlyvnplqdrfrqyglwdrYADLYPQNDLVYTIGVSDYRSDWFFAHVarnvgndty 484
Cdd:cd10317    1 WQIGTPDRTAAEFRNGDLLPNYHPS------------------DWRLAPPGDLTYTVGSSDSDFDWYYAQS--------- 53

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 485 QPTTWQIIFNLKNVNRIGRYTLRIALASA-ADSELQIRINDpkSDAIFTTGFIGKD-NAIARHGIHGLYRLYSIDVAGNL 562
Cdd:cd10317   54 VNGPWTIRFDLTAVQATGGATLRIALAGAsAGGRPQVRVND--NGPLLPTAPTGNDsRGIYRGAYRGNYHLYEFDIPASL 131

                        170       180       190
                 ....*....|....*....|....*....|
gi 334184375 563 LSVGDNTIFLTQTRSRTPFQGIMYDYIRLE 592
Cdd:cd10317  132 LVAGTNTITLTVVSGSSLSPGVMYDAIRLE 161
Rhamnogal_lyase pfam06045
Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the ...
 39-163 1.09e-49

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: 171.20  E-value: 1.09e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375   39 NITKPGQNIPALTVQLRRVghdtvVVDNGIVQVTFSNPEGLITGIKYHGIDNVLD--DKIDDRGYWDVVWYEPEKKQ--- 113
Cdd:pfam06045   7 TSPAGGQAGVSLKVQLRYV-----VVDNGIVEVTFSNPDGLVTGIKYNGVDNLLEilNKIDNRGYWDLVWSKPGERTgkt 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375  114 ------------------------------------------------------------------------------KT 115
Cdd:pfam06045  82 dvikgtkfeivyqneeqieisfsrtwdpslrgsavplnvdkrfiirrgvsgfymyailehlegwpdfdldqtrivfklRK 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 334184375  116 DKFDFMAISDDRQRSMPSMADRENSKS--LAYKEAVLLTNPSNPMFKGEV 163
Cdd:pfam06045 162 DKFDYMAIADNRQRIMPMPEDRVPPRGqpLAYPEAVLLVNPINPMLKGEV 211
RGL4_M cd10316
Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 294-393 3.48e-31

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: 116.58  E-value: 3.48e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 294 QRGTLEGQFLIKDsyvsrlKIYGKFAFVGLAPIGEAGSwQTESKGYQFWTKADRRGRFIIENVRAGNYSLYAWGSGfIGD 373
Cdd:cd10316    1 GRGTVSGRLLLPD------GASAAIAVVGLANPGEQGS-QFETKGYQYWTEADSDGRFTIPNVRPGTYRLTAYADG-IFG 72

                         90       100
                 ....*....|....*....|
gi 334184375 374 YKYEQNITITPGSEMNVGPL 393
Cdd:cd10316   73 YVAQDTVTVTAGGTTALGDL 92
fn3_3 pfam14686
Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase ...
 316-386 1.72e-24

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: 96.89  E-value: 1.72e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334184375  316 GKFAFVGLA-PIGEAGSWQTESKGYQFWTKADRRGRFIIENVRAGNYSLYAWGSGFIGDYKyEQNITITPGS 386
Cdd:pfam14686   1 GRGAVSGLAvGSGDVVSWQNESKGYQYWTRADSSGSFTIPNVRPGTYRLTAYADGLFGDYK-QDDVTVSAGS 71
 
Name Accession Description Interval E-value
CBM-like pfam14683
Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase ...
 403-591 3.94e-63

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: 204.74  E-value: 3.94e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375  403 TLWEIGVPDRTAGEFYIPDPYPtlmnKLYVNplqdrfrqyglwdryadlYPQNDLVYTIGVSDYrSDWFFAHVARNvgnd 482
Cdd:pfam14683   1 TLWQIGDPDRTAAGFLNADPNY----KNYRM------------------HPSDDLTYTVGTSDY-SDWFFAQVNRG---- 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375  483 tyqptTWQIIFNLKNVNRIGRYTLRIALASA-ADSELQIRINDPKSDaIFTTGFIGKDNAIARHGIH-GLYRLYSIDVAG 560
Cdd:pfam14683  54 -----TWTIKFTLDSVQAAGAATLRIALAGAfAGGRLQVRVNGWTGN-LPAAPTIGDSRGITRGGIYrGLYRLYEFDIPA 127

                         170       180       190
                  ....*....|....*....|....*....|.
gi 334184375  561 NLLSVGDNTIFLTQTRSRTPFQGIMYDYIRL 591
Cdd:pfam14683 128 SLLVAGENTITLTVIRFLSPFRGVMYDYIRL 158
RGL4_N cd10320
N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 61-261 8.25e-56

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: 189.52  E-value: 8.25e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375  61 TVVVDNGIVQVTFSNPEGLITGIKYHGiDNVLDDKIDDRGYWDVVWYEPEKKQKT------------------------- 115
Cdd:cd10320    9 AVVVDNGLLGLVFSVDGGIVTGILYGG-LLENDNGKGDRGYLDLVSIVYGGTEQTpgklshiesglgatvsatqsgdyiq 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 116 ------------------------------------------------DKFDFMAISDDRqrsmpsmADRENSKSLAYKE 147
Cdd:cd10320   88 isfsrtfetelhyvvrkgepgiymytvathpapepslgelrtvfrlnpDLFPNGAISDDR-------GDPPPGTALEGKE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 148 AVLLTNPSNPmfkGEVDDKYMYSMEDKDNNVHGWISSDppVGFWMITPSDEFRLGGPIKQDLTSHAGPITLSMFTSTHYA 227
Cdd:cd10320  161 VQDDTFPLPD---GEYDSKYYYSGYNRDNKVHGVYGDG--VGAWMIMPSREYSSGGPLKQDLTVHGGPILLNYFNSGHYG 235

                        250       260       270
                 ....*....|....*....|....*....|....
gi 334184375 228 GKemrmDYRNGEPWKKVFGPVLAYLNSVSPKDST 261
Cdd:cd10320  236 GK----DLNATEGWRKLFGPYLLYFNSGGAPSTL 265
RGL4_C cd10317
C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 405-592 2.15e-53

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: 179.39  E-value: 2.15e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 405 WEIGVPDRTAGEFYIPDPYPTLMNKlyvnplqdrfrqyglwdrYADLYPQNDLVYTIGVSDYRSDWFFAHVarnvgndty 484
Cdd:cd10317    1 WQIGTPDRTAAEFRNGDLLPNYHPS------------------DWRLAPPGDLTYTVGSSDSDFDWYYAQS--------- 53

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 485 QPTTWQIIFNLKNVNRIGRYTLRIALASA-ADSELQIRINDpkSDAIFTTGFIGKD-NAIARHGIHGLYRLYSIDVAGNL 562
Cdd:cd10317   54 VNGPWTIRFDLTAVQATGGATLRIALAGAsAGGRPQVRVND--NGPLLPTAPTGNDsRGIYRGAYRGNYHLYEFDIPASL 131

                        170       180       190
                 ....*....|....*....|....*....|
gi 334184375 563 LSVGDNTIFLTQTRSRTPFQGIMYDYIRLE 592
Cdd:cd10317  132 LVAGTNTITLTVVSGSSLSPGVMYDAIRLE 161
Rhamnogal_lyase pfam06045
Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the ...
 39-163 1.09e-49

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: 171.20  E-value: 1.09e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375   39 NITKPGQNIPALTVQLRRVghdtvVVDNGIVQVTFSNPEGLITGIKYHGIDNVLD--DKIDDRGYWDVVWYEPEKKQ--- 113
Cdd:pfam06045   7 TSPAGGQAGVSLKVQLRYV-----VVDNGIVEVTFSNPDGLVTGIKYNGVDNLLEilNKIDNRGYWDLVWSKPGERTgkt 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375  114 ------------------------------------------------------------------------------KT 115
Cdd:pfam06045  82 dvikgtkfeivyqneeqieisfsrtwdpslrgsavplnvdkrfiirrgvsgfymyailehlegwpdfdldqtrivfklRK 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 334184375  116 DKFDFMAISDDRQRSMPSMADRENSKS--LAYKEAVLLTNPSNPMFKGEV 163
Cdd:pfam06045 162 DKFDYMAIADNRQRIMPMPEDRVPPRGqpLAYPEAVLLVNPINPMLKGEV 211
RGL4_M cd10316
Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 294-393 3.48e-31

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: 116.58  E-value: 3.48e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184375 294 QRGTLEGQFLIKDsyvsrlKIYGKFAFVGLAPIGEAGSwQTESKGYQFWTKADRRGRFIIENVRAGNYSLYAWGSGfIGD 373
Cdd:cd10316    1 GRGTVSGRLLLPD------GASAAIAVVGLANPGEQGS-QFETKGYQYWTEADSDGRFTIPNVRPGTYRLTAYADG-IFG 72

                         90       100
                 ....*....|....*....|
gi 334184375 374 YKYEQNITITPGSEMNVGPL 393
Cdd:cd10316   73 YVAQDTVTVTAGGTTALGDL 92
fn3_3 pfam14686
Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase ...
 316-386 1.72e-24

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: 96.89  E-value: 1.72e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334184375  316 GKFAFVGLA-PIGEAGSWQTESKGYQFWTKADRRGRFIIENVRAGNYSLYAWGSGFIGDYKyEQNITITPGS 386
Cdd:pfam14686   1 GRGAVSGLAvGSGDVVSWQNESKGYQYWTRADSSGSFTIPNVRPGTYRLTAYADGLFGDYK-QDDVTVSAGS 71
CarboxypepD_reg pfam13620
Carboxypeptidase regulatory-like domain;
333-390 5.41e-03

Carboxypeptidase regulatory-like domain;


Pssm-ID: 433354 [Multi-domain]  Cd Length: 81  Bit Score: 36.10  E-value: 5.41e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 334184375  333 QTESKGYQFWTKADRRGRFIIENVRAGNYSLYAWGSGFIGDYKyeQNITITPGSEMNV 390
Cdd:pfam13620  22 TNTDTGTVRTTTTDADGRYRFPGLPPGTYTVTVSAPGFKTATR--TGVTVTAGQTTTL 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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