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Conserved domains on  [gi|644357970|ref|WP_025303061|]
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MULTISPECIES: D-lyxose/D-mannose family sugar isomerase [Serratia]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
cupin_YdaE cd20308
D-lyxose isomerase YdaE, cupin domain; This family includes D-lyxose isomerase (D-LI; EC 5.3.1. ...
 10-173 5.93e-91

D-lyxose isomerase YdaE, cupin domain; This family includes D-lyxose isomerase (D-LI; EC 5.3.1.15) homologous to YdaE from the sigma B regulon of Bacillus subtilis, a protein with an active site that is highly similar to the E. coli O157 z5688 D-lyxose isomerase. YdaE may have a synergistic role with ydaD, an NAD(P)-dependent alcohol dehydrogenase, in the adaptation to environment stresses; YdaD may be active against the ketose sugar produced by YdaE and function in providing resistance to oxidative stress through the production of reducing equivalents in the form of NAD(P)H. YdaE forms a cupin-type beta-barrel, with two alpha helices at the N-terminus. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


:

Pssm-ID: 380442  Cd Length: 160  Bit Score: 262.53  E-value: 5.93e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  10 ATLEYLREADIVLTEEEQQRIEIATFGLADYPVSGLQLLTYVNSPRYCAKELVLFPGQTCPEHLHPPFAGTPGKQETFRC 89
Cdd:cd20308    3 RALEMFEKAGIPLTEEEKESIEVADFGLGDLETEGLQILTYVNTERYCAKELVLLPNQTCPEHRHPPVGGYPGKEETFRV 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  90 RWGEVFLFVDDENlTLNdaggePVCRVPEGAEPWYTCNRYILLRPGEQYTIAPNTRHWFQAGKRGAVVSEFSSESRDELD 169
Cdd:cd20308   83 RWGTVYLYVEGEP-TPN-----PKAIPPEGKKEYYTVWHEIELKPGDQYTLPPNTKHWFQAGPEGAVVSEFSTKSRDELD 156


                 ....
gi 644357970 170 IFTD 173
Cdd:cd20308  157 IFTD 160
 
Name Accession Description Interval E-value
cupin_YdaE cd20308
D-lyxose isomerase YdaE, cupin domain; This family includes D-lyxose isomerase (D-LI; EC 5.3.1. ...
 10-173 5.93e-91

D-lyxose isomerase YdaE, cupin domain; This family includes D-lyxose isomerase (D-LI; EC 5.3.1.15) homologous to YdaE from the sigma B regulon of Bacillus subtilis, a protein with an active site that is highly similar to the E. coli O157 z5688 D-lyxose isomerase. YdaE may have a synergistic role with ydaD, an NAD(P)-dependent alcohol dehydrogenase, in the adaptation to environment stresses; YdaD may be active against the ketose sugar produced by YdaE and function in providing resistance to oxidative stress through the production of reducing equivalents in the form of NAD(P)H. YdaE forms a cupin-type beta-barrel, with two alpha helices at the N-terminus. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380442  Cd Length: 160  Bit Score: 262.53  E-value: 5.93e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  10 ATLEYLREADIVLTEEEQQRIEIATFGLADYPVSGLQLLTYVNSPRYCAKELVLFPGQTCPEHLHPPFAGTPGKQETFRC 89
Cdd:cd20308    3 RALEMFEKAGIPLTEEEKESIEVADFGLGDLETEGLQILTYVNTERYCAKELVLLPNQTCPEHRHPPVGGYPGKEETFRV 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  90 RWGEVFLFVDDENlTLNdaggePVCRVPEGAEPWYTCNRYILLRPGEQYTIAPNTRHWFQAGKRGAVVSEFSSESRDELD 169
Cdd:cd20308   83 RWGTVYLYVEGEP-TPN-----PKAIPPEGKKEYYTVWHEIELKPGDQYTLPPNTKHWFQAGPEGAVVSEFSTKSRDELD 156


                 ....
gi 644357970 170 IFTD 173
Cdd:cd20308  157 IFTD 160
YdaE COG3822
D-lyxose ketol-isomerase [Carbohydrate transport and metabolism];
1-184 3.12e-57

D-lyxose ketol-isomerase [Carbohydrate transport and metabolism];


Pssm-ID: 443034  Cd Length: 224  Bit Score: 179.31  E-value: 3.12e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970   1 MNKQQ--RAIAATLEYLREADIVLTE--------------------EEQQRIEIATFGLADYPVSGLQLLTYVNSP---- 54
Cdd:COG3822    1 MKRSEinRIIREAEAFFEEHGIVLPPfaywspdewkardaeadeirDEKLGWDVTDFGLGDFDRTGLTLFTLRNGSleda 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  55 ----RYCAKELVLFPGQTCPEHLHPPfagtpgKQETFRCRWGE---VFLFVDDENLTLNDAggePVCRVPEGAEPWYTCN 127
Cdd:COG3822   81 gygkPYAEKLMIVREGQTTPMHFHWP------KMEDIINRGGGtlvLELYNSDPDGTIDTS---PVTVVVDGVERTYTAG 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 644357970 128 RYILLRPGEQYTIAPNTRHWFQAGKRGAVVSEFSSESRDELD-IFTDPrINRLAGVNH 184
Cdd:COG3822  152 EELRLAPGESVTLPPGTYHWFWAEGGDVLIGEVSTVNDDLTDnIFLDP-IGRFPEIEE 208
Lyx_isomer pfam07385
D-lyxose isomerase; Members of this family of sugar isomerases belong to the cupin superfamily. ...
 32-174 6.89e-03

D-lyxose isomerase; Members of this family of sugar isomerases belong to the cupin superfamily. The enzyme from Cohnella laevoribosii has been shown to be specific for D-lyxose, L-ribose, and D-mannose. E. coli sugar isomerase (EcSI) has been structurally and functionally characterized and shows a preference for D-lyxose and D-mannose.


Pssm-ID: 429437  Cd Length: 223  Bit Score: 35.99  E-value: 6.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970   32 IATFGLADYPVSGLQLLTYVN-SPR-------YCAKELVLFPGQTCPEHLHPpfagtpGKQETFRCRWGE---VFLFVDD 100
Cdd:pfam07385  54 ITDFGQGDFDKLGLTLFTLRNgNLAdlkygkpYAEKIMIVREGQITPMHFHW------KKMEDIINRGGGnlvIELYNSD 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  101 ENLTLNDAGGEPVC-----RVPEGAEpwytcnryILLRPGEQYTIAPNTRHWFQAGKRGAVV--SEFSSESRDELD-IFT 172
Cdd:pfam07385 128 PDGSLADSDVTVVIdgirrTVPAGGK--------LRLSPGESITLTPGLYHSFWAEKGGGDVliGEVSMVNDDNTDnRFL 199


                  ..
gi 644357970  173 DP 174
Cdd:pfam07385 200 EP 201
 
Name Accession Description Interval E-value
cupin_YdaE cd20308
D-lyxose isomerase YdaE, cupin domain; This family includes D-lyxose isomerase (D-LI; EC 5.3.1. ...
 10-173 5.93e-91

D-lyxose isomerase YdaE, cupin domain; This family includes D-lyxose isomerase (D-LI; EC 5.3.1.15) homologous to YdaE from the sigma B regulon of Bacillus subtilis, a protein with an active site that is highly similar to the E. coli O157 z5688 D-lyxose isomerase. YdaE may have a synergistic role with ydaD, an NAD(P)-dependent alcohol dehydrogenase, in the adaptation to environment stresses; YdaD may be active against the ketose sugar produced by YdaE and function in providing resistance to oxidative stress through the production of reducing equivalents in the form of NAD(P)H. YdaE forms a cupin-type beta-barrel, with two alpha helices at the N-terminus. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380442  Cd Length: 160  Bit Score: 262.53  E-value: 5.93e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  10 ATLEYLREADIVLTEEEQQRIEIATFGLADYPVSGLQLLTYVNSPRYCAKELVLFPGQTCPEHLHPPFAGTPGKQETFRC 89
Cdd:cd20308    3 RALEMFEKAGIPLTEEEKESIEVADFGLGDLETEGLQILTYVNTERYCAKELVLLPNQTCPEHRHPPVGGYPGKEETFRV 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  90 RWGEVFLFVDDENlTLNdaggePVCRVPEGAEPWYTCNRYILLRPGEQYTIAPNTRHWFQAGKRGAVVSEFSSESRDELD 169
Cdd:cd20308   83 RWGTVYLYVEGEP-TPN-----PKAIPPEGKKEYYTVWHEIELKPGDQYTLPPNTKHWFQAGPEGAVVSEFSTKSRDELD 156


                 ....
gi 644357970 170 IFTD 173
Cdd:cd20308  157 IFTD 160
YdaE COG3822
D-lyxose ketol-isomerase [Carbohydrate transport and metabolism];
1-184 3.12e-57

D-lyxose ketol-isomerase [Carbohydrate transport and metabolism];


Pssm-ID: 443034  Cd Length: 224  Bit Score: 179.31  E-value: 3.12e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970   1 MNKQQ--RAIAATLEYLREADIVLTE--------------------EEQQRIEIATFGLADYPVSGLQLLTYVNSP---- 54
Cdd:COG3822    1 MKRSEinRIIREAEAFFEEHGIVLPPfaywspdewkardaeadeirDEKLGWDVTDFGLGDFDRTGLTLFTLRNGSleda 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  55 ----RYCAKELVLFPGQTCPEHLHPPfagtpgKQETFRCRWGE---VFLFVDDENLTLNDAggePVCRVPEGAEPWYTCN 127
Cdd:COG3822   81 gygkPYAEKLMIVREGQTTPMHFHWP------KMEDIINRGGGtlvLELYNSDPDGTIDTS---PVTVVVDGVERTYTAG 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 644357970 128 RYILLRPGEQYTIAPNTRHWFQAGKRGAVVSEFSSESRDELD-IFTDPrINRLAGVNH 184
Cdd:COG3822  152 EELRLAPGESVTLPPGTYHWFWAEGGDVLIGEVSTVNDDLTDnIFLDP-IGRFPEIEE 208
cupin_D-LI-like cd06998
sugar isomerase such as lyxose isomerase, cupin domain; This family includes D-lyxose ...
 59-162 1.02e-25

sugar isomerase such as lyxose isomerase, cupin domain; This family includes D-lyxose isomerase (D-LI; EC 5.3.1.15) homologous to YdaE from the sigma B regulon of Bacillus subtilis and to pathogenic Escherichia coli O157 z5688 D-lyxose isomerase (EcSI or Z5688), both having highly similar active sites. YdaE may have a synergistic role with ydaD, an NAD(P)-dependent alcohol dehydrogenase, in the adaptation to environment stresses, while EcSI has D-lyxose/D-mannose activity. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380402  Cd Length: 100  Bit Score: 95.00  E-value: 1.02e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  59 KELVLFPGQTCPEHLHPPfagtpgKQETFRCRWGEVFLFVddENLTLNDAGGEPVCRVPEGAE-PWYTCNRYILLRPGEQ 137
Cdd:cd06998    2 KLMIVHPGQFCPPHHHGR------KTESYEVRLGEMEVFY--SPTPSAESGVELLNALPKGRErSYETLTSYVRLRPGPK 73

                         90       100
                 ....*....|....*....|....*..
gi 644357970 138 YTIAPNTRHWFQAGK--RGAVVSEFSS 162
Cdd:cd06998   74 FVMPPKHLHAFRAPPdsVPLVVREVSS 100
cupin_EcSI cd20309
Escherichia coli sugar isomerase (EcSI), cupin domain; This family includes a sugar isomerase ...
 35-157 1.39e-05

Escherichia coli sugar isomerase (EcSI), cupin domain; This family includes a sugar isomerase homologous to pathogenic Escherichia coli O157 z5688 D-lyxose isomerase (EcSI or Z5688) which has an active site highly similar to YdaE from the sigma B regulon of Bacillus subtilis. Extensive substrate screening has revealed that EcSI is capable of acting on D-lyxose and D-mannose. Studies show that overexpression of EcSI enables cell growth on D-lyxose as the sole carbon source. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380443  Cd Length: 199  Bit Score: 43.71  E-value: 1.39e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  35 FGLADYPVSGLQLLTYVNSPR--------YCAKELVLFPGQTCPEHLHppfagtPGKQETFRCRWG---EVFLFVDDENL 103
Cdd:cd20309   56 FGSGDFDKVGLVLFTLRNGNLkdpkygkpYAEKILIVREGQVTPMHFH------WKKMEDIINRGGgnlVIRLYNSDPDG 129

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 644357970 104 TLNDaggEPV--------CRVPEGAEpwytcnryILLRPGEQYTIAPNTRHWFQAGKRGAVV 157
Cdd:cd20309  130 QLAD---TDVtvsvdgikRTVPAGEV--------IRLKPGESITLPPGLYHSFWAEGGTGDV 180
STKc_ULK3 cd14121
Catalytic domain of the Serine/Threonine kinase, Unc-51-like kinase 3; STKs catalyze the ...
 6-63 1.50e-03

Catalytic domain of the Serine/Threonine kinase, Unc-51-like kinase 3; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The ATG1/ULK complex is conserved from yeast to humans and it plays a critical role in the initiation of autophagy, the intracellular system that leads to the lysosomal degradation of cellular components and their recycling into basic metabolic units. ULK3 mRNA is up-regulated in fibroblasts after Ras-induced senescence, and its overexpression induces both autophagy and senescence in a fibroblast cell line. ULK3, through its kinase activity, positively regulates Gli proteins, mediators of the Sonic hedgehog (Shh) signaling pathway that is implicated in tissue homeostasis maintenance and neurogenesis. It is inhibited by binding to Suppressor of Fused (Sufu). The ULK3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.


Pssm-ID: 271023 [Multi-domain]  Cd Length: 252  Bit Score: 38.04  E-value: 1.50e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 644357970   6 RAIAATLEYLREADIV----------LTEEEQQRIEIATFGLADYPVSGLQLLTYVNSPRYCAKELVL 63
Cdd:cd14121  102 QQLASALQFLREHNIShmdlkpqnllLSSRYNPVLKLADFGFAQHLKPNDEAHSLRGSPLYMAPEMIL 169
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 60-157 1.84e-03

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 35.54  E-value: 1.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  60 ELVLFPGQTCPEHLHPpfagtpGKQETFRCRWGEVFLFVDDEnltlndaggepvcrvpegaepwytcnRYILLRPGEQYT 139
Cdd:cd02208    3 VVTLPPGTSSPPHWHP------EQDEIFYVLSGEGELTLDDG--------------------------ETVELKAGDIVL 50

                         90
                 ....*....|....*...
gi 644357970 140 IAPNTRHWFQAGKRGAVV 157
Cdd:cd02208   51 IPPGVPHSFVNTSDEPAV 68
Lyx_isomer pfam07385
D-lyxose isomerase; Members of this family of sugar isomerases belong to the cupin superfamily. ...
 32-174 6.89e-03

D-lyxose isomerase; Members of this family of sugar isomerases belong to the cupin superfamily. The enzyme from Cohnella laevoribosii has been shown to be specific for D-lyxose, L-ribose, and D-mannose. E. coli sugar isomerase (EcSI) has been structurally and functionally characterized and shows a preference for D-lyxose and D-mannose.


Pssm-ID: 429437  Cd Length: 223  Bit Score: 35.99  E-value: 6.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970   32 IATFGLADYPVSGLQLLTYVN-SPR-------YCAKELVLFPGQTCPEHLHPpfagtpGKQETFRCRWGE---VFLFVDD 100
Cdd:pfam07385  54 ITDFGQGDFDKLGLTLFTLRNgNLAdlkygkpYAEKIMIVREGQITPMHFHW------KKMEDIINRGGGnlvIELYNSD 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644357970  101 ENLTLNDAGGEPVC-----RVPEGAEpwytcnryILLRPGEQYTIAPNTRHWFQAGKRGAVV--SEFSSESRDELD-IFT 172
Cdd:pfam07385 128 PDGSLADSDVTVVIdgirrTVPAGGK--------LRLSPGESITLTPGLYHSFWAEKGGGDVliGEVSMVNDDNTDnRFL 199


                  ..
gi 644357970  173 DP 174
Cdd:pfam07385 200 EP 201
 
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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