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Conserved domains on  [gi|499272612|ref|WP_010970005|]
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LacI family DNA-binding transcriptional regulator [Sinorhizobium meliloti]

Protein Classification

LacI family DNA-binding transcriptional regulator( domain architecture ID 10105133)

LacI family DNA-binding transcriptional regulator functions as an activator or repressor by binding a specific effector ligand that either decreases (induction) or increases DNA-binding affinity (co-repression)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP1_sugar_binding cd06307
periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic ...
 59-327 1.58e-77

periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.


:

Pssm-ID: 380530 [Multi-domain]  Cd Length: 275  Bit Score: 238.23  E-value: 1.58e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612  59 RFEVLLGRRQMPLCARLSDAIVRFGRPFKDI-VAIERTFVDETRPELVAEAILKSRG--NALVVYGQDHELIIDAIAEVT 135
Cdd:cd06307    1 RFGFLLPSPENPFYELLRRAIEAAAAALRDRrVRLRIHFVDSLDPEALAAALRRLAAgcDGVALVAPDHPLVRAAIDELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 136 SAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAKMAG--EGSIVLLCSSLYYRAEAERISGCRDGMADHADRQSV 213
Cdd:cd06307   81 ARGIPVVTLVSDLPGSRRLAYVGIDNRAAGRTAAWLMGRFLGrrPGKVLVILGSHRFRGHEEREAGFRSVLRERFPDLTV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 214 SALVELDENDPFAGEELSKALEA-GKVTGIYNAGVSHAVLGRALAAHSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQN 292
Cdd:cd06307  161 LEVLEGLDDDELAYELLRELLARhPDLVGIYNAGGGNEGIARALREAGRARRVVFIGHELTPETRRLLRDGTIDAVIDQD 240

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 499272612 293 PDLQVRKALLILASRFGLPGGVAESPVVPFTVLVR 327
Cdd:cd06307  241 PELQARRAIEVLLAHLGGKGPAPPQPPIPIEIITR 275
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 7-46 8.75e-14

Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repressor binds its ligand, it undergoes a conformational change which affects the DNA-binding affinity of the repressor. In Escherichia coli, LacI represses transcription by binding with high affinity to the lac operon at a specific operator DNA sequence until it interacts with the physiological inducer allolactose or a non-degradable analog IPTG (isopropyl-beta-D-thiogalactopyranoside). Induction of the repressor lowers its affinity for the operator sequence, thereby allowing transcription of the lac operon structural genes (lacZ, lacY, and LacA). The lac repressor occurs as a tetramer made up of two functional dimers. Thus, two DNA binding domains of a dimer are required to bind the inverted repeat sequences of the operator DNA binding sites.


:

Pssm-ID: 143331 [Multi-domain]  Cd Length: 52  Bit Score: 64.74  E-value: 8.75e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 499272612   7 DVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGF 46
Cdd:cd01392    2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGY 41
 
Name Accession Description Interval E-value
PBP1_sugar_binding cd06307
periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic ...
 59-327 1.58e-77

periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.


Pssm-ID: 380530 [Multi-domain]  Cd Length: 275  Bit Score: 238.23  E-value: 1.58e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612  59 RFEVLLGRRQMPLCARLSDAIVRFGRPFKDI-VAIERTFVDETRPELVAEAILKSRG--NALVVYGQDHELIIDAIAEVT 135
Cdd:cd06307    1 RFGFLLPSPENPFYELLRRAIEAAAAALRDRrVRLRIHFVDSLDPEALAAALRRLAAgcDGVALVAPDHPLVRAAIDELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 136 SAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAKMAG--EGSIVLLCSSLYYRAEAERISGCRDGMADHADRQSV 213
Cdd:cd06307   81 ARGIPVVTLVSDLPGSRRLAYVGIDNRAAGRTAAWLMGRFLGrrPGKVLVILGSHRFRGHEEREAGFRSVLRERFPDLTV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 214 SALVELDENDPFAGEELSKALEA-GKVTGIYNAGVSHAVLGRALAAHSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQN 292
Cdd:cd06307  161 LEVLEGLDDDELAYELLRELLARhPDLVGIYNAGGGNEGIARALREAGRARRVVFIGHELTPETRRLLRDGTIDAVIDQD 240

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 499272612 293 PDLQVRKALLILASRFGLPGGVAESPVVPFTVLVR 327
Cdd:cd06307  241 PELQARRAIEVLLAHLGGKGPAPPQPPIPIEIITR 275
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
 107-305 6.82e-32

ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH domain [Carbohydrate transport and metabolism];


Pssm-ID: 441483 [Multi-domain]  Cd Length: 307  Bit Score: 120.80  E-value: 6.82e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 107 EAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVLLC 185
Cdd:COG1879   83 EDLIAQGVDAIIVSPVDPDALAPALKKAKAAGIPVVTVDSDVDGSDRVAYVGSDNYAAGRLAAEYLAKaLGGKGKVAILT 162

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 186 SSLYYRAEAERISGCRDGMADHADRQsVSALVELDENDPFAGEELSKALEA-GKVTGIYNAGVSHAV-LGRALAAHSLGP 263
Cdd:COG1879  163 GSPGAPAANERTDGFKEALKEYPGIK-VVAEQYADWDREKALEVMEDLLQAhPDIDGIFAANDGMALgAAQALKAAGRKG 241

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 499272612 264 PPVLVGHDISPDAERMLQEGVMTLVIDQNPDLQVRKALLILA 305
Cdd:COG1879  242 DVKVVGFDGSPEALQAIKDGTIDATVAQDPYLQGYLAVDAAL 283
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
 105-305 1.29e-24

Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic binding proteins. This domain recognizes fructose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433182 [Multi-domain]  Cd Length: 259  Bit Score: 100.46  E-value: 1.29e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612  105 VAEAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVL 183
Cdd:pfam13407  47 QIEDAIAQGVDAIIVAPVDPTALAPVLKKAKDAGIPVVTFDSDAPSSPRLAYVGFDNEAAGEAAGELLAEaLGGKGKVAI 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612  184 LCSSLYYRAEAERISGCRDGMADHADRQSVSALVELDENDPF-AGEELSKALEAGK--VTGIY--NAGVSHAVLgRALAA 258
Cdd:pfam13407 127 LSGSPGDPNANERIDGFKKVLKEKYPGIKVVAEVEGTNWDPEkAQQQMEALLTAYPnpLDGIIspNDGMAGGAA-QALEA 205

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 499272612  259 HSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQNPDLQVRKALLILA 305
Cdd:pfam13407 206 AGLAGKVVVTGFDATPEALEAIKDGTIDATVLQDPYGQGYAAVELAA 252
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 7-46 8.75e-14

Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repressor binds its ligand, it undergoes a conformational change which affects the DNA-binding affinity of the repressor. In Escherichia coli, LacI represses transcription by binding with high affinity to the lac operon at a specific operator DNA sequence until it interacts with the physiological inducer allolactose or a non-degradable analog IPTG (isopropyl-beta-D-thiogalactopyranoside). Induction of the repressor lowers its affinity for the operator sequence, thereby allowing transcription of the lac operon structural genes (lacZ, lacY, and LacA). The lac repressor occurs as a tetramer made up of two functional dimers. Thus, two DNA binding domains of a dimer are required to bind the inverted repeat sequences of the operator DNA binding sites.


Pssm-ID: 143331 [Multi-domain]  Cd Length: 52  Bit Score: 64.74  E-value: 8.75e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 499272612   7 DVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGF 46
Cdd:cd01392    2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGY 41
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
7-46 1.38e-10

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 56.44  E-value: 1.38e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 499272612     7 DVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGF 46
Cdd:smart00354   5 DVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGY 44
LacI pfam00356
Bacterial regulatory proteins, lacI family;
7-46 8.49e-10

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 53.41  E-value: 8.49e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 499272612    7 DVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGF 46
Cdd:pfam00356   4 DVARLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNY 43
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
7-127 1.32e-06

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 49.39  E-value: 1.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612   7 DVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGFDrklPTLYRQGLRFEV--LLGRRQMPlcarLSDAIvrFGR 84
Cdd:PRK10401   6 DVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYR---PNANAQALATQVsdTIGVVVMD----VSDAF--FGA 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499272612  85 PFK--DIVA--------IERTFVDETRPELVAEAILKSRGNALVVYGQ---DHELI 127
Cdd:PRK10401  77 LVKavDLVAqqhqkyvlIGNSYHEAEKERHAIEVLIRQRCNALIVHSKalsDDELA 132
PRK10014 PRK10014
DNA-binding transcriptional repressor MalI; Provisional
 2-48 6.40e-06

DNA-binding transcriptional repressor MalI; Provisional


Pssm-ID: 182193 [Multi-domain]  Cd Length: 342  Bit Score: 47.40  E-value: 6.40e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 499272612   2 KRKLIDVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGFDR 48
Cdd:PRK10014   6 KITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVR 52
 
Name Accession Description Interval E-value
PBP1_sugar_binding cd06307
periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic ...
 59-327 1.58e-77

periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.


Pssm-ID: 380530 [Multi-domain]  Cd Length: 275  Bit Score: 238.23  E-value: 1.58e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612  59 RFEVLLGRRQMPLCARLSDAIVRFGRPFKDI-VAIERTFVDETRPELVAEAILKSRG--NALVVYGQDHELIIDAIAEVT 135
Cdd:cd06307    1 RFGFLLPSPENPFYELLRRAIEAAAAALRDRrVRLRIHFVDSLDPEALAAALRRLAAgcDGVALVAPDHPLVRAAIDELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 136 SAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAKMAG--EGSIVLLCSSLYYRAEAERISGCRDGMADHADRQSV 213
Cdd:cd06307   81 ARGIPVVTLVSDLPGSRRLAYVGIDNRAAGRTAAWLMGRFLGrrPGKVLVILGSHRFRGHEEREAGFRSVLRERFPDLTV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 214 SALVELDENDPFAGEELSKALEA-GKVTGIYNAGVSHAVLGRALAAHSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQN 292
Cdd:cd06307  161 LEVLEGLDDDELAYELLRELLARhPDLVGIYNAGGGNEGIARALREAGRARRVVFIGHELTPETRRLLRDGTIDAVIDQD 240

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 499272612 293 PDLQVRKALLILASRFGLPGGVAESPVVPFTVLVR 327
Cdd:cd06307  241 PELQARRAIEVLLAHLGGKGPAPPQPPIPIEIITR 275
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
 107-305 6.82e-32

ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH domain [Carbohydrate transport and metabolism];


Pssm-ID: 441483 [Multi-domain]  Cd Length: 307  Bit Score: 120.80  E-value: 6.82e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 107 EAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVLLC 185
Cdd:COG1879   83 EDLIAQGVDAIIVSPVDPDALAPALKKAKAAGIPVVTVDSDVDGSDRVAYVGSDNYAAGRLAAEYLAKaLGGKGKVAILT 162

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 186 SSLYYRAEAERISGCRDGMADHADRQsVSALVELDENDPFAGEELSKALEA-GKVTGIYNAGVSHAV-LGRALAAHSLGP 263
Cdd:COG1879  163 GSPGAPAANERTDGFKEALKEYPGIK-VVAEQYADWDREKALEVMEDLLQAhPDIDGIFAANDGMALgAAQALKAAGRKG 241

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 499272612 264 PPVLVGHDISPDAERMLQEGVMTLVIDQNPDLQVRKALLILA 305
Cdd:COG1879  242 DVKVVGFDGSPEALQAIKDGTIDATVAQDPYLQGYLAVDAAL 283
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
 105-305 1.29e-24

Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic binding proteins. This domain recognizes fructose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433182 [Multi-domain]  Cd Length: 259  Bit Score: 100.46  E-value: 1.29e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612  105 VAEAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVL 183
Cdd:pfam13407  47 QIEDAIAQGVDAIIVAPVDPTALAPVLKKAKDAGIPVVTFDSDAPSSPRLAYVGFDNEAAGEAAGELLAEaLGGKGKVAI 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612  184 LCSSLYYRAEAERISGCRDGMADHADRQSVSALVELDENDPF-AGEELSKALEAGK--VTGIY--NAGVSHAVLgRALAA 258
Cdd:pfam13407 127 LSGSPGDPNANERIDGFKKVLKEKYPGIKVVAEVEGTNWDPEkAQQQMEALLTAYPnpLDGIIspNDGMAGGAA-QALEA 205

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 499272612  259 HSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQNPDLQVRKALLILA 305
Cdd:pfam13407 206 AGLAGKVVVTGFDATPEALEAIKDGTIDATVLQDPYGQGYAAVELAA 252
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
5-329 4.27e-23

DNA-binding transcriptional regulator, LacI/PurR family [Transcription];


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 97.58  E-value: 4.27e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612   5 LIDVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGFdrkLPTLYRQGLR------FEVLLGRRQMPLCARLSDA 78
Cdd:COG1609    6 IKDVARLAGVSVATVSRVLNGPPRVSEETRERVLAAAEELGY---RPNAAARSLRtgrtrtIGVVVPDLSNPFFAELLRG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612  79 IVRFGRPFKDIVAIERTFVDETRPELVAEAILKSRGNALVVYGQDHELiiDAIAEVTSAGKPVVTIVSDVPSaPRLSYVG 158
Cdd:COG1609   83 IEEAARERGYQLLLANSDEDPEREREALRLLLSRRVDGLILAGSRLDD--ARLERLAEAGIPVVLIDRPLPD-PGVPSVG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 159 IDHYKAGRCAAFFLAKmAGEGSIVLLCSSLYYRAEAERISGCRDGMADHaDRQSVSALVELDENDPFAGEELSKAL--EA 236
Cdd:COG1609  160 VDNRAGARLATEHLIE-LGHRRIAFIGGPADSSSARERLAGYREALAEA-GLPPDPELVVEGDFSAESGYEAARRLlaRG 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 237 GKVTGI--YNAGVSHAVLgRALAAHSLGPPP--VLVGHDISPDAeRMLQEGVMTlvIDQNPDLQVRKALLILASRFGLPG 312
Cdd:COG1609  238 PRPTAIfcANDLMALGAL-RALREAGLRVPEdvSVVGFDDIPLA-RYLTPPLTT--VRQPIEEMGRRAAELLLDRIEGPD 313

                        330
                 ....*....|....*..
gi 499272612 313 GVAESPVVPFTVLVRDS 329
Cdd:COG1609  314 APPERVLLPPELVVRES 330
PBP1_ABC_sugar_binding-like cd01536
periplasmic sugar-binding domain of active transport systems that are members of the type 1 ...
 107-301 4.16e-19

periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily; Periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2) receptors such as LsrB and LuxP which are highly homologous to periplasmic pentose/hexose sugar-binding proteins.


Pssm-ID: 380478 [Multi-domain]  Cd Length: 268  Bit Score: 85.31  E-value: 4.16e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 107 EAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVP-SAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVLL 184
Cdd:cd01536   49 EDLIAQGVDAIIIAPVDSEALVPAVKKANAAGIPVVAVDTDIDgGGDVVAFVGTDNYEAGKLAGEYLAEaLGGKGKVAIL 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 185 CSSLYYRAEAERISGCRDGMADHADRQSVSALveldendpFAGEELSKALEA--------GKVTGIYNAGVSHAvLG--R 254
Cdd:cd01536  129 EGPPGSSTAIDRTKGFKEALKKYPDIEIVAEQ--------PANWDRAKALTVtenllqanPDIDAVFAANDDMA-LGaaE 199

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 499272612 255 ALAAHSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQNPDLQVRKAL 301
Cdd:cd01536  200 ALKAAGRTGDIKIVGVDGTPEALKAIKDGELDATVAQDPYLQGYLAV 246
PBP1_ABC_sugar_binding-like cd20006
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 103-304 2.77e-18

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380661 [Multi-domain]  Cd Length: 274  Bit Score: 83.03  E-value: 2.77e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 103 ELVAEAIlKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAKMAGE-GSI 181
Cdd:cd20006   50 ELIEEAI-AQKPDAIVLAASDYDRLVEAVERAKKAGIPVITIDSPVNSKKADSFVATDNYEAGKKAGEKLASLLGEkGKV 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 182 VLLCSSLYYRAEAERISGCRDGMADHADRQSVSALVELDENDPfAGEELSKALEAGK-VTGI--YNAGVSHAVlGRALAA 258
Cdd:cd20006  129 AIVSFVKGSSTAIEREEGFKQALAEYPNIKIVETEYCDSDEEK-AYEITKELLSKYPdINGIvaLNEQSTLGA-ARALKE 206

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 499272612 259 HSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQNP----DLQVRKALLIL 304
Cdd:cd20006  207 LGLGGKVKVVGFDSSVEEIQLLEEGIIDALVVQNPfnmgYLSVQAAVDLL 256
PBP1_tmGBP cd06314
periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and ...
 115-293 4.47e-17

periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs; Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are members of the type 1 periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).


Pssm-ID: 380537 [Multi-domain]  Cd Length: 271  Bit Score: 79.55  E-value: 4.47e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 115 NALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVLLCSSLYYRAE 193
Cdd:cd06314   58 DGIAISPNDPEAVTPVINKAADKGIPVITFDSDAPDSKRLAYIGTDNYEAGREAGELMKKaLPGGGKVAIITGGLGADNL 137

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 194 AERISGCRDGMADHADRQSVSalVELDENDPFAGEELSKALEAG--KVTGIYNAGvSHAVLGRALAAHSLGPP--PVLVG 269
Cdd:cd06314  138 NERIQGFKDALKGSPGIEIVD--PLSDNDDIAKAVQNVEDILKAnpDLDAIFGVG-AYNGPAIAAALKDAGKVgkVKIVG 214

                        170       180
                 ....*....|....*....|....
gi 499272612 270 HDISPDAERMLQEGVMTLVIDQNP 293
Cdd:cd06314  215 FDTLPETLQGIKDGVIAATVGQRP 238
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 7-46 8.75e-14

Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repressor binds its ligand, it undergoes a conformational change which affects the DNA-binding affinity of the repressor. In Escherichia coli, LacI represses transcription by binding with high affinity to the lac operon at a specific operator DNA sequence until it interacts with the physiological inducer allolactose or a non-degradable analog IPTG (isopropyl-beta-D-thiogalactopyranoside). Induction of the repressor lowers its affinity for the operator sequence, thereby allowing transcription of the lac operon structural genes (lacZ, lacY, and LacA). The lac repressor occurs as a tetramer made up of two functional dimers. Thus, two DNA binding domains of a dimer are required to bind the inverted repeat sequences of the operator DNA binding sites.


Pssm-ID: 143331 [Multi-domain]  Cd Length: 52  Bit Score: 64.74  E-value: 8.75e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 499272612   7 DVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGF 46
Cdd:cd01392    2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGY 41
PBP1_ABC_sugar_binding-like cd19965
monosaccharide ABC transporter substrate binding protein CUT2 family and similar proteins; ...
 107-311 1.93e-13

monosaccharide ABC transporter substrate binding protein CUT2 family and similar proteins; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380620 [Multi-domain]  Cd Length: 272  Bit Score: 69.22  E-value: 1.93e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 107 EAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAP--RLSYVGIDHYKAGRCAAFFLAKMAGEGS---I 181
Cdd:cd19965   50 EAAIASGPDGIATTIVDPEAFDEVIKRALDAGIPVVAFNVDAPGGEnaRLAFVGQDLYPAGYVLGKRIAEKFKPGGghvL 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 182 VLLCSSLYYRAEaERISGCRDGMADHADRqsvsalVELDENDPfaGEELSKALEAGK--------VTGIYNAGVS-HAVL 252
Cdd:cd19965  130 LGISTPGQSALE-QRLDGIKQALKEYGRG------ITYDVIDT--GTDLAEALSRIEayytahpdIKAIFATGAFdTAGA 200

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499272612 253 GRALAAHSLgPPPVLV-GHDISPDAERMLQEGVMTLVIDQNPDLQ--VRKALLILASRFGLP 311
Cdd:cd19965  201 GQAIKDLGL-KGKVLVgGFDLVPEVLQGIKAGYIDFTIDQQPYLQgfYPVMQLFLYKKFGLS 261
PBP1_ABC_sugar_binding-like cd20005
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 103-293 3.53e-13

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380660 [Multi-domain]  Cd Length: 274  Bit Score: 68.42  E-value: 3.53e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 103 ELVAEAILKsRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAKMAG-EGSI 181
Cdd:cd20005   48 EMLDNAIAK-KPDAIALAALDTNALLPQLEKAKEKGIPVVTFDSGVPSDLPLATVATDNYAAGALAADHLAELIGgKGKV 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 182 VLLCSSLYYRAEAERISGCRDGM-ADHADRQSVSalVELDENDPFAGEELSKA--LEAGKVTGIY--NAGVSHAVLgRAL 256
Cdd:cd20005  127 AIVAHDATSETGIDRRDGFKDEIkEKYPDIKVVN--VQYGVGDHAKAADIAKAilQANPDLKGIYatNEGAAIGVA-NAL 203

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 499272612 257 AAHSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQNP 293
Cdd:cd20005  204 KEMGKLGKIKVVGFDSGEAQIDAIKNGVIAGSVTQNP 240
PBP1_ABC_sugar_binding-like cd20004
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 107-293 9.48e-13

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380659 [Multi-domain]  Cd Length: 273  Bit Score: 67.26  E-value: 9.48e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 107 EAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVLLC 185
Cdd:cd20004   51 EYFIDQGVDGIVLAPLDRKALVAPVERARAQGIPVVIIDSDLGGDAVISFVATDNYAAGRLAAKRMAKlLNGKGKVALLR 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 186 SSLYYRAEAERISGCRDGMADHADRQSVSALVELDENDPFAGEELSKAL-EAGKVTGIY--NAGVSHAVLgRALAAHSLG 262
Cdd:cd20004  131 LAKGSASTTDRERGFLEALKKLAPGLKVVDDQYAGGTVGEARSSAENLLnQYPDVDGIFtpNESTTIGAL-RALRRLGLA 209

                        170       180       190
                 ....*....|....*....|....*....|.
gi 499272612 263 PPPVLVGHDISPDAERMLQEGVMTLVIDQNP 293
Cdd:cd20004  210 GKVKFIGFDASDLLLDALRAGEISALVVQDP 240
PBP1_ABC_sugar_binding-like cd19969
monosaccharide ABC transporter substrate binding protein; Periplasmic sugar-binding domain of ...
 107-296 1.98e-12

monosaccharide ABC transporter substrate binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380624 [Multi-domain]  Cd Length: 278  Bit Score: 66.59  E-value: 1.98e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 107 EAILKsRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLA-KMAGEGSIVLLC 185
Cdd:cd19969   51 QAIAK-NPDGIAVSAIDPEALTPTINKAVDAGIPVVTFDSDAPESKRISYVGTDNYEAGYAAAEKLAeLLGGKGKVAVLT 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 186 SSLYYRAEaERISGCRDGMADHADRQSVSalVELDENDPFAGEELSKALEAGK--VTGIY----NAGVshavlGRALAAH 259
Cdd:cd19969  130 GPGQPNHE-ERVEGFKEAFAEYPGIEVVA--VGDDNDDPEKAAQNTSALLQAHpdLVGIFgvdaSGGV-----GAAQAVR 201

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 499272612 260 SLGPPPVL--VGHDISPDAERMLQEGVMTLVIDQNPDLQ 296
Cdd:cd19969  202 EAGKTGKVkiVAFDDDPETLDLIKDGVIDASIAQRPWMM 240
PBP1_ABC_sugar_binding-like cd06310
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 107-293 1.24e-11

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380533 [Multi-domain]  Cd Length: 272  Bit Score: 63.90  E-value: 1.24e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 107 EAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGR-CAAFFLAKMAGEGSIVLL- 184
Cdd:cd06310   51 EELINKKPDAIVVAPLDSEDLVDPLKDAKDKGIPVIVIDSGIKGDAYLSYIATDNYAAGRlAAQKLAEALGGKGKVAVLs 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 185 ----CSSLYYRAEaerisGCRDGMADHADRQSVSAlveldenDPFAGEELSKALEA--------GKVTGIYNAGVSHAV- 251
Cdd:cd06310  131 ltagNSTTDQREE-----GFKEYLKKHPGGIKVLA-------SQYAGSDYAKAANEtedllgkyPDIDGIFATNEITALg 198

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 499272612 252 LGRALAAHSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQNP 293
Cdd:cd06310  199 AAVAIKSRKLSGQIKIVGFDSQEELLDALKNGKIDALVVQNP 240
PBP1_ABC_IbpA-like cd19968
periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The ...
 116-304 1.47e-11

periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The periplasmic binding protein (PBP) IbpA mediates the uptake of myo-inositol by an ABC transporter that consists of the PBP IbpA, the transmembrane permease IatP, and the ABC IatA. IbpA shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge.


Pssm-ID: 380623 [Multi-domain]  Cd Length: 271  Bit Score: 63.94  E-value: 1.47e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 116 ALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLA-KMAGEGSIVLLCSSLYYRAEA 194
Cdd:cd19968   58 GIIVSPIDVKALVPAIEAAIKAGIPVVTVDRRAEGAAPVPHVGADNVAGGREVAKFVVdKLPNGAKVIELTGTPGSSPAI 137

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 195 ERISGCRDGMADHADRQSVsalveLDENDPFAGEELSKALEA--GKVTGIYNAGVSH---AVLGRALAAHSLGPPP---V 266
Cdd:cd19968  138 DRTKGFHEELAAGPKIKVV-----FEQTGNFERDEGLTVMENilTSLPGPPDAIICAnddMALGAIEAMRAAGLDLkkvK 212

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 499272612 267 LVGHDISPDAERMLQEGVMTLVIDQNPDLQVRKALLIL 304
Cdd:cd19968  213 VIGFDAVPDALQAIKDGELYATVEQPPGGQARTALRIL 250
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
7-46 1.38e-10

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 56.44  E-value: 1.38e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 499272612     7 DVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGF 46
Cdd:smart00354   5 DVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGY 44
PBP1_ABC_sugar_binding-like cd06322
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 115-295 3.00e-10

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380545 [Multi-domain]  Cd Length: 270  Bit Score: 59.98  E-value: 3.00e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 115 NALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVLLCSSLYYRAE 193
Cdd:cd06322   57 DAIILAPVDSGGIVPAIEAANEAGIPVFTVDVKADGAKVVTHVGTDNYAGGKLAGEYALKaLLGGGGKIAIIDYPEVESV 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 194 AERISGCRDGMADHADRQSVSalvELDENDpfAGEELSKALE-----AGKVTGIYNAGVSHA--VLGRALAAHSLGPPPV 266
Cdd:cd06322  137 VLRVNGFKEAIKKYPNIEIVA---EQPGDG--RREEALAATEdmlqaNPDLDGIFAIGDPAAlgALTAIESAGKEDKIKV 211

                        170       180       190
                 ....*....|....*....|....*....|
gi 499272612 267 lVGHDISPDAERMLQE-GVMTLVIDQNPDL 295
Cdd:cd06322  212 -IGFDGNPEAIKAIAKgGKIKADIAQQPDK 240
PBP1_ABC_sugar_binding-like cd20007
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 105-301 3.34e-10

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380662 [Multi-domain]  Cd Length: 271  Bit Score: 59.94  E-value: 3.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 105 VAEAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDV--PSAPrLSYVGIDHYKAGRCAAFFLAKMAGE-GSI 181
Cdd:cd20007   48 IVNAVIAKKPDALLIAPTDPQALIAPLKRAADAGIKVVTVDTTLgdPSFV-LSQIASDNVAGGALAAEALAELIGGkGKV 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 182 VLLCSSLYYRAEAERISGCRDGMADHADRQSVSalVELDENDPF-AGEELSKALEA-GKVTGIYNAGVSHAvLGRALA-- 257
Cdd:cd20007  127 LVINSTPGVSTTDARVKGFAEEMKKYPGIKVLG--VQYSENDPAkAASIVAAALQAnPDLAGIFGTNTFSA-EGAAAAlr 203

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 499272612 258 -AHSLGPPPVlVGHDISPDAERMLQEGVMTLVIDQNPDLQVRKAL 301
Cdd:cd20007  204 nAGKTGKVKV-VGFDASPAQVEQLKAGTIDALIAQKPAEIGYLAV 247
PBP1_ribose_binding cd06323
periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose ...
 105-300 5.14e-10

periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis D-ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group belong to the type 1 periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.


Pssm-ID: 380546 [Multi-domain]  Cd Length: 268  Bit Score: 59.23  E-value: 5.14e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 105 VAEAILKsRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVL 183
Cdd:cd06323   48 VEDLIVR-KVDALLINPTDSDAVSPAVEEANEAGIPVITVDRSVTGGKVVSHIASDNVAGGEMAAEYIAKkLGGKGKVVE 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 184 LCSSLYYRAEAERISGCRDGMADHADRQSVSALVeldendpfAGEELSKALEA--------GKVTGIYnAGVSHAVLGRA 255
Cdd:cd06323  127 LQGIPGTSAARERGKGFHNAIAKYPKINVVASQT--------ADFDRTKGLNVmenllqahPDIDAVF-AHNDEMALGAI 197

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 499272612 256 LAAHSLGPPPVL-VGHDISPDAERMLQEGVMTLVIDQNPDLQVRKA 300
Cdd:cd06323  198 QALKAAGRKDVIvVGFDGTPDAVKAVKDGKLAATVAQQPEEMGAKA 243
PBP1_ABC_sugar_binding-like cd06312
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 107-296 7.20e-10

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380535 [Multi-domain]  Cd Length: 272  Bit Score: 58.78  E-value: 7.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 107 EAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIVS-DVPSAPR---LSYVGIDHYKAGRCAAfflAKMAGEGSIV 182
Cdd:cd06312   51 EQAIAAKPDGIIVTIPDPDALEPALKRAVAAGIPVIAINSgDDRSKERlgaLTYVGQDEYLAGQAAG---ERALEAGPKN 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 183 LLCSSLYYRAEA--ERISGCRDGMADhadrqSVSALVELD--ENDPFAGEELSKALEAGK-VTGIY--NAGVSHAVLgRA 255
Cdd:cd06312  128 ALCVNHEPGNPGleARCKGFADAFKG-----AGILVELLDvgGDPTEAQEAIKAYLQADPdTDAVLtlGPVGADPAL-KA 201

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 499272612 256 LAAHSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQNPDLQ 296
Cdd:cd06312  202 VKEAGLKGKVKIGTFDLSPETLEAIKDGKILFAIDQQPYLQ 242
LacI pfam00356
Bacterial regulatory proteins, lacI family;
7-46 8.49e-10

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 53.41  E-value: 8.49e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 499272612    7 DVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGF 46
Cdd:pfam00356   4 DVARLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNY 43
PBP1_ABC_sugar_binding-like cd19966
monosaccharide ABC transporter substrate binding protein CUT2 family and simialr proteins; ...
 103-312 3.01e-09

monosaccharide ABC transporter substrate binding protein CUT2 family and simialr proteins; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380621 [Multi-domain]  Cd Length: 278  Bit Score: 56.95  E-value: 3.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 103 ELVAEAIlKSRGNALVVYG-QDHELIIDAIAEVTSAGKPVVTIVSDVP----SAPRLSYVGIDHYKAGRCAAFFLAKMAG 177
Cdd:cd19966   47 EQFKEAI-AAKPDGIAIMGhPGDGAYTPLIEAAKKAGIIVTSFNTDLPkleyGDCGLGYVGADLYAAGYTLAKELVKRGG 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 178 --EGSIVLLCSSLY---YRAEaeRISGCRDGMADH---ADRQSVSalveLDENDPFAGEE-LSKALEAGKVTG--IYNAG 246
Cdd:cd19966  126 lkTGDRVFVPGLLPgqpYRVL--RTKGVIDALKEAgikVDYLEIS----LEPNKPAEGIPvMTGYLAANPDVKaiVGDGG 199

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499272612 247 VSHAVLGRALAAHSLGPPPV-LVGHDISPDAERMLQEGVMTLVIDQNPDLQ--VRKALLILASRFGLPG 312
Cdd:cd19966  200 GLTANVAKYLKAAGKKPGEIpVAGFDLSPATVQAIKSGYVNATIDQQPYLQgyLPVLQIYLTKKYGFSG 268
PBP1_ABC_sugar_binding-like cd20008
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 103-294 6.76e-08

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380663 [Multi-domain]  Cd Length: 277  Bit Score: 53.00  E-value: 6.76e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 103 ELVAEAIlkSRG-NALVVYGQDHELIIdAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAKM-----A 176
Cdd:cd20008   48 NLVENAI--SRKpDAIVLAPNDTAALV-PAVEAADAGIPVVLVDSGANTDDYDAFLATDNVAAGALAADELAELlkasgG 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 177 GEGSIVLLCSSLYYRAEAERISGCRDGMADHADRQSVSAlVELDENDpfAGEELSKA---LEAGK-VTGIYNAGVSHAV- 251
Cdd:cd20008  125 GKGKVAIISFQAGSQTLVDREEGFRDYIKEKYPDIEIVD-VQYSDGD--IAKALNQTtdlLTANPdLVGIFGANNPSAVg 201

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 499272612 252 LGRALAAHSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQNPD 294
Cdd:cd20008  202 VAQALAEAGKAGKIVLVGFDSSPDEVALLKSGVIKALVVQDPY 244
PBP1_ABC_sugar_binding-like cd19970
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 107-297 6.95e-08

monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380625 [Multi-domain]  Cd Length: 275  Bit Score: 53.02  E-value: 6.95e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 107 EAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTIvsDVPSAPRLS--------YVGIDHYKAGRCAAFFLAKMAGE 178
Cdd:cd19970   52 ENLIAQKVDAIVIAPADSKALVPVLKKAVDAGIAVINI--DNRLDADALkegginvpFVGPDNRQGAYLAGDYLAKKLGK 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 179 GSIVLLCS--SLYYRAEaERISGCRDGMADHADR--QSVSALVELDEndpfAGEELSKALEAGK-VTGIYNAGVSHAvLG 253
Cdd:cd19970  130 GGKVAIIEgiPGADNAQ-QRKAGFLKAFEEAGMKivASQSANWEIDE----ANTVAANLLTAHPdIRGILCANDNMA-LG 203

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 499272612 254 --RALAAHSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQNPDLQV 297
Cdd:cd19970  204 aiKAVDAAGKAGKVLVVGFDNIPAVRPLLKDGKMLATIDQHPAKQA 249
PBP1_ABC_sugar_binding-like cd19971
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 107-293 3.71e-07

monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380626 [Multi-domain]  Cd Length: 267  Bit Score: 50.66  E-value: 3.71e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 107 EAILKSRGNALVVYGQDHELIIDAIAEVTSAGKPVVTI---VSDVPSAprLSYVGIDHYKAGR-CAAFFLAKMAGEGSIV 182
Cdd:cd19971   49 EDMINQGVDAIFLNPVDSEGIRPALEAAKEAGIPVINVdtpVKDTDLV--DSTIASDNYNAGKlCGEDMVKKLPEGAKIA 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 183 LLCSSLyyrAEA--ERISGCRDGMADHADRQSVsALVELDENDPFAGEELSKALEAG-KVTGIYnAGVSHAVLG--RALA 257
Cdd:cd19971  127 VLDHPT---AEScvDRIDGFLDAIKKNPKFEVV-AQQDGKGQLEVAMPIMEDILQAHpDLDAVF-ALNDPSALGalAALK 201

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 499272612 258 AHSLGPPPVLVGHDISPDAERMLQEGVMTLVIDQNP 293
Cdd:cd19971  202 AAGKLGDILVYGVDGSPDAKAAIKDGKMTATAAQSP 237
PBP1_allose_binding cd06320
periplasmic allose-binding domain of bacterial transport systems that function as a primary ...
 127-315 7.86e-07

periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis; Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.


Pssm-ID: 380543 [Multi-domain]  Cd Length: 283  Bit Score: 49.57  E-value: 7.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 127 IIDAIAEVTSAGKPVVTIVSDVPSAPR-------LSYVGIDHYKAGRCAAFFLAKMAGEGSIVLLCSSLYYRAEAE-RIS 198
Cdd:cd06320   71 LIPPIEKANKKGIPVINLDDAVDADALkkaggkvTSFIGTDNVAAGALAAEYIAEKLPGGGKVAIIEGLPGNAAAEaRTK 150

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 199 GCRDGMADHADRQSVSALveldendPfAGEELSKALEAGK--------VTGIY--NAGVSHAVLgRALAAHSLGPPPVLV 268
Cdd:cd06320  151 GFKETFKKAPGLKLVASQ-------P-ADWDRTKALDAATailqahpdLKGIYaaNDTMALGAV-EAVKAAGKTGKVLVV 221

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 499272612 269 GHDISPDAERMLQEGVMTLVIDQNPDLQ----VRKALLILASRfGLPGGVA 315
Cdd:cd06320  222 GTDGIPEAKKSIKAGELTATVAQYPYLEgamaVEAALRLLQGQ-KVPAVVA 271
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
7-127 1.32e-06

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 49.39  E-value: 1.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612   7 DVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGFDrklPTLYRQGLRFEV--LLGRRQMPlcarLSDAIvrFGR 84
Cdd:PRK10401   6 DVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYR---PNANAQALATQVsdTIGVVVMD----VSDAF--FGA 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499272612  85 PFK--DIVA--------IERTFVDETRPELVAEAILKSRGNALVVYGQ---DHELI 127
Cdd:PRK10401  77 LVKavDLVAqqhqkyvlIGNSYHEAEKERHAIEVLIRQRCNALIVHSKalsDDELA 132
PBP1_ABC_sugar_binding-like cd06321
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 130-326 1.75e-06

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380544 [Multi-domain]  Cd Length: 270  Bit Score: 48.44  E-value: 1.75e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 130 AIAEVTSAGKPVVTIvsDVPSAPRLSYVGIDHYKAGRCAAFFLA-KMAGEGSIVLLcSSLYYRAEAERISGCRDGMADHA 208
Cdd:cd06321   74 AIKRAKDAGIIVVAV--DVAAEGADATVTTDNVQAGYLACEYLVeQLGGKGKVAII-DGPPVSAVIDRVNGCKEALAEYP 150

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 209 DrqsvsALVELDENdpfAGEELSKALEA--------GKVTGIYNAGVSHAvLGRALAAHSLGPPP-VLVGHDISPDAERM 279
Cdd:cd06321  151 G-----IKLVDDQN---GKGSRAGGLSVmtrmltahPDVDGVFAINDPGA-IGALLAAQQAGRDDiVITSVDGSPEAVAA 221

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 499272612 280 LQEGvMTLVI---DQNPDLQVRKAL-LILASRFGLPggVAESPVVPFTVLV 326
Cdd:cd06321  222 LKRE-GSPFIataAQDPYDMARKAVeLALKILNGQE--PAPELVLIPSTLV 269
PBP1_sensor_kinase-like cd06308
periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic ...
 110-286 2.48e-06

periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.


Pssm-ID: 380531 [Multi-domain]  Cd Length: 268  Bit Score: 48.31  E-value: 2.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 110 LKSRG-NALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVLLCSS 187
Cdd:cd06308   52 LIAQGvDLLIVSPNEADALTPVVKKAYDAGIPVIVLDRKVSGDDYTAFIGADNVEIGRQAGEYIAElLNGKGNVVEIQGL 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 188 LYYRAEAERISGCRDGMADHADRQSVsALVELDENDPFAGEELSKALEAG-KVTGIYnagvSHA---VLGRALAAHSLG- 262
Cdd:cd06308  132 PGSSPAIDRHKGFLEAIAKYPGIKIV-ASQDGDWLRDKAIKVMEDLLQAHpDIDAVY----AHNdemALGAYQALKKAGr 206

                        170       180
                 ....*....|....*....|....*.
gi 499272612 263 -PPPVLVGHDISPDA-ERMLQEGVMT 286
Cdd:cd06308  207 eKEIKIIGVDGLPEAgEKAVKDGILA 232
PBP1_ABC_ThpA_XypA cd06313
periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group ...
 116-328 2.74e-06

periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group includes periplasmic D-threitol-binding protein ThpA and xylitol/L-sorbitol-binding protein XypA, which are part of sugar ABC-type transport systems. Both ThpA and XypA share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge.


Pssm-ID: 380536 [Multi-domain]  Cd Length: 277  Bit Score: 48.04  E-value: 2.74e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 116 ALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLA-KMAGEGSIVLLCSSLYYRAEA 194
Cdd:cd06313   58 AIIVVPVDADALAPAVEKAKEAGIPLVGVNALIENEDLTAYVGSDDVVAGELEGQAVAdRLGGKGNVVILEGPIGQSAQI 137

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 195 ERISGCRDGMADHADrqsvsalVELDENDP--FAGEELSKALEA------GKVTGIynagVSH---AVLG--RALAAHSL 261
Cdd:cd06313  138 DRGKGIENVLKKYPD-------IKVLAEQTanWSRDEAMSLMENwlqaygDEIDGI----IAQnddMALGalQAVKAAGR 206

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499272612 262 GPPPVlVGHDISPDAERMLQEGVMTLVIDQNPDLQVRKAL-LILASRFGlpGGVAESPVVPFTVLVRD 328
Cdd:cd06313  207 DDIPV-VGIDGIEDALQAVKSGELIATVLQDAEAQGKGAVeVAVDAVKG--EGVEKKYYIPFVLVTKD 271
PBP1_LacI-like cd06285
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 98-329 3.53e-06

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380508 [Multi-domain]  Cd Length: 269  Bit Score: 47.61  E-value: 3.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612  98 DETRPELVAEAILKSRGNALVVygQDHELIIDAIAEVTSAGKPVVTIVSDVPSaPRLSYVGIDHYKAGRCAAFFLAKMaG 177
Cdd:cd06285   40 DPERELAALDSLLSRRVDGLII--TPARDDAPDLQELAARGVPVVLVDRRIGD-TALPSVTVDNELGGRLATRHLLEL-G 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 178 EGSIVLLCSSLYYRAEAERISGCRDGMADHADRQSVSALVElDENDPFAGEELSKAL--EAGKVTGIYnAGVSHAVLGRA 255
Cdd:cd06285  116 HRRIAVVAGPLNASTGRDRLRGYRRALAEAGLPVPDERIVP-GGFTIEAGREAAYRLlsRPERPTAVF-AANDLMAIGVL 193

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499272612 256 LAAHSLG---PPPV-LVGHDISPDAeRMLQEGVMTlvIDQNPDLQVRKALLILASRFGLPGGVAESPVVPFTVLVRDS 329
Cdd:cd06285  194 RAARDLGlrvPEDLsVVGFDDIPLA-AFLPPPLTT--VRQPKYEMGRRAAELLLQLIEGGGRPPRSITLPPELVVRES 268
PBP1_rhizopine_binding-like cd06301
periplasmic binding proteins specific to rhizopines; Periplasmic binding proteins specific to ...
 115-301 4.06e-06

periplasmic binding proteins specific to rhizopines; Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily.


Pssm-ID: 380524 [Multi-domain]  Cd Length: 272  Bit Score: 47.61  E-value: 4.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 115 NALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRL-SYVGIDHYKAGRCAAFFLAKMAG-EGSIVLLCSSLYYRA 192
Cdd:cd06301   59 DAIIVNPVDTDASAPAVDAAADAGIPLVYVNREPDSKPKGvAFVGSDDIESGELQMEYLAKLLGgKGNIAILDGVLGHEA 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 193 EAERISGCRDGMADHADRQsvsalVELDENDPFAGEELSKALEAGKVTGI-YNAGVSHA---VLGRALAAHSLGPPP--V 266
Cdd:cd06301  139 QILRTEGNKDVLAKYPGMK-----IVAEQTANWSREKAMDIVENWLQSGDkIDAIVANNdemAIGAILALEAAGKKDdiL 213

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 499272612 267 LVGHDISPDAERMLQEGVMTLVIDQNPDLQVRKAL 301
Cdd:cd06301  214 VAGIDATPDALKAMKAGRLDATVFQDAAGQGETAV 248
PRK10014 PRK10014
DNA-binding transcriptional repressor MalI; Provisional
 2-48 6.40e-06

DNA-binding transcriptional repressor MalI; Provisional


Pssm-ID: 182193 [Multi-domain]  Cd Length: 342  Bit Score: 47.40  E-value: 6.40e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 499272612   2 KRKLIDVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGFDR 48
Cdd:PRK10014   6 KITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVR 52
lacI PRK09526
lac repressor; Reviewed
 1-46 6.62e-06

lac repressor; Reviewed


Pssm-ID: 181929 [Multi-domain]  Cd Length: 342  Bit Score: 47.30  E-value: 6.62e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 499272612   1 MKRKLI---DVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGF 46
Cdd:PRK09526   1 MKSKPVtlyDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNY 49
PBP1_ABC_sugar_binding-like cd19996
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
 115-184 1.39e-05

monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.


Pssm-ID: 380651 [Multi-domain]  Cd Length: 302  Bit Score: 46.08  E-value: 1.39e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499272612 115 NALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVLL 184
Cdd:cd19996   60 DAIIVSPNSPTALLPAIEKAAAAGIPVVLFDSGVGSDKYTAFVGVDDAAFGRVGAEWLVKqLGGKGNIIAL 130
PBP1_ABC_sugar_binding-like cd06317
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 116-293 2.93e-05

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380540 [Multi-domain]  Cd Length: 281  Bit Score: 45.06  E-value: 2.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 116 ALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGR-----CAAFFLAKMAGEGSIVLLcsslyy 190
Cdd:cd06317   58 AIILDAIDVNGSIPAIKRASEAGIPVIAYDAVIPSDFQAAQVGVDNLEGGKeigkyAADYIKAELGGQAKIGVV------ 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 191 RAEAERISGCR-DGMADHA-DRQSVSALVELD-----ENDPFAGEELSKAleAGKVTGIYNAGvSHAVLGRALAAHSLGP 263
Cdd:cd06317  132 GALSSLIQNQRqKGFEEALkANPGVEIVATVDgqnvqEKALSAAENLLTA--NPDLDAIYATG-EPALLGAVAAVRSQGR 208

                        170       180       190
                 ....*....|....*....|....*....|...
gi 499272612 264 PP--VLVGHDISPD-AERMLQEGVMTLVIDQNP 293
Cdd:cd06317  209 QGkiKVFGWDLTKQaIFLGIDEGVLQAVVQQDP 241
PBP1_LacI-like cd06279
ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium ...
 116-234 5.67e-05

ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium glutamicum and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium glutamicum and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380502 [Multi-domain]  Cd Length: 284  Bit Score: 44.12  E-value: 5.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 116 ALVVYGQDHELiiDAIAEVTSAGKPVVTIvsDVPSAPRLSYVGIDHYKAGRCAA-----------------FFLAKMAGE 178
Cdd:cd06279   59 GFIVYGLSDDD--PAVAALRRRGLPLVVV--DGPAPPGIPSVGIDDRAAARAAArhlldlghrriailslrLDRGRERGP 134

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499272612 179 GSIVLLCSSlYYRAEAERISGCRDGMADHADRQSVSALVELDENDPFAGEELSKAL 234
Cdd:cd06279  135 VSAERLAAA-TNSVARERLAGYRDALEEAGLDLDDVPVVEAPGNTEEAGRAAARAL 189
PBP1_TorT-like cd06306
TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor ...
 129-301 1.27e-04

TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria; TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type 1 periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.


Pssm-ID: 380529 [Multi-domain]  Cd Length: 269  Bit Score: 42.95  E-value: 1.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 129 DAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAKMAGEGSIVLLCSSLYYRAE--AERISGCRDGMAD 206
Cdd:cd06306   73 PKVAEAAAAGIPVIDLVNGIDSPKVAARVLVDFYDMGYLAGEYLVEHHPGKPVKVAWFPGPAGAGwaEDREKGFKEALAG 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 207 HA-----------DRQSVSALVEldendpfageelsKALEAGKVTGIYNA-GVSHAVLGRALAAHSLGPPPVLVGHDISP 274
Cdd:cd06306  153 SNveivatkygdtGKAVQLNLVE-------------DALQAHPDIDYIVGnAVAAEAAVGALREAGLTGKVKVVSTYLTP 219

                        170       180
                 ....*....|....*....|....*..
gi 499272612 275 DAERMLQEGVMTLVIDQNPDLQVRKAL 301
Cdd:cd06306  220 GVYRGIKRGKILAAPSDQPVLQGRIAV 246
PBP1_LacI-like cd06284
ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus ...
 126-207 1.29e-04

ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380507 [Multi-domain]  Cd Length: 267  Bit Score: 42.91  E-value: 1.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 126 LIIDAIAEVTSAGKPVVtIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAKMaGEGSIVLLCSSLYYRAEAERISGCRDGMA 205
Cdd:cd06284   65 RLDAELLSELSKRYPIV-QCCEYIPDSGVPSVSIDNEAAAYDATEYLISL-GHRRIAHINGPLDNVYARERLEGYRRALA 142


                 ..
gi 499272612 206 DH 207
Cdd:cd06284  143 EA 144
PBP1_ABC_sugar_binding-like cd06300
periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are ...
 115-269 2.09e-04

periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.


Pssm-ID: 380523 [Multi-domain]  Cd Length: 302  Bit Score: 42.31  E-value: 2.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 115 NALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVpSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVLLCSSLYYRAE 193
Cdd:cd06300   62 DAIIINPSSPTALNAVIEQAADAGIPVVAFDGAV-TSPDAYNVSNDQVEWGRLGAKWLFEaLGGKGNVLVVRGIAGAPAS 140

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499272612 194 AERISGCRDGMADHADRQsVSALVELDENDPFAGEELSKALEAG-KVTGIYNAGVSHAVLGRALAAHSLGPPPVLVG 269
Cdd:cd06300  141 ADRHAGVKEALAEYPGIK-VVGEVFGGWDEATAQTAMLDFLATHpQVDGVWTQGGEDTGVLQAFQQAGRPPVPIVGG 216
PBP1_galactofuranose_YtfQ-like cd06309
periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ...
 129-305 3.25e-04

periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.


Pssm-ID: 380532 [Multi-domain]  Cd Length: 285  Bit Score: 41.82  E-value: 3.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 129 DAIAEVTSAGKPVVTI---VSDVPSAPRLSYVGIDHYKAGRCAAFFLAK--MAGEGSIVLLCSSLYYRAEAERISGCRDG 203
Cdd:cd06309   71 PVLKEAKDAGIPVILVdrtIDGEDGSLYVTFIGSDFVEEGRRAAEWLVKnyKGGKGNVVELQGTAGSSVAIDRSKGFREV 150

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 204 MADHADRQSVSAlveldENDPFAGEELSKALEA------GKVTGIYnagvSH---AVLG--RALAAHSLGPPP--VLVGH 270
Cdd:cd06309  151 IKKHPNIKIVAS-----QSGNFTREKGQKVMENllqagpGDIDVIY----AHnddMALGaiQALKEAGLKPGKdvLVVGI 221

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 499272612 271 DISPDAERMLQEGVMTLVIDQNPdLQVRKALLILA 305
Cdd:cd06309  222 DGQKDALEAIKAGELNATVECNP-LFGPTAFDTIA 255
PBP1_ABC_sugar_binding-like cd06311
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 115-209 4.57e-04

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380534 [Multi-domain]  Cd Length: 270  Bit Score: 41.20  E-value: 4.57e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 115 NALVVYGQDHELIIDAIAEVTSAGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLA-KMAGEGSIVLL----CSSLy 189
Cdd:cd06311   57 DAIVILPQDSEELTVAAQKAKDAGIPVVNFDRGLNVLIYDLYVAGDNPGMGVVSAEYIGkKLGGKGNVVVLevpsSGSV- 135

                         90       100
                 ....*....|....*....|
gi 499272612 190 yraEAERISGCRDGMADHAD 209
Cdd:cd06311  136 ---NEERVAGFKEVIKGNPG 152
PBP1_ABC_sugar_binding-like cd19972
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 137-305 7.43e-04

monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380627 [Multi-domain]  Cd Length: 269  Bit Score: 40.50  E-value: 7.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 137 AGKPVVTIVSDVPSAPRLSYVGIDHYKAGRCAAFFLAK-MAGEGSIVLLCSSLYYRAEAERISGCRDGMADHADRQSVSA 215
Cdd:cd19972   79 AGIPVIAVDRNPEDAPGDTFIATDSVAAAKELGEWVIKqTGGKGEIAILHGQLGTTPEVDRTKGFQEALAEAPGIKVVAE 158

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 216 L-VELDENDPFAGEElsKALEAG-KVTGIYnaGVSHAV-LGRALAAHSLGPPP--VLVGHDISPDAERMLQEGVMTLVID 290
Cdd:cd19972  159 QtADWDQDEGFKVAQ--DMLQANpNITVFF--GQSDAMaLGAAQAVKVAGLDHkiWVVGFDGDVAGLKAVKDGVLDATMT 234

                        170
                 ....*....|....*....
gi 499272612 291 QNP----DLQVRKALLILA 305
Cdd:cd19972  235 QQTqkmgRLAVDSAIDLLN 253
PBP1_ABC_sugar_binding-like cd19999
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
 126-209 1.02e-03

monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.


Pssm-ID: 380654 [Multi-domain]  Cd Length: 313  Bit Score: 40.37  E-value: 1.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 126 LIIDA---------IAEVTSAGKPVVtIVSDVPSAPRLSYVGIDHYKAGRCAAFFLA-KMAGEGSIVLLCSSLYYRAEAE 195
Cdd:cd19999   64 ILIDPvsatalnpvIEKAQAAGILVV-SFDQPVSSPDAINVVIDQYKWAAIQAQWLAeQLGGKGNIVAINGVAGNPANEA 142

                         90
                 ....*....|....
gi 499272612 196 RISGCRDGMADHAD 209
Cdd:cd19999  143 RVKAADDVFAKYPG 156
PBP1_LacI_sugar_binding-like cd06267
ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 ...
 129-207 1.23e-03

ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily; Ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.


Pssm-ID: 380491 [Multi-domain]  Cd Length: 264  Bit Score: 39.81  E-value: 1.23e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499272612 129 DAIAEVTSAGKPVVTIVSDVPSaPRLSYVGIDHYKAGRCAAFFLAKMaGEGSIVLLCSSLYYRAEAERISGCRDGMADH 207
Cdd:cd06267   69 ELLEELLAAGIPVVLIDRRLDG-LGVDSVVVDNYAGAYLATEHLIEL-GHRRIAFIGGPLDLSTSRERLEGYRDALAEA 145
PBP1_MalI-like cd06289
ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia ...
 129-277 1.26e-03

ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria; This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380512 [Multi-domain]  Cd Length: 268  Bit Score: 39.86  E-value: 1.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 129 DAIAEVTSAGKPVVTIVSDVPSAPrLSYVGIDHYKAGRCAAFFLAKMaGEGSIVLLCSSLYYRAEAERISGCRDGMADHa 208
Cdd:cd06289   70 ELLRRLKAWGIPVVLALRDVPGSD-LDYVGIDNRLGAQLATEHLIAL-GHRRIAFLGGLSDSSTRRERLAGFRAALAEA- 146

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499272612 209 DRQSVSALVELDENDPFAGEELSKAL--EAGKVTGI--YNAGVSHAVLgRALAAHSLGPPP--VLVGHDISPDAE 277
Cdd:cd06289  147 GLPLDESLIVPGPATREAGAEAARELldAAPPPTAVvcFNDLVALGAM-LALRRRGLEPGRdiAVVGFDDVPEAA 220
PBP1_GntR cd01575
ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of ...
 103-219 1.79e-03

ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding, which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380489 [Multi-domain]  Cd Length: 269  Bit Score: 39.40  E-value: 1.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 103 ELVaEAILKSRGNALVVYGQDHELiiDAIAEVTSAGKPVVTIVsDVPSAPRLSYVGIDHYKAGRCAAFFLAKmAGEGSIV 182
Cdd:cd01575   46 ELI-RALLSRRPAGLILTGTEHTP--ATRKLLRAAGIPVVETW-DLPDDPIDMAVGFSNFAAGRAMARHLIE-RGYRRIA 120

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 499272612 183 LLCSSL--YYRAeAERISGCRDGMADHADRQSVSALVEL 219
Cdd:cd01575  121 FVGARLdgDSRA-RQRLEGFRDALAEAGLPLPLVLLVEL 158
PBP1_ABC_xylose_binding-like cd19993
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ...
 110-184 1.87e-03

periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380648 [Multi-domain]  Cd Length: 287  Bit Score: 39.38  E-value: 1.87e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499272612 110 LKSRG-NALVVYGQDHELIIDAIAEVTSAGKPVvtIVSDVP-SAPRLSYVGIDHYKAGRCAAFFLAKMAGEGSIVLL 184
Cdd:cd19993   51 LISQGaKALIVLAQDGDAILPAVEKAAAEGIPV--IAYDRLiENPIAFYISFDNVEVGRMQARGVLKAKPEGNYVFI 125
PBP1_XylR cd01543
ligand-binding domain of DNA transcription repressor specific for xylose (XylR); ...
 96-174 1.89e-03

ligand-binding domain of DNA transcription repressor specific for xylose (XylR); Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380485 [Multi-domain]  Cd Length: 265  Bit Score: 39.49  E-value: 1.89e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612  96 FVDETRPELVAEAILKSRGNALVVYGQDHELIidaiAEVTSAGKPVVtIVSDVPSAPRLSYVGIDHYKAGRCAA-FFLAK 174
Cdd:cd01543   33 YLEPPGYEELLDLLKGWKGDGIIARLDDPELA----EALRRLGIPVV-NVSGSRPEPGFPRVTTDNEAIGRMAAeHLLER 107
PRK10339 PRK10339
DNA-binding transcriptional repressor EbgR; Provisional
 5-68 1.94e-03

DNA-binding transcriptional repressor EbgR; Provisional


Pssm-ID: 182389 [Multi-domain]  Cd Length: 327  Bit Score: 39.36  E-value: 1.94e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612   5 LIDVARRAGVGHATVDRVLNERG--GVRPETAKRVLDAARDLGF----DRKLPTLYRQGLRFEVLLGRRQ 68
Cdd:PRK10339   4 LKDIAIEAGVSLATVSRVLNDDPtlNVKEETKHRILEIAEKLEYktssARKLQTGAVNQHHILAIYSYQQ 73
PBP1_Qymf-like cd06291
ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing ...
 129-207 2.26e-03

ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs; This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380514 [Multi-domain]  Cd Length: 264  Bit Score: 39.04  E-value: 2.26e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499272612 129 DAIAEVTSAGKPVVTIvsDVPSAPRLSYVGIDHYKAGRCAAFFLAKmAGEGSIVLLCSSLYYRAEAERISGCRDGMADH 207
Cdd:cd06291   66 LDIEEYKKLNIPIVSI--DRYLSEGIPSVSSDNYQGGRLAAEHLIE-KGCKKILHIGGPSNNSPANERYRGFEDALKEA 141
PRK10703 PRK10703
HTH-type transcriptional repressor PurR;
7-46 3.16e-03

HTH-type transcriptional repressor PurR;


Pssm-ID: 236739 [Multi-domain]  Cd Length: 341  Bit Score: 38.94  E-value: 3.16e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 499272612   7 DVARRAGVGHATVDRVLNERGGVRPETAKRVLDAARDLGF 46
Cdd:PRK10703   6 DVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHY 45
PBP1_ABC_sugar_binding-like cd06319
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 136-300 7.87e-03

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380542 [Multi-domain]  Cd Length: 278  Bit Score: 37.34  E-value: 7.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 136 SAGKPVVtiVSDV--PSAPRLSYVGIDHYKAGRCAAFFLAKMAGE-----GSIVLLCSSLYYRAEAERISGCRDGMADH- 207
Cdd:cd06319   78 EAKIPVV--IADIgtGGGDYVSYIISDNYDGGYQAGEYLAEALKEngwggGSVGIIAIPQSRVNGQARTAGFEDALEEAg 155

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499272612 208 ----ADRQSVSALVEldENDPFAGEELSkalEAGKVTGIYNAGVSHAV-LGRALAAHSLGPPPVLVGHDISPDAERMLQE 282
Cdd:cd06319  156 veevALRQTPNSTVE--ETYSAAQDLLA---ANPDIKGIFAQNDQMAQgALQAIEEAGRTGDILVVGFDGDPEALDLIKD 230

                        170
                 ....*....|....*...
gi 499272612 283 GVMTLVIDQNPDLQVRKA 300
Cdd:cd06319  231 GKLDGTVAQQPFGMGARA 248
 
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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