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Conserved domains on  [gi|742479139|ref|WP_038934192|]
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MULTISPECIES: LacI family DNA-binding transcriptional regulator [Bradyrhizobium]

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 ...
 69-343 1.97e-104

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: 307.57  E-value: 1.97e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  69 RLLFLLPAGTNRFLSTLGQLIAHSDGRLAPFNVHCQVDTIKSFNPDLLARQLWRARDKADGIAFMALEHPVVREAVDRLA 148
Cdd:cd06307    1 RFGFLLPSPENPFYELLRRAIEAAAAALRDRRVRLRIHFVDSLDPEALAAALRRLAAGCDGVALVAPDHPLVRAAIDELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 149 EHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERPAKVAMIAGSRSYRAHEEREMGFLHVFEELFPAIKV 228
Cdd:cd06307   81 ARGIPVVTLVSDLPGSRRLAYVGIDNRAAGRTAAWLMGRFLGRRPGKVLVILGSHRFRGHEEREAGFRSVLRERFPDLTV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 229 VGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGGAADGVARALNEMNRARDVVFIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:cd06307  161 LEVLEGLDDDELAYELLRELLARHPDLVGIYNAGGGNEGIARALREAGRARRVVFIGHELTPETRRLLRDGTIDAVIDQD 240

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 742479139 309 QLNTMMSCVGIFDNLRAGRSAMHGIEAPRSEIIFR 343
Cdd:cd06307  241 PELQARRAIEVLLAHLGGKGPAPPQPPIPIEIITR 275
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 14-62 1.28e-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: 67.43  E-value: 1.28e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 742479139  14 DVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMPaeNLLAA 62
Cdd:cd01392    2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRP--NAAAR 48
 
Name Accession Description Interval E-value
PBP1_sugar_binding cd06307
periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic ...
 69-343 1.97e-104

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: 307.57  E-value: 1.97e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  69 RLLFLLPAGTNRFLSTLGQLIAHSDGRLAPFNVHCQVDTIKSFNPDLLARQLWRARDKADGIAFMALEHPVVREAVDRLA 148
Cdd:cd06307    1 RFGFLLPSPENPFYELLRRAIEAAAAALRDRRVRLRIHFVDSLDPEALAAALRRLAAGCDGVALVAPDHPLVRAAIDELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 149 EHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERPAKVAMIAGSRSYRAHEEREMGFLHVFEELFPAIKV 228
Cdd:cd06307   81 ARGIPVVTLVSDLPGSRRLAYVGIDNRAAGRTAAWLMGRFLGRRPGKVLVILGSHRFRGHEEREAGFRSVLRERFPDLTV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 229 VGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGGAADGVARALNEMNRARDVVFIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:cd06307  161 LEVLEGLDDDELAYELLRELLARHPDLVGIYNAGGGNEGIARALREAGRARRVVFIGHELTPETRRLLRDGTIDAVIDQD 240

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 742479139 309 QLNTMMSCVGIFDNLRAGRSAMHGIEAPRSEIIFR 343
Cdd:cd06307  241 PELQARRAIEVLLAHLGGKGPAPPQPPIPIEIITR 275
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
 61-308 1.60e-52

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: 175.88  E-value: 1.60e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  61 AAMRPKPMRLLFLLPAGTNRFLSTLGQLIAHsdgRLAPFNVHCQVdTIKSFNPDLLARQLWRARD-KADGIAFMALEHPV 139
Cdd:COG1879   27 AAAAAKGKTIGFVVKTLGNPFFVAVRKGAEA---AAKELGVELIV-VDAEGDAAKQISQIEDLIAqGVDAIIVSPVDPDA 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 140 VREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGErPAKVAMIAGSRSYRAHEEREMGFLHVF 219
Cdd:COG1879  103 LAPALKKAKAAGIPVVTVDSDVDGSDRVAYVGSDNYAAGRLAAEYLAKALGG-KGKVAILTGSPGAPAANERTDGFKEAL 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 220 EElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNI-GGAADGVARALNEMNRARDVVFIGHGLTSDTRSFLLD 298
Cdd:COG1879  182 KE-YPGIKVVAEQYADWDREKALEVMEDLLQAHPDIDGIFAAnDGMALGAAQALKAAGRKGDVKVVGFDGSPEALQAIKD 260

                        250
                 ....*....|
gi 742479139 299 GTMDAVITQN 308
Cdd:COG1879  261 GTIDATVAQD 270
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
 126-308 5.46e-39

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: 138.98  E-value: 5.46e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  126 KADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSY 205
Cdd:pfam13407  55 GVDAIIVAPVDPTALAPVLKKAKDAGIPVVTFDSDAPSSPRLAYVGFDNEAAGEAAGELLAEALGGK-GKVAILSGSPGD 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  206 RAHEEREMGFLHVFEELFPAIKVVGLREG-HDDADRNYRQTRMLLGQHPD-LAGIYNIG-GAADGVARALNEMNRARDVV 282
Cdd:pfam13407 134 PNANERIDGFKKVLKEKYPGIKVVAEVEGtNWDPEKAQQQMEALLTAYPNpLDGIISPNdGMAGGAAQALEAAGLAGKVV 213

                         170       180
                  ....*....|....*....|....*.
gi 742479139  283 FIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:pfam13407 214 VTGFDATPEALEAIKDGTIDATVLQD 239
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 14-62 1.28e-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: 67.43  E-value: 1.28e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 742479139  14 DVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMPaeNLLAA 62
Cdd:cd01392    2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRP--NAAAR 48
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
12-63 2.10e-14

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 67.23  E-value: 2.10e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 742479139    12 IVDVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMPaeNLLAAM 63
Cdd:smart00354   3 IKDVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGYIP--NRVARS 52
LacI pfam00356
Bacterial regulatory proteins, lacI family;
12-55 8.69e-13

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 61.88  E-value: 8.69e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 742479139   12 IVDVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMP 55
Cdd:pfam00356   2 IKDVARLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNYIP 45
lacI PRK09526
lac repressor; Reviewed
 14-295 5.07e-11

lac repressor; Reviewed


Pssm-ID: 181929 [Multi-domain]  Cd Length: 342  Bit Score: 63.09  E-value: 5.07e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  14 DVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMP--AENLLAAMRPKPMRLlfllpAGTNRFLSTLGQLIA- 90
Cdd:PRK09526  10 DVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPnrVAQQLAGKQSLTIGL-----ATTSLALHAPSQIAAa 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  91 -HSDGRLAPFNV------HCQVDTIKSFNPDLLARqlwrardKADGIafmALEHPVVREAVDRLAEHGVPTVTLI----- 158
Cdd:PRK09526  85 iKSRADQLGYSVvismveRSGVEACQAAVNELLAQ-------RVSGV---IINVPLEDADAEKIVADCADVPCLFldvsp 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 159 -SDILNARRAAYIGldnrsIGRTAGYLIArfLGERpaKVAMIAGSRSYRAHEEREMGFLHVFEELfpAIKVVGLREGHDD 237
Cdd:PRK09526 155 qSPVNSVSFDPEDG-----TRLGVEHLVE--LGHQ--RIALLAGPESSVSARLRLAGWLEYLTDY--QLQPIAVREGDWS 223

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 742479139 238 ADRNYRQTRMLLGQHPDLAGIYNiggAAD----GVARALNEMNRA--RDVVFIGHGLTSDTRSF 295
Cdd:PRK09526 224 AMSGYQQTLQMLREGPVPSAILV---ANDqmalGVLRALHESGLRvpGQISVIGYDDTEDSSYF 284
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
12-61 8.74e-09

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 56.32  E-value: 8.74e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 742479139  12 IVDVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMPAENLLA 61
Cdd:PRK10401   4 IRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPNANAQA 53
 
Name Accession Description Interval E-value
PBP1_sugar_binding cd06307
periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic ...
 69-343 1.97e-104

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: 307.57  E-value: 1.97e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  69 RLLFLLPAGTNRFLSTLGQLIAHSDGRLAPFNVHCQVDTIKSFNPDLLARQLWRARDKADGIAFMALEHPVVREAVDRLA 148
Cdd:cd06307    1 RFGFLLPSPENPFYELLRRAIEAAAAALRDRRVRLRIHFVDSLDPEALAAALRRLAAGCDGVALVAPDHPLVRAAIDELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 149 EHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERPAKVAMIAGSRSYRAHEEREMGFLHVFEELFPAIKV 228
Cdd:cd06307   81 ARGIPVVTLVSDLPGSRRLAYVGIDNRAAGRTAAWLMGRFLGRRPGKVLVILGSHRFRGHEEREAGFRSVLRERFPDLTV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 229 VGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGGAADGVARALNEMNRARDVVFIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:cd06307  161 LEVLEGLDDDELAYELLRELLARHPDLVGIYNAGGGNEGIARALREAGRARRVVFIGHELTPETRRLLRDGTIDAVIDQD 240

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 742479139 309 QLNTMMSCVGIFDNLRAGRSAMHGIEAPRSEIIFR 343
Cdd:cd06307  241 PELQARRAIEVLLAHLGGKGPAPPQPPIPIEIITR 275
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
 61-308 1.60e-52

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: 175.88  E-value: 1.60e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  61 AAMRPKPMRLLFLLPAGTNRFLSTLGQLIAHsdgRLAPFNVHCQVdTIKSFNPDLLARQLWRARD-KADGIAFMALEHPV 139
Cdd:COG1879   27 AAAAAKGKTIGFVVKTLGNPFFVAVRKGAEA---AAKELGVELIV-VDAEGDAAKQISQIEDLIAqGVDAIIVSPVDPDA 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 140 VREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGErPAKVAMIAGSRSYRAHEEREMGFLHVF 219
Cdd:COG1879  103 LAPALKKAKAAGIPVVTVDSDVDGSDRVAYVGSDNYAAGRLAAEYLAKALGG-KGKVAILTGSPGAPAANERTDGFKEAL 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 220 EElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNI-GGAADGVARALNEMNRARDVVFIGHGLTSDTRSFLLD 298
Cdd:COG1879  182 KE-YPGIKVVAEQYADWDREKALEVMEDLLQAHPDIDGIFAAnDGMALGAAQALKAAGRKGDVKVVGFDGSPEALQAIKD 260

                        250
                 ....*....|
gi 742479139 299 GTMDAVITQN 308
Cdd:COG1879  261 GTIDATVAQD 270
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
 126-308 5.46e-39

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: 138.98  E-value: 5.46e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  126 KADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSY 205
Cdd:pfam13407  55 GVDAIIVAPVDPTALAPVLKKAKDAGIPVVTFDSDAPSSPRLAYVGFDNEAAGEAAGELLAEALGGK-GKVAILSGSPGD 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  206 RAHEEREMGFLHVFEELFPAIKVVGLREG-HDDADRNYRQTRMLLGQHPD-LAGIYNIG-GAADGVARALNEMNRARDVV 282
Cdd:pfam13407 134 PNANERIDGFKKVLKEKYPGIKVVAEVEGtNWDPEKAQQQMEALLTAYPNpLDGIISPNdGMAGGAAQALEAAGLAGKVV 213

                         170       180
                  ....*....|....*....|....*.
gi 742479139  283 FIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:pfam13407 214 VTGFDATPEALEAIKDGTIDATVLQD 239
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
12-287 1.77e-30

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


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 118.38  E-value: 1.77e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  12 IVDVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMPaeNLLA-AMRPKPMRLL-FLLPAGTNRFLStlgQLI 89
Cdd:COG1609    6 IKDVARLAGVSVATVSRVLNGPPRVSEETRERVLAAAEELGYRP--NAAArSLRTGRTRTIgVVVPDLSNPFFA---ELL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  90 AHSDGRLAPFNVH---CQVDTiksfNPDLLARQLWRARDK-ADGIAFMALEHPvvREAVDRLAEHGVPTVtLISDILNAR 165
Cdd:COG1609   81 RGIEEAARERGYQlllANSDE----DPEREREALRLLLSRrVDGLILAGSRLD--DARLERLAEAGIPVV-LIDRPLPDP 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 166 RAAYIGLDNRSIGRTAG-YLIArfLGERpaKVAMIAGSRSYRAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQ 244
Cdd:COG1609  154 GVPSVGVDNRAGARLATeHLIE--LGHR--RIAFIGGPADSSSARERLAGYREALAEAGLPPDPELVVEGDFSAESGYEA 229

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 742479139 245 TRMLLGQHPDLAGI--YNIGGAAdGVARALNEMNRA--RDVVFIGHG 287
Cdd:COG1609  230 ARRLLARGPRPTAIfcANDLMAL-GALRALREAGLRvpEDVSVVGFD 275
PBP1_ABC_sugar_binding-like cd01536
periplasmic sugar-binding domain of active transport systems that are members of the type 1 ...
 126-308 6.92e-30

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: 114.97  E-value: 6.92e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 126 KADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDI-LNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRS 204
Cdd:cd01536   55 GVDAIIIAPVDSEALVPAVKKANAAGIPVVAVDTDIdGGGDVVAFVGTDNYEAGKLAGEYLAEALGGK-GKVAILEGPPG 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 205 YRAHEEREMGFLHVFEElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIG-GAADGVARALNEMNRARDVVF 283
Cdd:cd01536  134 SSTAIDRTKGFKEALKK-YPDIEIVAEQPANWDRAKALTVTENLLQANPDIDAVFAANdDMALGAAEALKAAGRTGDIKI 212

                        170       180
                 ....*....|....*....|....*
gi 742479139 284 IGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:cd01536  213 VGVDGTPEALKAIKDGELDATVAQD 237
PBP1_ABC_sugar_binding-like cd19969
monosaccharide ABC transporter substrate binding protein; Periplasmic sugar-binding domain of ...
 126-315 2.40e-28

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: 111.28  E-value: 2.40e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 126 KADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSY 205
Cdd:cd19969   56 NPDGIAVSAIDPEALTPTINKAVDAGIPVVTFDSDAPESKRISYVGTDNYEAGYAAAEKLAELLGGK-GKVAVLTGPGQP 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 206 RaHEEREMGFLHVFEElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIY-NIGGAADGVARALNEMNRARDVVFI 284
Cdd:cd19969  135 N-HEERVEGFKEAFAE-YPGIEVVAVGDDNDDPEKAAQNTSALLQAHPDLVGIFgVDASGGVGAAQAVREAGKTGKVKIV 212

                        170       180       190
                 ....*....|....*....|....*....|.
gi 742479139 285 GHGLTSDTRSFLLDGTMDAVITQNQlnTMMS 315
Cdd:cd19969  213 AFDDDPETLDLIKDGVIDASIAQRP--WMMG 241
PBP1_tmGBP cd06314
periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and ...
 104-308 6.51e-28

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: 109.98  E-value: 6.51e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 104 QVDTIKsfnpDLLARqlwrardKADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGY 183
Cdd:cd06314   45 QVQLIE----DLIAR-------GVDGIAISPNDPEAVTPVINKAADKGIPVITFDSDAPDSKRLAYIGTDNYEAGREAGE 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 184 LIARFLGErPAKVAMIAGSRSYRAHEEREMGFLHVFEELfPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGG 263
Cdd:cd06314  114 LMKKALPG-GGKVAIITGGLGADNLNERIQGFKDALKGS-PGIEIVDPLSDNDDIAKAVQNVEDILKANPDLDAIFGVGA 191

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 742479139 264 -AADGVARALNEMNRARDVVFIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:cd06314  192 yNGPAIAAALKDAGKVGKVKIVGFDTLPETLQGIKDGVIAATVGQR 237
PBP1_ABC_sugar_binding-like cd06310
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 126-308 5.82e-26

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: 104.73  E-value: 5.82e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 126 KADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSY 205
Cdd:cd06310   57 KPDAIVVAPLDSEDLVDPLKDAKDKGIPVIVIDSGIKGDAYLSYIATDNYAAGRLAAQKLAEALGGK-GKVAVLSLTAGN 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 206 RAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGG-AADGVARALNEMNRARDVVFI 284
Cdd:cd06310  136 STTDQREEGFKEYLKKHPGGIKVLASQYAGSDYAKAANETEDLLGKYPDIDGIFATNEiTALGAAVAIKSRKLSGQIKIV 215

                        170       180
                 ....*....|....*....|....
gi 742479139 285 GHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:cd06310  216 GFDSQEELLDALKNGKIDALVVQN 239
PBP1_ABC_sugar_binding-like cd20006
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 124-311 8.20e-26

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: 104.22  E-value: 8.20e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 124 RDKADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERPaKVAMIAGSR 203
Cdd:cd20006   57 AQKPDAIVLAASDYDRLVEAVERAKKAGIPVITIDSPVNSKKADSFVATDNYEAGKKAGEKLASLLGEKG-KVAIVSFVK 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 204 SYRAHEEREMGFLHVFEElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIynIG---GAADGVARALNEMNRARD 280
Cdd:cd20006  136 GSSTAIEREEGFKQALAE-YPNIKIVETEYCDSDEEKAYEITKELLSKYPDINGI--VAlneQSTLGAARALKELGLGGK 212

                        170       180       190
                 ....*....|....*....|....*....|.
gi 742479139 281 VVFIGHGLTSDTRSFLLDGTMDAVITQNQLN 311
Cdd:cd20006  213 VKVVGFDSSVEEIQLLEEGIIDALVVQNPFN 243
PBP1_ABC_sugar_binding-like cd20005
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 126-308 3.57e-24

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: 100.01  E-value: 3.57e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 126 KADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSigrtAGYLIARFLGE---RPAKVAMIAGS 202
Cdd:cd20005   57 KPDAIALAALDTNALLPQLEKAKEKGIPVVTFDSGVPSDLPLATVATDNYA----AGALAADHLAEligGKGKVAIVAHD 132

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 203 RSYRAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIY--NiGGAADGVARALNEMNRARD 280
Cdd:cd20005  133 ATSETGIDRRDGFKDEIKEKYPDIKVVNVQYGVGDHAKAADIAKAILQANPDLKGIYatN-EGAAIGVANALKEMGKLGK 211

                        170       180
                 ....*....|....*....|....*...
gi 742479139 281 VVFIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:cd20005  212 IKVVGFDSGEAQIDAIKNGVIAGSVTQN 239
PBP1_ABC_sugar_binding-like cd20008
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 126-309 2.47e-23

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: 97.69  E-value: 2.47e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 126 KADGIAFMALEHPVVREAVDRlAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERP---AKVAMIAGS 202
Cdd:cd20008   57 KPDAIVLAPNDTAALVPAVEA-ADAGIPVVLVDSGANTDDYDAFLATDNVAAGALAADELAELLKASGggkGKVAIISFQ 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 203 RSYRAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIY-NIGGAADGVARALNEMNRARDV 281
Cdd:cd20008  136 AGSQTLVDREEGFRDYIKEKYPDIEIVDVQYSDGDIAKALNQTTDLLTANPDLVGIFgANNPSAVGVAQALAEAGKAGKI 215

                        170       180
                 ....*....|....*....|....*...
gi 742479139 282 VFIGHGLTSDTRSFLLDGTMDAVITQNQ 309
Cdd:cd20008  216 VLVGFDSSPDEVALLKSGVIKALVVQDP 243
PBP1_sensor_kinase-like cd06308
periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic ...
 140-306 5.27e-21

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: 91.07  E-value: 5.27e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 140 VREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFLHVF 219
Cdd:cd06308   70 LTPVVKKAYDAGIPVIVLDRKVSGDDYTAFIGADNVEIGRQAGEYIAELLNGK-GNVVEIQGLPGSSPAIDRHKGFLEAI 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 220 EElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYnigGAAD----GVARALNEMNRARDVVFIGH-GLTSDTRS 294
Cdd:cd06308  149 AK-YPGIKIVASQDGDWLRDKAIKVMEDLLQAHPDIDAVY---AHNDemalGAYQALKKAGREKEIKIIGVdGLPEAGEK 224

                        170
                 ....*....|..
gi 742479139 295 FLLDGTMDAVIT 306
Cdd:cd06308  225 AVKDGILAATFL 236
PBP1_LsrB_Quorum_Sensing-like cd06302
periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium ...
 104-305 1.53e-19

periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs; Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling.


Pssm-ID: 380525 [Multi-domain]  Cd Length: 296  Bit Score: 87.30  E-value: 1.53e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 104 QVDTIKsfnpDLLARqlwrardKADGIAF-----MALEhPVVREAVDRlaehGVPTVTLISDILNARRAAYI-GLDNRSI 177
Cdd:cd06302   45 QVQIVE----NLIAQ-------GVDAIAVspndaDALA-PVLKKAKDA----GIKVITWDSDAPPSARDYFVnQADDEGL 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 178 GRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAG 257
Cdd:cd06302  109 GEALVDSLAKEIGGK-GKVAILSGSLTATNLNAWIKAMKEYLKSKYPDIELVDTYYTDDDQQKAYTQAQNLIQAYPDLKG 187

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 742479139 258 IYNIGGAAD-GVARALNEMNRARDVVFIGHGLTSDTRSFLLDGTMDAVI 305
Cdd:cd06302  188 IIGVSTTAPpAAAQAVEEAGKTGKVAVTGIGLPNTARPYLKDGSVKEGV 236
PBP1_ABC_sugar_binding-like cd20004
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 121-308 2.56e-17

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: 80.74  E-value: 2.56e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 121 WRARDKADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERPaKVAMI- 199
Cdd:cd20004   52 YFIDQGVDGIVLAPLDRKALVAPVERARAQGIPVVIIDSDLGGDAVISFVATDNYAAGRLAAKRMAKLLNGKG-KVALLr 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 200 --AGSRSYRaheEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGGA-ADGVARALNEMN 276
Cdd:cd20004  131 laKGSASTT---DRERGFLEALKKLAPGLKVVDDQYAGGTVGEARSSAENLLNQYPDVDGIFTPNEStTIGALRALRRLG 207

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 742479139 277 RARDVVFIGHgltsDTRSFLLD----GTMDAVITQN 308
Cdd:cd20004  208 LAGKVKFIGF----DASDLLLDalraGEISALVVQD 239
PBP1_ABC_sugar_binding-like cd06322
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 116-308 7.65e-16

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: 76.55  E-value: 7.65e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 116 LARQLWRARD----KADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGE 191
Cdd:cd06322   41 LAKQLSQIEDfiqqGVDAIILAPVDSGGIVPAIEAANEAGIPVFTVDVKADGAKVVTHVGTDNYAGGKLAGEYALKALLG 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 192 RPAKVAMIagsrSYRAHE---EREMGFLHVFEElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGG-AADG 267
Cdd:cd06322  121 GGGKIAII----DYPEVEsvvLRVNGFKEAIKK-YPNIEIVAEQPGDGRREEALAATEDMLQANPDLDGIFAIGDpAALG 195

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 742479139 268 VARALNEMNRARDVVFIGHGLTSDTRSFLL-DGTMDAVITQN 308
Cdd:cd06322  196 ALTAIESAGKEDKIKVIGFDGNPEAIKAIAkGGKIKADIAQQ 237
PBP1_ABC_sugar_binding-like cd19970
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 138-307 9.91e-16

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: 76.13  E-value: 9.91e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 138 PVVREAVDRlaehGVPTVTlISDILNARRAA-------YIGLDNRSIGRTAGYLIARFLGErPAKVAMIAGSRSYRAHEE 210
Cdd:cd19970   74 PVLKKAVDA----GIAVIN-IDNRLDADALKegginvpFVGPDNRQGAYLAGDYLAKKLGK-GGKVAIIEGIPGADNAQQ 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 211 REMGFLHVFEElfPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGGA-ADGVARALNEMNRARDVVFIGHGLT 289
Cdd:cd19970  148 RKAGFLKAFEE--AGMKIVASQSANWEIDEANTVAANLLTAHPDIRGILCANDNmALGAIKAVDAAGKAGKVLVVGFDNI 225

                        170
                 ....*....|....*...
gi 742479139 290 SDTRSFLLDGTMDAVITQ 307
Cdd:cd19970  226 PAVRPLLKDGKMLATIDQ 243
PBP1_ABC_sugar_binding-like cd06317
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 126-307 2.44e-15

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: 75.11  E-value: 2.44e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 126 KADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDN----RSIGR-TAGYLIARFLGerPAKVAMIa 200
Cdd:cd06317   55 GVDAIILDAIDVNGSIPAIKRASEAGIPVIAYDAVIPSDFQAAQVGVDNleggKEIGKyAADYIKAELGG--QAKIGVV- 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 201 GSRSYRAHEEREMGFLHVFEELfPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIG-GAADGVARALNEMNRAR 279
Cdd:cd06317  132 GALSSLIQNQRQKGFEEALKAN-PGVEIVATVDGQNVQEKALSAAENLLTANPDLDAIYATGePALLGAVAAVRSQGRQG 210

                        170       180
                 ....*....|....*....|....*....
gi 742479139 280 DVVFIGHGLTSDTRSFLLD-GTMDAVITQ 307
Cdd:cd06317  211 KIKVFGWDLTKQAIFLGIDeGVLQAVVQQ 239
PBP1_allose_binding cd06320
periplasmic allose-binding domain of bacterial transport systems that function as a primary ...
 140-307 9.86e-15

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: 73.45  E-value: 9.86e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 140 VREAVDRLAEHGVPTVTL----ISDILNARR---AAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEERE 212
Cdd:cd06320   71 LIPPIEKANKKGIPVINLddavDADALKKAGgkvTSFIGTDNVAAGALAAEYIAEKLPGG-GKVAIIEGLPGNAAAEART 149

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 213 MGFLHVFEELfPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIY-NIGGAADGVARALNEMNRARDVVFIGHGLTSD 291
Cdd:cd06320  150 KGFKETFKKA-PGLKLVASQPADWDRTKALDAATAILQAHPDLKGIYaANDTMALGAVEAVKAAGKTGKVLVVGTDGIPE 228

                        170
                 ....*....|....*.
gi 742479139 292 TRSFLLDGTMDAVITQ 307
Cdd:cd06320  229 AKKSIKAGELTATVAQ 244
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 14-62 1.28e-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: 67.43  E-value: 1.28e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 742479139  14 DVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMPaeNLLAA 62
Cdd:cd01392    2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRP--NAAAR 48
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
12-63 2.10e-14

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 67.23  E-value: 2.10e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 742479139    12 IVDVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMPaeNLLAAM 63
Cdd:smart00354   3 IKDVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGYIP--NRVARS 52
PBP1_ABC_sugar_binding-like cd06324
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 101-303 5.63e-14

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 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: 380547 [Multi-domain]  Cd Length: 317  Bit Score: 71.48  E-value: 5.63e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 101 VHCQVDTIKSFNpdlLARQLWRARDKADGIAFMAlEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNR----- 175
Cdd:cd06324   36 LYANRNRFKMLE---LAEELLARPPKPDYLILVN-EKGVAPELLELAEQAKIPVFLINNDLTDEERALLGKPREKfkywl 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 176 -SIG---RTAGYLIARFLGER--------PAKVAMIAGSRSYRAHEEREMGFLHVFEElFPAIKVVGLREGHDDADRNYR 243
Cdd:cd06324  112 gSIVpdnEQAGYLLAKALIKAarkksddgKIRVLAISGDKSTPASILREQGLRDALAE-HPDVTLLQIVYANWSEDEAYQ 190

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 742479139 244 QTRMLLGQHPDLAGI--YNiGGAADGVARALNEMNRA--RDVVFIGHGLTSDTRSFLLDGTMDA 303
Cdd:cd06324  191 KTEKLLQRYPDIDIVwaAN-DAMALGAIDALEEAGLKpgKDVLVGGIDWSPEALQAVKDGELTA 253
PBP1_ABC_sugar_binding-like cd06316
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 149-309 1.03e-13

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: 380539 [Multi-domain]  Cd Length: 294  Bit Score: 70.73  E-value: 1.03e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 149 EHGVPTVTLISDilnarraayiglDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFLHVFEELFPAIKV 228
Cdd:cd06316   95 EAGKDYVSVVSS------------DNRGNGQIAAELLAEAIGGK-GKVGIIYHDADFYATNQRDKAFKDTLKEKYPDIKI 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 229 VGlREGHDDADRNYRQTRMLLGQHPDLAGIYNI-GGAADGVARALNEMNRaRDVVFIGHGLTSDTRSFLLDGTMDAVITQ 307
Cdd:cd06316  162 VA-EQGFADPNDAEEVASAMLTANPDIDGIYVSwDTPALGVISALRAAGR-SDIKITTVDLGTEIALDMAKGGNVKGIGA 239


                 ..
gi 742479139 308 NQ 309
Cdd:cd06316  240 QR 241
PBP1_ABC_sugar_binding-like cd20007
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 138-308 3.17e-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: 380662 [Multi-domain]  Cd Length: 271  Bit Score: 68.80  E-value: 3.17e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 138 PVVREAVDRlaehGVPTVTLISDILNAR-RAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFL 216
Cdd:cd20007   72 APLKRAADA----GIKVVTVDTTLGDPSfVLSQIASDNVAGGALAAEALAELIGGK-GKVLVINSTPGVSTTDARVKGFA 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 217 HVFEElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNI-GGAADGVARALNEMNRARDVVFIGHGLTSDTRSF 295
Cdd:cd20007  147 EEMKK-YPGIKVLGVQYSENDPAKAASIVAAALQANPDLAGIFGTnTFSAEGAAAALRNAGKTGKVKVVGFDASPAQVEQ 225

                        170
                 ....*....|...
gi 742479139 296 LLDGTMDAVITQN 308
Cdd:cd20007  226 LKAGTIDALIAQK 238
PBP1_TorT-like cd06306
TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor ...
 123-308 6.20e-13

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: 67.99  E-value: 6.20e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 123 ARDKADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERPAKVAMIAGS 202
Cdd:cd06306   54 VASGADAILLGAISFDGLDPKVAEAAAAGIPVIDLVNGIDSPKVAARVLVDFYDMGYLAGEYLVEHHPGKPVKVAWFPGP 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 203 RSYRAHEEREMGFLHVFEElfPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGGAADGVARALNEMNRARDVV 282
Cdd:cd06306  134 AGAGWAEDREKGFKEALAG--SNVEIVATKYGDTGKAVQLNLVEDALQAHPDIDYIVGNAVAAEAAVGALREAGLTGKVK 211

                        170       180
                 ....*....|....*....|....*.
gi 742479139 283 FIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:cd06306  212 VVSTYLTPGVYRGIKRGKILAAPSDQ 237
LacI pfam00356
Bacterial regulatory proteins, lacI family;
12-55 8.69e-13

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 61.88  E-value: 8.69e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 742479139   12 IVDVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMP 55
Cdd:pfam00356   2 IKDVARLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNYIP 45
PBP1_ribose_binding cd06323
periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose ...
 140-307 1.15e-12

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: 67.32  E-value: 1.15e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 140 VREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGErPAKVAMIAGSRSYRAHEEREMGFLHVF 219
Cdd:cd06323   69 VSPAVEEANEAGIPVITVDRSVTGGKVVSHIASDNVAGGEMAAEYIAKKLGG-KGKVVELQGIPGTSAARERGKGFHNAI 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 220 EElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIY--NiGGAADGVARALNEMNRaRDVVFIGHGLTSDTRSFLL 297
Cdd:cd06323  148 AK-YPKINVVASQTADFDRTKGLNVMENLLQAHPDIDAVFahN-DEMALGAIQALKAAGR-KDVIVVGFDGTPDAVKAVK 224

                        170
                 ....*....|
gi 742479139 298 DGTMDAVITQ 307
Cdd:cd06323  225 DGKLAATVAQ 234
PBP1_LsrB_Quorum_Sensing-like cd20001
ligand-binding protein LsrB-like of ABC transporter periplasmic binding protein; ...
 173-304 1.04e-11

ligand-binding protein LsrB-like of ABC transporter periplasmic binding protein; Ligand-binding protein LsrB-like of a transport system, similar to periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling.


Pssm-ID: 380656  Cd Length: 296  Bit Score: 64.61  E-value: 1.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 173 DNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFLHVFEELFPAIKVVGLR-EGHDDADRNYRQTRMLLGQ 251
Cdd:cd20001  103 DNAAYGAFIMDKLAEAMGGK-GKYVTFVGSLTSTSHMEWANAAVAYQKANYPDMLLVTDRvETNDDSETAYEKAKELLKT 181

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 742479139 252 HPDLAGIynIGGAAD---GVARALNEMNRARDVVFIGHGLTSDTRSFLLDGTMDAV 304
Cdd:cd20001  182 YPDLKGI--VGCSSSdvpGAARAVEELGLQGKIAVVGTGLPSVAGEYLEDGTIDYI 235
PBP1_ABC_sugar_binding-like cd06319
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 144-307 1.34e-11

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: 64.30  E-value: 1.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 144 VDRLAEHGVPTVtlISDI--LNARRAAYIGLDNRSIGRTAGYLIARFLGER---PAKVAMIAGSRSYRAHEEREMGFLHV 218
Cdd:cd06319   73 LDLANEAKIPVV--IADIgtGGGDYVSYIISDNYDGGYQAGEYLAEALKENgwgGGSVGIIAIPQSRVNGQARTAGFEDA 150

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 219 FEElfPAIKVVGLRE-GHDDADRNYRQTRMLLGQHPDLAGIYNIGG-AADGVARALNEMNRARDVVFIGHGLTSDTRSFL 296
Cdd:cd06319  151 LEE--AGVEEVALRQtPNSTVEETYSAAQDLLAANPDIKGIFAQNDqMAQGALQAIEEAGRTGDILVVGFDGDPEALDLI 228

                        170
                 ....*....|.
gi 742479139 297 LDGTMDAVITQ 307
Cdd:cd06319  229 KDGKLDGTVAQ 239
PBP1_LsrB_Quorum_Sensing cd20003
ligand-binding protein LsrB of ABC transporter periplasmic binding protein; Periplasmic ...
 100-305 1.79e-11

ligand-binding protein LsrB of ABC transporter periplasmic binding protein; Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling.


Pssm-ID: 380658  Cd Length: 298  Bit Score: 64.22  E-value: 1.79e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 100 NVHCQVDTIKSF---NPDLLARqlwrARDKADGIAfmalehPVVREAVDRlaehGVPTVTLISDILNARRAAYIGL-DNR 175
Cdd:cd20003   41 SVSKQVEVINNFinqGYDVIAV----SANDPDALA------PALKKAMKK----GIKVVTWDSDVNPDARDFFVNQaTPE 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 176 SIGRTAGYLIARFLGERpAKVAMIAGSRS------YRAHEEREMgflhvfEELFPAIKVVGLREGHDDADRNYRQTRMLL 249
Cdd:cd20003  107 GIGKTLVDMVAEQTGEK-GKVAIVTSSPTatnqnaWIKAMKAYI------AEKYPDMKIVTTQYGQEDPAKSLQVAENIL 179

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 742479139 250 GQHPDLAGIYNIGGAA-DGVARALNEMNRARDVVFIGHGLTSDTRSFLLDGTMDAVI 305
Cdd:cd20003  180 KAYPDLKAIIAPDSVAlPGAAEAVEQLGRTGKVAVTGLSTPNVMRPYVKDGTVKSVV 236
lacI PRK09526
lac repressor; Reviewed
 14-295 5.07e-11

lac repressor; Reviewed


Pssm-ID: 181929 [Multi-domain]  Cd Length: 342  Bit Score: 63.09  E-value: 5.07e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  14 DVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMP--AENLLAAMRPKPMRLlfllpAGTNRFLSTLGQLIA- 90
Cdd:PRK09526  10 DVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPnrVAQQLAGKQSLTIGL-----ATTSLALHAPSQIAAa 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  91 -HSDGRLAPFNV------HCQVDTIKSFNPDLLARqlwrardKADGIafmALEHPVVREAVDRLAEHGVPTVTLI----- 158
Cdd:PRK09526  85 iKSRADQLGYSVvismveRSGVEACQAAVNELLAQ-------RVSGV---IINVPLEDADAEKIVADCADVPCLFldvsp 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 159 -SDILNARRAAYIGldnrsIGRTAGYLIArfLGERpaKVAMIAGSRSYRAHEEREMGFLHVFEELfpAIKVVGLREGHDD 237
Cdd:PRK09526 155 qSPVNSVSFDPEDG-----TRLGVEHLVE--LGHQ--RIALLAGPESSVSARLRLAGWLEYLTDY--QLQPIAVREGDWS 223

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 742479139 238 ADRNYRQTRMLLGQHPDLAGIYNiggAAD----GVARALNEMNRA--RDVVFIGHGLTSDTRSF 295
Cdd:PRK09526 224 AMSGYQQTLQMLREGPVPSAILV---ANDqmalGVLRALHESGLRvpGQISVIGYDDTEDSSYF 284
PRK10703 PRK10703
HTH-type transcriptional repressor PurR;
12-251 2.69e-10

HTH-type transcriptional repressor PurR;


Pssm-ID: 236739 [Multi-domain]  Cd Length: 341  Bit Score: 60.89  E-value: 2.69e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  12 IVDVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMPAenllAAMRPkpmrllflLPAGTNRflsTLGQLIAH 91
Cdd:PRK10703   4 IKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPS----AVARS--------LKVNHTK---SIGLLATS 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  92 SDgrlAPF----------------------NVHCQVDTIKSFnPDLLARQlwrardKADGIAFMALEHPvvREAVDRLAE 149
Cdd:PRK10703  69 SE---APYfaeiieavekncyqkgytlilcNAWNNLEKQRAY-LSMLAQK------RVDGLLVMCSEYP--EPLLAMLEE 136

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 150 H-GVPTVTLISDILNARRAAYIgLDNRSIGrtaGYLIARFLGERPAK-VAMIAGSRSYRAHEEREMGFLHVFEELFPAIK 227
Cdd:PRK10703 137 YrHIPMVVMDWGEAKADFTDAI-IDNAFEG---GYLAGRYLIERGHRdIGVIPGPLERNTGAGRLAGFMKAMEEANIKVP 212

                        250       260
                 ....*....|....*....|....
gi 742479139 228 VVGLREGHDDADRNYRQTRMLLGQ 251
Cdd:PRK10703 213 EEWIVQGDFEPESGYEAMQQILSQ 236
PBP1_ABC_sugar_binding-like cd19966
monosaccharide ABC transporter substrate binding protein CUT2 family and simialr proteins; ...
 125-309 1.20e-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: 58.49  E-value: 1.20e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 125 DKADGIAFMAleHP---VVREAVDRLAEHGVPTVTLISDI----LNARRAAYIGLDNRSIGRT-AGYLIARFlGERPAKV 196
Cdd:cd19966   55 AKPDGIAIMG--HPgdgAYTPLIEAAKKAGIIVTSFNTDLpkleYGDCGLGYVGADLYAAGYTlAKELVKRG-GLKTGDR 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 197 AMI---AGSRSYRAheEREMGFLHVFEELfpAIKVVGLREGHDDADRNYRQTRM--LLGQHPDLAGIYNIGGA-ADGVAR 270
Cdd:cd19966  132 VFVpglLPGQPYRV--LRTKGVIDALKEA--GIKVDYLEISLEPNKPAEGIPVMtgYLAANPDVKAIVGDGGGlTANVAK 207

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 742479139 271 ALNEMN-RARDVVFIGHGLTSDTRSFLLDGTMDAVITQNQ 309
Cdd:cd19966  208 YLKAAGkKPGEIPVAGFDLSPATVQAIKSGYVNATIDQQP 247
PBP1_galactofuranose_YtfQ-like cd06309
periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ...
 114-308 1.35e-09

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: 58.38  E-value: 1.35e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 114 DLLARqlwrardKADGIAFMALE----HPVVREAVDRlaehGVPTVTLISDILNAR---RAAYIGLDNRSIGRTAGYLIA 186
Cdd:cd06309   50 DLIAQ-------GVDAILISPIDatgwDPVLKEAKDA----GIPVILVDRTIDGEDgslYVTFIGSDFVEEGRRAAEWLV 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 187 RFLGERPAKVAMIAGSRSYRAHEEREMGFLHVFEElFPAIKVVglREGHDDADRNYRQTRM--LLGQHP-DLAGIYnigG 263
Cdd:cd06309  119 KNYKGGKGNVVELQGTAGSSVAIDRSKGFREVIKK-HPNIKIV--ASQSGNFTREKGQKVMenLLQAGPgDIDVIY---A 192

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 742479139 264 AAD----GVARALNEMNR--ARDVVFIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:cd06309  193 HNDdmalGAIQALKEAGLkpGKDVLVVGIDGQKDALEAIKAGELNATVECN 243
PBP1_ABC_rhamnose cd20000
rhamnose ABC transporter substrate-binding protein; Rhamnose ABC transporter substrate-binding ...
 123-305 1.64e-09

rhamnose ABC transporter substrate-binding protein; Rhamnose ABC transporter substrate-binding protein similar to periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling.


Pssm-ID: 380655  Cd Length: 298  Bit Score: 58.04  E-value: 1.64e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 123 ARDKADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIG-LDNRSIGRTAGYLIARFLGERpAKVAMIAG 201
Cdd:cd20000   53 IQQGVDAIAISANDPDALAPALKKARAAGIKVVTFDSDVAPEARDLFVNqADADGIGRAQVDMMAELIGGE-GEFAILSA 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 202 S------RSYRAHEEREMGflhvfEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIY---NIGGAAdgVARAL 272
Cdd:cd20000  132 TptatnqNAWIDAMKKELA-----SPEYAGMKLVKVAYGDDDAQKSYQEAEALLQAYPDLKGIIaptTVGIAA--AARAL 204

                        170       180       190
                 ....*....|....*....|....*....|...
gi 742479139 273 NEMNRARDVVFIGHGLTSDTRSFLLDGTMDAVI 305
Cdd:cd20000  205 EDSGLKGKVKVTGLGLPSEMAKYVKDGTVPAFA 237
PBP1_LacI_sugar_binding-like cd06267
ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 ...
 126-285 1.94e-09

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: 57.53  E-value: 1.94e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 126 KADGIAFMALEHPvvREAVDRLAEHGVPTVtLISDILNARRAAYIGLDNRSIGRTAG-YLIArfLGERpaKVAMIAGSRS 204
Cdd:cd06267   55 RVDGIILAPSSLD--DELLEELLAAGIPVV-LIDRRLDGLGVDSVVVDNYAGAYLATeHLIE--LGHR--RIAFIGGPLD 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 205 YRAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYniggAAD-----GVARALNEMNRA- 278
Cdd:cd06267  128 LSTSRERLEGYRDALAEAGLPVDPELVVEGDFSEESGYEAARELLALPPRPTAIF----AANdlmaiGALRALRELGLRv 203


                 ....*...
gi 742479139 279 -RDVVFIG 285
Cdd:cd06267  204 pEDISVVG 211
PBP1_ABC_sugar_binding-like cd19965
monosaccharide ABC transporter substrate binding protein CUT2 family and similar proteins; ...
 99-308 2.03e-09

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: 57.67  E-value: 2.03e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  99 FNVHCQVDTIKSFNPDLLARQLWRA-RDKADGIAFMALE----HPVVREAVDRlaehGVPTVTLISDILNARRA--AYIG 171
Cdd:cd19965   28 LGAECQFTGPQTFDVAEQVSLLEAAiASGPDGIATTIVDpeafDEVIKRALDA----GIPVVAFNVDAPGGENArlAFVG 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 172 LDNRSIGRTAGYLIARFLGERPAKVAMIAGSRSYRAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGq 251
Cdd:cd19965  104 QDLYPAGYVLGKRIAEKFKPGGGHVLLGISTPGQSALEQRLDGIKQALKEYGRGITYDVIDTGTDLAEALSRIEAYYTA- 182

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 742479139 252 HPDLAGIYNIGGAAD-GVARALNEMNRARDVVFIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:cd19965  183 HPDIKAIFATGAFDTaGAGQAIKDLGLKGKVLVGGFDLVPEVLQGIKAGYIDFTIDQQ 240
PBP1_ABC_sugar_binding-like cd19972
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 151-307 2.87e-09

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: 57.07  E-value: 2.87e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 151 GVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFLHVFEElFPAIKVVG 230
Cdd:cd19972   80 GIPVIAVDRNPEDAPGDTFIATDSVAAAKELGEWVIKQTGGK-GEIAILHGQLGTTPEVDRTKGFQEALAE-APGIKVVA 157

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 231 LREGHDDADRNYRQTRMLLGQHPDLAGIYnigGAAD----GVARALNEMNRARDVVFIGH-GLTSDTRSfLLDGTMDAVI 305
Cdd:cd19972  158 EQTADWDQDEGFKVAQDMLQANPNITVFF---GQSDamalGAAQAVKVAGLDHKIWVVGFdGDVAGLKA-VKDGVLDATM 233


                 ..
gi 742479139 306 TQ 307
Cdd:cd19972  234 TQ 235
PBP1_ABC_sugar_binding-like cd06300
periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are ...
 138-278 3.63e-09

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: 57.33  E-value: 3.63e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 138 PVVREAVDRlaehGVPTVTLiSDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFLH 217
Cdd:cd06300   76 AVIEQAADA----GIPVVAF-DGAVTSPDAYNVSNDQVEWGRLGAKWLFEALGGK-GNVLVVRGIAGAPASADRHAGVKE 149

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 742479139 218 VFEElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGGAADGVARALNEMNRA 278
Cdd:cd06300  150 ALAE-YPGIKVVGEVFGGWDEATAQTAMLDFLATHPQVDGVWTQGGEDTGVLQAFQQAGRP 209
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
12-61 8.74e-09

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 56.32  E-value: 8.74e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 742479139  12 IVDVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMPAENLLA 61
Cdd:PRK10401   4 IRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPNANAQA 53
PBP1_LsrB_Quorum_Sensing-like cd20002
ligand-binding protein LsrB-like of ABC transporter periplasmic binding protein; ...
 172-308 1.99e-08

ligand-binding protein LsrB-like of ABC transporter periplasmic binding protein; Ligand-binding protein LsrB-like of a transport system, similar to periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling.


Pssm-ID: 380657  Cd Length: 295  Bit Score: 55.02  E-value: 1.99e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 172 LDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFLHVFEELFPAIKVVGLR-EGHDDADRNYRQTRMLLG 250
Cdd:cd20002  102 IDNEKFGEAQMELLAKEMGGK-GEYAIFVGSLTVPLHNLWADAAVEYQKEKYPNMKQVTDRiPGGEDVDVSRQTTLELLK 180

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 742479139 251 QHPDLAGIYNIGGA-ADGVARALNEMNRARDVVFIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:cd20002  181 AYPDLKGIISFGSLgPIGAGQALREKGLKGKVAVVGTVIPSQAAAYLKEGSITEGYLWD 239
PBP1_ABC_sugar_binding-like cd19999
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
 138-296 2.89e-08

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: 54.62  E-value: 2.89e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 138 PVVREAVDRlaehGVPTVTlISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFLH 217
Cdd:cd19999   76 PVIEKAQAA----GILVVS-FDQPVSSPDAINVVIDQYKWAAIQAQWLAEQLGGK-GNIVAINGVAGNPANEARVKAADD 149

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 218 VFEElFPAIKVVGlrEGHDDADRNYRQTRM--LLGQHPDLAGIYNIGGAADGVARALNEMNRARDVVfighglTSDTR-S 294
Cdd:cd19999  150 VFAK-YPGIKVLA--SVPGGWDQATAQQVMatLLATYPDIDGVLTQDGMAEGVLRAFQAAGKDPPVM------TGDYRkG 220


                 ..
gi 742479139 295 FL 296
Cdd:cd19999  221 FL 222
PBP1_ABC_D-talitol-like cd06318
periplasmic D-talitol-binding protein of an ABC transport system and similar proteins; ...
 139-304 2.91e-08

periplasmic D-talitol-binding protein of an ABC transport system 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: 380541 [Multi-domain]  Cd Length: 282  Bit Score: 54.34  E-value: 2.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 139 VVREAVDRLAEHGVPTVTLISDIL-NARRAAYIGLDNRSIGRTAGYLIARFLGERPAKVAMIAGSRSYRAHEEREMGFLH 217
Cdd:cd06318   68 GLTPAVKAAKAAGIPVITVDSALDpSANVATQVGRDNKQNGVLVGKEAAKALGGDPGKIIELSGDKGNEVSRDRRDGFLA 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 218 VFEE------LFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYnigGAAD----GVARALNEMNRARDVVFIGhg 287
Cdd:cd06318  148 GVNEyqlrkyGKSNIKVVAQPYGNWIRSGAVAAMEDLLQAHPDINVVY---AENDdmalGAMKALKAAGMLDKVKVAG-- 222

                        170
                 ....*....|....*..
gi 742479139 288 ltsdtrsflLDGTMDAV 304
Cdd:cd06318  223 ---------ADGQKEAL 230
PBP1_ABC_sugar_binding-like cd06311
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 126-287 3.65e-08

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: 53.91  E-value: 3.65e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 126 KADGIAFMALEHPVVREAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSY 205
Cdd:cd06311   55 KVDAIVILPQDSEELTVAAQKAKDAGIPVVNFDRGLNVLIYDLYVAGDNPGMGVVSAEYIGKKLGGK-GNVVVLEVPSSG 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 206 RAHEEREMGFLHVFEElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGG-AADGVARALNEMNRARDVVFI 284
Cdd:cd06311  134 SVNEERVAGFKEVIKG-NPGIKILAMQAGDWTREDGLKVAQDILTKNKKIDAVWAADDdMAIGVLQAIKEAGRTDIKVMT 212


                 ...
gi 742479139 285 GHG 287
Cdd:cd06311  213 GGG 215
PBP1_Qymf-like cd06291
ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing ...
 138-285 4.88e-08

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: 53.29  E-value: 4.88e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 138 PVVreAVDRLAEHGVPTVTliSDilnarraayigldNRSigrtAGYLIARFLGERPAK-VAMIAGSRSYRAHEEREMGFL 216
Cdd:cd06291   77 PIV--SIDRYLSEGIPSVS--SD-------------NYQ----GGRLAAEHLIEKGCKkILHIGGPSNNSPANERYRGFE 135

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 742479139 217 HVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYnigGAAD----GVARALNEMNRA--RDVVFIG 285
Cdd:cd06291  136 DALKEAGIEYEIIEIDENDFSEEDAYELAKELLEKYPDIDGIF---ASNDllaiGVLKALQKLGIRvpEDVQIIG 207
PBP1_ABC_sugar_binding-like cd19996
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
 138-277 1.11e-07

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: 52.63  E-value: 1.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 138 PVVREAVDRlaehGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFLH 217
Cdd:cd19996   74 PAIEKAAAA----GIPVVLFDSGVGSDKYTAFVGVDDAAFGRVGAEWLVKQLGGK-GNIIALRGIAGVSVSEDRWAGAKE 148

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 742479139 218 VFEElFPAIKVVGlregHDDADRNY----RQTRMLLGQHPDLAGIYNIGGA-ADGVARALNEMNR 277
Cdd:cd19996  149 VFKE-YPGIKIVG----EVYADWDYakakQAVESLLAAYPDIDGVWSDGGAmTLGAIEAFEEAGR 208
PRK09701 PRK09701
D-allose transporter substrate-binding protein;
129-308 2.33e-07

D-allose transporter substrate-binding protein;


Pssm-ID: 182037 [Multi-domain]  Cd Length: 311  Bit Score: 51.80  E-value: 2.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 129 GIAFMALEHPVVREAVDRLAEHGVPTVTLIS--DILNARRA-----AYIGLDNRSIGRTAGYLIARFLGERPAKVAMIAG 201
Cdd:PRK09701  85 GIAFAPLSSVNLVMPVARAWKKGIYLVNLDEkiDMDNLKKAggnveAFVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEG 164

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 202 SRSYRAHEEREMGFLHVFEELfPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGGA-ADGVARALNEMNRARD 280
Cdd:PRK09701 165 KAGNASGEARRNGATEAFKKA-SQIKLVASQPADWDRIKALDVATNVLQRNPNIKAIYCANDTmAMGVAQAVANAGKTGK 243

                        170       180
                 ....*....|....*....|....*...
gi 742479139 281 VVFIGHGLTSDTRSFLLDGTMDAVITQN 308
Cdd:PRK09701 244 VLVVGTDGIPEARKMVEAGQMTATVAQN 271
PBP1_MalI-like cd06289
ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia ...
 141-286 2.89e-07

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: 51.03  E-value: 2.89e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 141 REAVDRLAEHGVPTVTLISDILNARrAAYIGLDNRSIGRTAG-YLIArfLGERpaKVAMIAGSRSYRAHEEREMGFLHVF 219
Cdd:cd06289   69 AELLRRLKAWGIPVVLALRDVPGSD-LDYVGIDNRLGAQLATeHLIA--LGHR--RIAFLGGLSDSSTRRERLAGFRAAL 143

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742479139 220 EE---LFPAIKVVglrEGHDDADRNYRQTRMLLGQHPDLAGI--YN--IggaADGVARALNEMNRA--RDVVFIGH 286
Cdd:cd06289  144 AEaglPLDESLIV---PGPATREAGAEAARELLDAAPPPTAVvcFNdlV---ALGAMLALRRRGLEpgRDIAVVGF 213
PBP1_LacI-like cd06285
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 124-275 1.24e-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: 49.15  E-value: 1.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 124 RDKADGIAFMALEhpVVREAVDRLAEHGVPtVTLISDILNARRAAYIGLDNRsigrTAGYLIARFL---GERpaKVAMIA 200
Cdd:cd06285   53 SRRVDGLIITPAR--DDAPDLQELAARGVP-VVLVDRRIGDTALPSVTVDNE----LGGRLATRHLlelGHR--RIAVVA 123

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742479139 201 GSRSYRAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGG-AADGVARALNEM 275
Cdd:cd06285  124 GPLNASTGRDRLRGYRRALAEAGLPVPDERIVPGGFTIEAGREAAYRLLSRPERPTAVFAANDlMAIGVLRAARDL 199
PBP1_LuxPQ_Quorum_Sensing cd06303
periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi ...
 169-305 3.39e-06

periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs; Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type 1 periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LuxPQ to control light production as well as its motility behavior.


Pssm-ID: 380526 [Multi-domain]  Cd Length: 320  Bit Score: 48.14  E-value: 3.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 169 YIGLDNrSIGRT--AGYLIARFLGErpAKVAMIAGSRSYRAHEeREMGFLHVFEElFPAIKVVGLREGHDDADRNYRQTR 246
Cdd:cd06303  136 YVGFDH-AEGSRmlAKHFIKIFPEE--GKYAILYLTEGYVSDQ-RGDTFIDEVAR-HSNLELVSAYYTDFDRESAREAAR 210

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 247 MLLGQHPDLAGIYNIG-GAADGVARALNEMNRARDVVFIGHGLTSDTRSFLLDGTMDAVI 305
Cdd:cd06303  211 ALLARHPDLDFIYACStDIALGAIDALQELGRETDIMINGWGGGSAELDALQKGGLDVTV 270
PRK10423 PRK10423
transcriptional repressor RbsR; Provisional
 14-85 3.58e-06

transcriptional repressor RbsR; Provisional


Pssm-ID: 182448 [Multi-domain]  Cd Length: 327  Bit Score: 48.16  E-value: 3.58e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 742479139  14 DVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMPAEnLLAAMRPKPMRLL-FLLPAGTNRFLSTL 85
Cdd:PRK10423   3 DVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSA-LARSLKLNQTRTIgMLITASTNPFYSEL 74
PBP1_sucrose_transcription_regulator cd06288
ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members ...
 111-274 6.33e-06

ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose 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: 380511 [Multi-domain]  Cd Length: 268  Bit Score: 47.16  E-value: 6.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 111 FNPDLLARQLWRARD-KADGIAFMALEHpvvREAVDRLAEHGVPTVtlisdILNARRAA----YIGLDNRSIGRTA-GYL 184
Cdd:cd06288   40 GDPELEAEAIRELLSrRVDGIIYASMHH---REVTLPPELTDIPLV-----LLNCFDDDpslpSVVPDDEQGGYLAtRHL 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 185 IARflGERpaKVAMIAGSRSYRAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGI--YNig 262
Cdd:cd06288  112 IEA--GHR--RIAFIGGPEDSLATRLRLAGYRAALAEAGIPYDPSLVVHGDWGRESGYEAAKRLLSAPDRPTAIfcGN-- 185

                        170
                 ....*....|....*.
gi 742479139 263 gaaD----GVARALNE 274
Cdd:cd06288  186 ---DrmamGVYQAAAE 198
PBP1_ABC_sugar_binding-like cd06312
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 99-309 6.57e-06

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: 46.84  E-value: 6.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  99 FNVHCQVDTIKSFNPDLLARQLWRAR-DKADGIA----FMALEHPVVREAVDRlaehGVPTVtlisdILNARRA------ 167
Cdd:cd06312   29 LGVTVQYLGPQNNDIADQARLIEQAIaAKPDGIIvtipDPDALEPALKRAVAA----GIPVI-----AINSGDDrskerl 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 168 ---AYIGLDNRSIGRTAGyliARFLgERPAKVAMI----AGSRsyrAHEEREMGFLHVFEElfPAIKVVGLREGHDDAD- 239
Cdd:cd06312  100 galTYVGQDEYLAGQAAG---ERAL-EAGPKNALCvnhePGNP---GLEARCKGFADAFKG--AGILVELLDVGGDPTEa 170

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 742479139 240 ----RNYrqtrmlLGQHPDLAGIYNIGGA-ADGVARALNEMNRARDVVFIGHGLTSDTRSFLLDGTMDAVITQNQ 309
Cdd:cd06312  171 qeaiKAY------LQADPDTDAVLTLGPVgADPALKAVKEAGLKGKVKIGTFDLSPETLEAIKDGKILFAIDQQP 239
PRK10727 PRK10727
HTH-type transcriptional regulator GalR;
12-61 9.55e-06

HTH-type transcriptional regulator GalR;


Pssm-ID: 182681 [Multi-domain]  Cd Length: 343  Bit Score: 47.06  E-value: 9.55e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 742479139  12 IVDVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMPAENLLA 61
Cdd:PRK10727   4 IKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNANARA 53
PBP1_ABC_xylose_binding-like cd19995
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ...
 144-313 1.16e-05

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: 380650 [Multi-domain]  Cd Length: 294  Bit Score: 46.51  E-value: 1.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 144 VDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFL---GERPAKVAMIAGSRS-YRAHEEREmGFLHVF 219
Cdd:cd19995   76 VAKAAQAGVPVIAYDRLILGGPADYYVSFDNVAVGEAQAQSLVDHLkaiGKKGVNIVMINGSPTdNNAGLFKK-GAHEVL 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 220 EELFPAIKVVGLREGH------DDADRNYRQtrMLLGQHPDLAGIY--NIGGAADGVArALNEMNRARDVVFIGhgltsd 291
Cdd:cd19995  155 DPLGDSGELKLVCEYDtpdwdpANAQTAMEQ--ALTKLGNNIDGVLsaNDGLAGGAIA-ALKAQGLAGKVPVTG------ 225

                        170       180
                 ....*....|....*....|....*
gi 742479139 292 trsflLDGTMDAV---ITQNQLNTM 313
Cdd:cd19995  226 -----QDATVAGLqriLAGDQYMTV 245
PBP1_LacI-like cd06278
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 112-259 2.76e-05

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: 380501 [Multi-domain]  Cd Length: 266  Bit Score: 45.22  E-value: 2.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 112 NPDLLARQLWRARdkADGIAFMALEHPvvREAVDRLAEHGVPTVTLISDILNARrAAYIGLDNRSIGRTAG-YLIARflG 190
Cdd:cd06278   42 DVDDALRQLLQYR--VDGVIVTSATLS--SELAEECARRGIPVVLFNRVVEDPG-VDSVSCDNRAGGRLAAdLLLAA--G 114

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 742479139 191 ERpaKVAMIAGSRSYRAHEEREMGFLHVFEELfpAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIY 259
Cdd:cd06278  115 HR--RIAFLGGPEGTSTSRERERGFRAALAEL--GLPPPAVEAGDYSYEGGYEAARRLLAAPDRPDAIF 179
PBP1_SalR cd01545
ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of ...
 144-216 3.45e-05

ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-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: 380487 [Multi-domain]  Cd Length: 270  Bit Score: 44.85  E-value: 3.45e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 742479139 144 VDRLAEHGVPTVtLISDILNARRAAYIGLDNRSIGRTAG-YLIArfLGERpaKVAMIAGSRSYRAHEEREMGFL 216
Cdd:cd01545   73 LDALDELGIPYV-RIAPGTDDDRSPSVRIDDRAAAREMTrHLIA--LGHR--RIGFIAGPPDHGASAERLEGFR 141
PRK10339 PRK10339
DNA-binding transcriptional repressor EbgR; Provisional
 14-53 4.14e-05

DNA-binding transcriptional repressor EbgR; Provisional


Pssm-ID: 182389 [Multi-domain]  Cd Length: 327  Bit Score: 44.75  E-value: 4.14e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 742479139  14 DVARRAGVSTATVDRVLNRRP--GVRAITQQRVLAAASELDY 53
Cdd:PRK10339   6 DIAIEAGVSLATVSRVLNDDPtlNVKEETKHRILEIAEKLEY 47
PBP1_ABC_sugar_binding-like cd06321
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 116-285 8.14e-05

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: 43.82  E-value: 8.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 116 LARQLWRARD----KADGIAFMALEHPVVREAVDRLAEHGVPTVTLisDIlNARRA-AYIGLDNRSIGRTAGYLIARFLG 190
Cdd:cd06321   43 LAKQFSQIDDfiaqGVDLILLNAADSAGIEPAIKRAKDAGIIVVAV--DV-AAEGAdATVTTDNVQAGYLACEYLVEQLG 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 191 ERpAKVAMIAGSrSYRAHEEREMGFLHVFEElFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIG-GAADGVA 269
Cdd:cd06321  120 GK-GKVAIIDGP-PVSAVIDRVNGCKEALAE-YPGIKLVDDQNGKGSRAGGLSVMTRMLTAHPDVDGVFAINdPGAIGAL 196

                        170
                 ....*....|....*.
gi 742479139 270 RALNEMNRaRDVVFIG 285
Cdd:cd06321  197 LAAQQAGR-DDIVITS 211
PRK10014 PRK10014
DNA-binding transcriptional repressor MalI; Provisional
 12-55 1.00e-04

DNA-binding transcriptional repressor MalI; Provisional


Pssm-ID: 182193 [Multi-domain]  Cd Length: 342  Bit Score: 43.54  E-value: 1.00e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 742479139  12 IVDVARRAGVSTATVDRVLNRRPGVRAITQQRVLAAASELDYMP 55
Cdd:PRK10014   9 IHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVR 52
PBP1_repressor_sugar_binding-like cd01537
Ligand-binding domain of the LacI-GalR family of transcription regulators and the ...
 123-295 1.73e-04

Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems; Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type 1 periplasmic binding protein-like fold. Their specific ligands include 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 general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type 1, which has six beta strands, and type 2, which has five beta strands. These two distinct structural arrangements may have originated from a common ancestor.


Pssm-ID: 380479 [Multi-domain]  Cd Length: 265  Bit Score: 42.62  E-value: 1.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 123 ARDKADGIAFMALEHPVVREAVDRLAEHgVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARfLGERpaKVAMIAGS 202
Cdd:cd01537   52 LAKRVKGLAINLVDPAAAGVAEKARGQN-VPVVFFDKEPSRYDKAYYVITDSKEGGIIQGDLLAK-HGHI--QIVLLKGP 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 203 RSYRAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTR-MLLGQHPDLAGIYNIGGAADGVARALNEMNR--AR 279
Cdd:cd01537  128 LGHPDAEARLAGVIKELNDKGIKTEQLQLDTGDWDTASGKDKMDqWLSGPNKPTAVIANNDAMAMGAVEALKEHGLrvPS 207

                        170
                 ....*....|....*.
gi 742479139 280 DVVFIGHGLTSDTRSF 295
Cdd:cd01537  208 DISVFGYDALPEALKS 223
PBP1_MalR-like cd06294
ligand-binding domain of maltose transcription regulator MalR which is a member of the ...
 96-285 1.78e-04

ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors; This group includes the ligand-binding domain of maltose transcription regulator MalR which 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: 380517 [Multi-domain]  Cd Length: 269  Bit Score: 42.57  E-value: 1.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139  96 LAPFNVHCQVDTIKSFNPDLLARQLWRARDKADGIAFM-ALEHPVVREAvdrLAEHGVPTVtLISDILNARRAAYIGLDN 174
Cdd:cd06294   30 ANENGYSLLLATGNTEEELLEEVKRMVRGRRVDGFILLySKEDDPLIEY---LKEEGFPFV-VIGKPLDDNDVLYVDNDN 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 175 RSIGRTA-GYLIARflGERpaKVAMIAGSRSYRAHEEREMGFLHVFEE---LFPAIKVVGLREGHDDadrNYRQTRMLLG 250
Cdd:cd06294  106 VQAGYEAtEYLIDK--GHK--RIAFIGGDKNLVVSIDRLQGYKQALKEaglPLDDDYILLLDFSEED---GYDALQELLS 178

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 742479139 251 QHPDLAGIYniggAAD-----GVARALNEMNR--ARDVVFIG 285
Cdd:cd06294  179 KPPPPTAIV----ATDdllalGVLRYLQELGLrvPEDVSIIS 216
PBP1_ABC_IbpA-like cd19968
periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The ...
 143-308 2.30e-04

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: 42.37  E-value: 2.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 143 AVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFlhvFEEL 222
Cdd:cd19968   72 AIEAAIKAGIPVVTVDRRAEGAAPVPHVGADNVAGGREVAKFVVDKLPNG-AKVIELTGTPGSSPAIDRTKGF---HEEL 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 223 --FPAIKVVGLREGHDDADRNYRQTRMLLGQHPDlaGIYNIGGAAD----GVARALNEMN-RARDVVFIGHGLTSDTRSF 295
Cdd:cd19968  148 aaGPKIKVVFEQTGNFERDEGLTVMENILTSLPG--PPDAIICANDdmalGAIEAMRAAGlDLKKVKVIGFDAVPDALQA 225

                        170
                 ....*....|...
gi 742479139 296 LLDGTMDAVITQN 308
Cdd:cd19968  226 IKDGELYATVEQP 238
PBP1_AglR_RafR-like cd06292
Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that ...
 118-285 2.52e-04

Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the repressors specific raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins highly similar to DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR). Members of this group belong to 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 I 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: 380515 [Multi-domain]  Cd Length: 273  Bit Score: 42.25  E-value: 2.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 118 RQLWRARDkADGIAFMALEHPVVReaVDRLAEHGVPTVTlISDILNARRAAYIGLDNRS-IGRTAGYLIArfLGERpaKV 196
Cdd:cd06292   52 RDLVRSRR-VDGFVLASTRHDDPR--VRYLHEAGVPFVA-FGRANPDLDFPWVDVDGAAgMRQAVRHLIA--LGHR--RI 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 197 AMIAGSRSYRAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGGA-ADGVARALNEM 275
Cdd:cd06292  124 GLIGGPEGSVPSDDRLAGYRAALEEAGLPFDPGLVVEGENTEEGGYAAAARLLDLGPPPTAIVCVSDLlALGAMRAARER 203

                        170
                 ....*....|..
gi 742479139 276 NRA--RDVVFIG 285
Cdd:cd06292  204 GLRvgRDVSVVG 215
PBP1_AglR-like cd20010
Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and ...
 144-300 3.10e-04

Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and similar proteins; Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) which is a member of the LacI-GalR family of bacterial transcription regulators. 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 I 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: 380665 [Multi-domain]  Cd Length: 269  Bit Score: 41.77  E-value: 3.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 144 VDRLAEHGVPTVTLISDILNARRAaYIGLDNRSIGRTAgylIARF--LGERpaKVAMIAGSRSYRAHEEREMGFLHVFEE 221
Cdd:cd20010   75 IAYLLERGIPFVVHGRSESGAPYA-WVDIDNEGAFRRA---TRRLlaLGHR--RIALLNGPEELNFAHQRRDGYRAALAE 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 222 LFPAIKVVGLREGHDDADRNYRQTRMLLGQHPD-LAGIYNIGGAADGVARALNEMNRA--RDVVFIGHGLTSDTRSFLLD 298
Cdd:cd20010  149 AGLPVDPALVREGPLTEEGGYQAARRLLALPPPpTAIVCGSDLLALGAYRALREAGLSpgKDVSVIGHDDLLPALEYFSP 228


                 ..
gi 742479139 299 GT 300
Cdd:cd20010  229 PL 230
PBP1_ABC_ThpA_XypA cd06313
periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group ...
 143-308 3.56e-04

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: 41.87  E-value: 3.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 143 AVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFLHVFEEl 222
Cdd:cd06313   72 AVEKAKEAGIPLVGVNALIENEDLTAYVGSDDVVAGELEGQAVADRLGGK-GNVVILEGPIGQSAQIDRGKGIENVLKK- 149

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 223 FPAIKVVGLREGHDDADRNYRQTRMLLGQHPDlaGIYNIGGAADGVA----RALNEMNRArDVVFIGHGLTSDTRSFLLD 298
Cdd:cd06313  150 YPDIKVLAEQTANWSRDEAMSLMENWLQAYGD--EIDGIIAQNDDMAlgalQAVKAAGRD-DIPVVGIDGIEDALQAVKS 226

                        170
                 ....*....|
gi 742479139 299 GTMDAVITQN 308
Cdd:cd06313  227 GELIATVLQD 236
PBP1_DegA_Like cd19976
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
 128-276 4.49e-04

ligand-binding domain of putative DNA transcription regulators highly similar to that of the transcription regulator DegA; This group includes the ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the transcription regulator DegA, which is involved in the control of degradation of Bacillus subtilis amidophosphoribosyltransferase (purF). 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: 380631 [Multi-domain]  Cd Length: 268  Bit Score: 41.47  E-value: 4.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 128 DGIAFMAlEHPVVREAVDRLAEHGVPTVTLISDIlNARRAAYIGLDNRSIGRTAG-YLIArfLGERpaKVAMIAGSRSYR 206
Cdd:cd19976   57 DGIIIAS-SNISDEAIIKLLKEEKIPVVVLDRYI-EDNDSDSVGVDDYRGGYEATkYLIE--LGHT--RIGCIVGPPSTY 130

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 742479139 207 AHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHP--------DLAGIyniggaadGVARALNEMN 276
Cdd:cd19976  131 NEHERIEGYKNALQDHNLPIDESWIYSGESSLEGGYKAAEELLKSKNptaifagnDLIAM--------GVYRAALELG 200
PBP1_PurR cd06275
ligand-binding domain of purine repressor, PurR, which functions as the master regulatory ...
 128-275 4.96e-04

ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan 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 purine transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380499 [Multi-domain]  Cd Length: 269  Bit Score: 41.09  E-value: 4.96e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 128 DGIAFM-ALEHPVVREAVDRLAEhgVPTVTLISDILNARrAAYIGLDNRSIGRTAG-YLIArfLGERpaKVAMIAGSRSY 205
Cdd:cd06275   57 DGLLLMcSEMTDDDAELLAALRS--IPVVVLDREIAGDN-ADAVLDDSFQGGYLATrHLIE--LGHR--RIGCITGPLEH 129

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 742479139 206 RAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYNIGGA-ADGVARALNEM 275
Cdd:cd06275  130 SVSRERLAGFRRALAEAGIEVPPSWIVEGDFEPEGGYEAMQRLLSQPPRPTAVFACNDMmALGALRAAQEQ 200
PRK10653 PRK10653
ribose ABC transporter substrate-binding protein RbsB;
152-307 1.43e-03

ribose ABC transporter substrate-binding protein RbsB;


Pssm-ID: 182620 [Multi-domain]  Cd Length: 295  Bit Score: 40.07  E-value: 1.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 152 VPTVTLISDILNARRAAYIGLDNRSIGRTAGYLIARFLGERpAKVAMIAGSRSYRAHEEREMGFLHVFEelfpAIKVVGL 231
Cdd:PRK10653 108 IPVITLDRGATKGEVVSHIASDNVAGGKMAGDFIAKKLGEG-AKVIQLEGIAGTSAARERGEGFKQAVA----AHKFNVL 182

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 742479139 232 REGHDDADRNYRQTRM--LLGQHPDLAGIYNIGGA-ADGVARALNEMNRArDVVFIGHGLTSDTRSFLLDGTMDAVITQ 307
Cdd:PRK10653 183 ASQPADFDRTKGLNVMqnLLTAHPDVQAVFAQNDEmALGALRALQTAGKS-DVMVVGFDGTPDGIKAVNRGKLAATIAQ 260
PBP1_LacI cd01574
ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of ...
 140-285 2.87e-03

ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI 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: 380488 [Multi-domain]  Cd Length: 265  Bit Score: 38.72  E-value: 2.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 140 VREAVDRLAEHGV-----------------------PTVTLISDIlnARRAAYIGLDNRSIGRTA-GYLIArfLGERpaK 195
Cdd:cd01574   45 VREALDRLLSQRVdgiiviapdeavlealrrlppglPVVIVGSGP--SPGVPTVSIDQEEGARLAtRHLLE--LGHR--R 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 196 VAMIAGSRSYRAHEEREMGFLHVFEELfpAIKVVGLREGHDDADRNYRQTRMLLGQhPDLAGIYniggAAD-----GVAR 270
Cdd:cd01574  119 IAHIAGPLDWVDARARLRGWREALEEA--GLPPPPVVEGDWSAASGYRAGRRLLDD-GPVTAVF----AANdqmalGALR 191

                        170
                 ....*....|....*..
gi 742479139 271 ALNEMNRA--RDVVFIG 285
Cdd:cd01574  192 ALHERGLRvpEDVSVVG 208
PBP1_CelR cd06295
ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly ...
 126-285 4.65e-03

ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators; This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. 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: 380518 [Multi-domain]  Cd Length: 273  Bit Score: 38.39  E-value: 4.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 126 KADGIAFMALEHPvvREAVDRLAEHGVPTVTLISDiLNARRAAYIGLDNRsigrTAGYLIARFLGERPAKVAMIAGSRSY 205
Cdd:cd06295   63 RADGLIVLGQGLD--HDALRELAQQGLPMVVWGAP-EDGQSYCSVGSDNV----KGGALATEHLIEIGRRRIAFLGDPPH 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 206 RAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIY-NIGGAADGVARALNEMNRA--RDVV 282
Cdd:cd06295  136 PEVADRLQGYRDALAEAGLEADPSLLLSCDFTEESGYAAMRALLDSGTAFDAIFaASDLIAMGAIRALRERGISvpGDVA 215


                 ...
gi 742479139 283 FIG 285
Cdd:cd06295  216 VVG 218
PBP1_LacI-like cd06287
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 134-278 5.13e-03

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: 380510 [Multi-domain]  Cd Length: 268  Bit Score: 38.17  E-value: 5.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 134 ALEHPVVReavdRLAEHGVPTVTLISDILNARRAAYIglDNRSiGRTAGYLIARFLGERPAKVAMIAGSRSYRAHEEREM 213
Cdd:cd06287   66 TVEDPILA----RLRQRGVPVVSIGRAPGTDEPVPYV--DLQS-AATARLLLEHLHGAGARQVALLTGSSRRNSSLESEA 138

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742479139 214 GFLHVFEELFPAIKVVGLREGHDDADrNYRQTRMLLGQHPDLAGIYN-IGGAADGVARALNEMNRA 278
Cdd:cd06287  139 AYLRFAQEYGTTPVVYKVPESEGERA-GYEAAAALLAAHPDIDAVCVpVDAFAVGAMRAARDSGRS 203
PBP1_LacI-like cd06284
ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus ...
 112-285 7.04e-03

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: 37.52  E-value: 7.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 112 NPDLLARQLWRARdkADGIAFMALEHPvvREAVDRLAeHGVPTVtLISDILNARRAAYIGLDNRSIGRTAG-YLIArfLG 190
Cdd:cd06284   43 REDDLLDMLRSRR--VDGVILLSGRLD--AELLSELS-KRYPIV-QCCEYIPDSGVPSVSIDNEAAAYDATeYLIS--LG 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 191 ERpaKVAMIAGSRSYRAHEEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIYnigGAAD---- 266
Cdd:cd06284  115 HR--RIAHINGPLDNVYARERLEGYRRALAEAGLPVDEDLIIEGDFSFEAGYAAARALLALPERPTAIF---CASDelai 189

                        170       180
                 ....*....|....*....|.
gi 742479139 267 GVARALNEMNRA--RDVVFIG 285
Cdd:cd06284  190 GAIKALRRAGLRvpEDVSVIG 210
PBP1_ABC_xylose_binding-like cd19992
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ...
 142-285 7.53e-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: 380647 [Multi-domain]  Cd Length: 284  Bit Score: 37.56  E-value: 7.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 142 EAVDRLAEHGVPTVTLISDILNARRAAYIGLDNRSIGRtagyLIARFLGERPAK--VAMIAG-SRSYRAHEEREmGFLHV 218
Cdd:cd19992   71 NIVDKAKAAGVPVISYDRLILNADVDLYVGRDNYKVGQ----LQAEYALEAVPKgnYVILSGdPGDNNAQLITA-GAMDV 145

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 742479139 219 FEELFPA--IKVVgLREGHD--DADRNYRQTRMLLGQ-HPDLAGIY-NIGGAADGVARALNEMNRARDVVFIG 285
Cdd:cd19992  146 LQPAIDSgdIKIV-LDQYVKgwSPDEAMKLVENALTAnNNNIDAVLaPNDGMAGGAIQALKAQGLAGKVFVTG 217
PBP1_GntR cd01575
ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of ...
 115-259 9.83e-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: 37.09  E-value: 9.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742479139 115 LLARQlwrardkADGIAFMALEHPvvREAVDRLAEHGVPTVTlISDILNARRAAYIGLDNRsigrTAGYLIARFLGERPA 194
Cdd:cd01575   51 LLSRR-------PAGLILTGTEHT--PATRKLLRAAGIPVVE-TWDLPDDPIDMAVGFSNF----AAGRAMARHLIERGY 116

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 742479139 195 K-VAMIAGS--RSYRAHeEREMGFLHVFEELFPAIKVVGLREGHDDADRNYRQTRMLLGQHPDLAGIY 259
Cdd:cd01575  117 RrIAFVGARldGDSRAR-QRLEGFRDALAEAGLPLPLVLLVELPSSFALGREALAELLARHPDLDAIF 183
 
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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