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Conserved domains on  [gi|1125163609|gb|OLB19315|]
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sugar ABC transporter substrate-binding protein [Acidobacteria bacterium 13_2_20CM_57_7]

Protein Classification

HTH_LacI and PBP1_ABC_sugar_binding_like domain-containing protein( domain architecture ID 11545747)

HTH_LacI and PBP1_ABC_sugar_binding_like domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
 79-335 2.13e-53

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: 177.50  E-value: 2.13e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPREIHFFYDQLWSGVLDEARrvgQLGIQFVdrpVQALGEGDTEAFKE----LVRSGVDGIILTAGNPKDLSPLID 154
Cdd:pfam13407   1 IGVVPKSTGNPFFQAAEEGAEEAAK---ELGGEVI---VVGPAEADAAEQVAqiedAIAQGVDAIIVAPVDPTALAPVLK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 155 DAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHCAGG 234
Cdd:pfam13407  75 KAKDAGIPVVTFDSDAPSSPRLAYVGFDNEAAGEAAGELLAEALGGKGKVAILSGSPGDPNANERIDGFKKVLKEKYPGI 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 235 KIVSVVEG-HEEEDESFQKTFALLTRVP-GLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITA 311
Cdd:pfam13407 155 KVVAEVEGtNWDPEKAQQQMEALLTAYPnPLDGIIsPNDGMAGGAAQALEAAGLAGKVVVTGFDATPEALEAIKDGTIDA 234

                         250       260
                  ....*....|....*....|....
gi 1125163609 312 SIYQQPHRQGQIAVRLMADKLTNK 335
Cdd:pfam13407 235 TVLQDPYGQGYAAVELAAALLKGK 258
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 23-71 6.75e-16

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: 70.90  E-value: 6.75e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1125163609  23 IAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALS 71
Cdd:cd01392     3 IARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNAAARSLR 51
 
Name Accession Description Interval E-value
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
 79-335 2.13e-53

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: 177.50  E-value: 2.13e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPREIHFFYDQLWSGVLDEARrvgQLGIQFVdrpVQALGEGDTEAFKE----LVRSGVDGIILTAGNPKDLSPLID 154
Cdd:pfam13407   1 IGVVPKSTGNPFFQAAEEGAEEAAK---ELGGEVI---VVGPAEADAAEQVAqiedAIAQGVDAIIVAPVDPTALAPVLK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 155 DAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHCAGG 234
Cdd:pfam13407  75 KAKDAGIPVVTFDSDAPSSPRLAYVGFDNEAAGEAAGELLAEALGGKGKVAILSGSPGDPNANERIDGFKKVLKEKYPGI 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 235 KIVSVVEG-HEEEDESFQKTFALLTRVP-GLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITA 311
Cdd:pfam13407 155 KVVAEVEGtNWDPEKAQQQMEALLTAYPnPLDGIIsPNDGMAGGAAQALEAAGLAGKVVVTGFDATPEALEAIKDGTIDA 234

                         250       260
                  ....*....|....*....|....
gi 1125163609 312 SIYQQPHRQGQIAVRLMADKLTNK 335
Cdd:pfam13407 235 TVLQDPYGQGYAAVELAAALLKGK 258
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
 66-354 4.56e-44

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: 154.70  E-value: 4.56e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  66 AARALSFAKASARVGVCIPREIHFFYDQLWSGVLDEARrvgQLGIQFVDRPvqalGEGDTE----AFKELVRSGVDGIIL 141
Cdd:COG1879    23 AAEAAAAAAKGKTIGFVVKTLGNPFFVAVRKGAEAAAK---ELGVELIVVD----AEGDAAkqisQIEDLIAQGVDAIIV 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 142 TAGNPKDLSPLIDDAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTD 221
Cdd:COG1879    96 SPVDPDALAPALKKAKAAGIPVVTVDSDVDGSDRVAYVGSDNYAAGRLAAEYLAKALGGKGKVAILTGSPGAPAANERTD 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 222 GFSESFPRHcAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEM 300
Cdd:COG1879   176 GFKEALKEY-PGIKVVAEQYADWDREKALEVMEDLLQAHPDIDGIFaANDGMALGAAQALKAAGRKGDVKVVGFDGSPEA 254

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1125163609 301 SPYFQKGTITASIYQQPHRQGQIAVRLMADKLTNKIhLPPAVHLSPGLVMSSNL 354
Cdd:COG1879   255 LQAIKDGTIDATVAQDPYLQGYLAVDAALKLLKGKE-VPKEILTPPVLVTKENV 307
PBP1_sugar_binding cd06307
periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic ...
 78-351 2.17e-38

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: 138.46  E-value: 2.17e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  78 RVGVCIPREIHFFYDQLWSGVLDEARRVGQLGIQFVdrpVQALGEGDTEAFKELVRS---GVDGIILTAGNPKDLSPLID 154
Cdd:cd06307     1 RFGFLLPSPENPFYELLRRAIEAAAAALRDRRVRLR---IHFVDSLDPEALAAALRRlaaGCDGVALVAPDHPLVRAAID 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 155 DAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGK-LVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHCAG 233
Cdd:cd06307    78 ELAARGIPVVTLVSDLPGSRRLAYVGIDNRAAGRTAAWLMGRfLGRRPGKVLVILGSHRFRGHEEREAGFRSVLRERFPD 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 234 GKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYVNTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASI 313
Cdd:cd06307   158 LTVLEVLEGLDDDELAYELLRELLARHPDLVGIYNAGGGNEGIARALREAGRARRVVFIGHELTPETRRLLRDGTIDAVI 237

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1125163609 314 YQQPHRQGQIAVRLMADKLTNKIHLPPAVHLSPGLVMS 351
Cdd:cd06307   238 DQDPELQARRAIEVLLAHLGGKGPAPPQPPIPIEIITR 275
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 23-71 6.75e-16

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: 70.90  E-value: 6.75e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1125163609  23 IAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALS 71
Cdd:cd01392     3 IARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNAAARSLR 51
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
20-85 1.28e-13

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 65.30  E-value: 1.28e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1125163609   20 IHLIAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALSfAKASARVGVCIPR 85
Cdd:smart00354   3 IKDVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGYIPNRVARSLK-GKKTKTIGLIVPD 67
PRK10014 PRK10014
DNA-binding transcriptional repressor MalI; Provisional
 16-167 9.14e-13

DNA-binding transcriptional repressor MalI; Provisional


Pssm-ID: 182193 [Multi-domain]  Cd Length: 342  Bit Score: 68.58  E-value: 9.14e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  16 KRSGIHLIAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALSfAKASARVGVcIPREIHF-FYDQL 94
Cdd:PRK10014    5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRNRQASALR-GGQSGVIGL-IVRDLSApFYAEL 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1125163609  95 WSGVLDEARRVGQLgiQFVDRPVQAlGEGDTEAFKELVRSGVDGIILtAGNPKDLSPLIDDAEEKGIRVVCVS 167
Cdd:PRK10014   83 TAGLTEALEAQGRM--VFLLQGGKD-GEQLAQRFSTLLNQGVDGVVI-AGAAGSSDDLREMAEEKGIPVVFAS 151
LacI pfam00356
Bacterial regulatory proteins, lacI family;
20-64 2.93e-09

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 52.25  E-value: 2.93e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1125163609  20 IHLIAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPN 64
Cdd:pfam00356   2 IKDVARLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNYIPN 46
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
20-83 1.07e-04

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 44.00  E-value: 1.07e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1125163609  20 IHLIAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALSfAKASARVGVCI 83
Cdd:PRK10401    4 IRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPNANAQALA-TQVSDTIGVVV 66
 
Name Accession Description Interval E-value
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
 79-335 2.13e-53

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: 177.50  E-value: 2.13e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPREIHFFYDQLWSGVLDEARrvgQLGIQFVdrpVQALGEGDTEAFKE----LVRSGVDGIILTAGNPKDLSPLID 154
Cdd:pfam13407   1 IGVVPKSTGNPFFQAAEEGAEEAAK---ELGGEVI---VVGPAEADAAEQVAqiedAIAQGVDAIIVAPVDPTALAPVLK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 155 DAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHCAGG 234
Cdd:pfam13407  75 KAKDAGIPVVTFDSDAPSSPRLAYVGFDNEAAGEAAGELLAEALGGKGKVAILSGSPGDPNANERIDGFKKVLKEKYPGI 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 235 KIVSVVEG-HEEEDESFQKTFALLTRVP-GLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITA 311
Cdd:pfam13407 155 KVVAEVEGtNWDPEKAQQQMEALLTAYPnPLDGIIsPNDGMAGGAAQALEAAGLAGKVVVTGFDATPEALEAIKDGTIDA 234

                         250       260
                  ....*....|....*....|....
gi 1125163609 312 SIYQQPHRQGQIAVRLMADKLTNK 335
Cdd:pfam13407 235 TVLQDPYGQGYAAVELAAALLKGK 258
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
 66-354 4.56e-44

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: 154.70  E-value: 4.56e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  66 AARALSFAKASARVGVCIPREIHFFYDQLWSGVLDEARrvgQLGIQFVDRPvqalGEGDTE----AFKELVRSGVDGIIL 141
Cdd:COG1879    23 AAEAAAAAAKGKTIGFVVKTLGNPFFVAVRKGAEAAAK---ELGVELIVVD----AEGDAAkqisQIEDLIAQGVDAIIV 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 142 TAGNPKDLSPLIDDAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTD 221
Cdd:COG1879    96 SPVDPDALAPALKKAKAAGIPVVTVDSDVDGSDRVAYVGSDNYAAGRLAAEYLAKALGGKGKVAILTGSPGAPAANERTD 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 222 GFSESFPRHcAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEM 300
Cdd:COG1879   176 GFKEALKEY-PGIKVVAEQYADWDREKALEVMEDLLQAHPDIDGIFaANDGMALGAAQALKAAGRKGDVKVVGFDGSPEA 254

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1125163609 301 SPYFQKGTITASIYQQPHRQGQIAVRLMADKLTNKIhLPPAVHLSPGLVMSSNL 354
Cdd:COG1879   255 LQAIKDGTIDATVAQDPYLQGYLAVDAALKLLKGKE-VPKEILTPPVLVTKENV 307
PBP1_sugar_binding cd06307
periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic ...
 78-351 2.17e-38

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: 138.46  E-value: 2.17e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  78 RVGVCIPREIHFFYDQLWSGVLDEARRVGQLGIQFVdrpVQALGEGDTEAFKELVRS---GVDGIILTAGNPKDLSPLID 154
Cdd:cd06307     1 RFGFLLPSPENPFYELLRRAIEAAAAALRDRRVRLR---IHFVDSLDPEALAAALRRlaaGCDGVALVAPDHPLVRAAID 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 155 DAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGK-LVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHCAG 233
Cdd:cd06307    78 ELAARGIPVVTLVSDLPGSRRLAYVGIDNRAAGRTAAWLMGRfLGRRPGKVLVILGSHRFRGHEEREAGFRSVLRERFPD 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 234 GKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYVNTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASI 313
Cdd:cd06307   158 LTVLEVLEGLDDDELAYELLRELLARHPDLVGIYNAGGGNEGIARALREAGRARRVVFIGHELTPETRRLLRDGTIDAVI 237

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1125163609 314 YQQPHRQGQIAVRLMADKLTNKIHLPPAVHLSPGLVMS 351
Cdd:cd06307   238 DQDPELQARRAIEVLLAHLGGKGPAPPQPPIPIEIITR 275
PBP1_ABC_sugar_binding-like cd01536
periplasmic sugar-binding domain of active transport systems that are members of the type 1 ...
 78-335 5.55e-35

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: 129.22  E-value: 5.55e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  78 RVGVCIPREIHFFYDQLWSGVLDEARrvgQLGIQFVdrpVQAlGEGDTE----AFKELVRSGVDGIILTAGNPKDLSPLI 153
Cdd:cd01536     1 KIGVVVKDLTNPFWVAVKKGAEAAAK---ELGVELV---VLD-AQGDVAkqisQIEDLIAQGVDAIIIAPVDSEALVPAV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 154 DDAEEKGIRVVCVSTDAPE-SRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHCa 232
Cdd:cd01536    74 KKANAAGIPVVAVDTDIDGgGDVVAFVGTDNYEAGKLAGEYLAEALGGKGKVAILEGPPGSSTAIDRTKGFKEALKKYP- 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 233 GGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITA 311
Cdd:cd01536   153 DIEIVAEQPANWDRAKALTVTENLLQANPDIDAVFaANDDMALGAAEALKAAGRTGDIKIVGVDGTPEALKAIKDGELDA 232

                         250       260
                  ....*....|....*....|....
gi 1125163609 312 SIYQQPHRQGQIAVRLMADKLTNK 335
Cdd:cd01536   233 TVAQDPYLQGYLAVEAAVKLLNGE 256
PBP1_tmGBP cd06314
periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and ...
 90-343 2.28e-34

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: 127.70  E-value: 2.28e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  90 FYDQLWSGVLDEARrvgQLGIQ-FVDRPVQALGEGDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVST 168
Cdd:cd06314    13 FWDLAEAGAEKAAK---ELGVNvEFVGPQKSDAAEQVQLIEDLIARGVDGIAISPNDPEAVTPVINKAADKGIPVITFDS 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 169 DAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHcAGGKIVSVVEGHEEEDE 248
Cdd:cd06314    90 DAPDSKRLAYIGTDNYEAGREAGELMKKALPGGGKVAIITGGLGADNLNERIQGFKDALKGS-PGIEIVDPLSDNDDIAK 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 249 SFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRL 327
Cdd:cd06314   169 AVQNVEDILKANPDLDAIFgVGAYNGPAIAAALKDAGKVGKVKIVGFDTLPETLQGIKDGVIAATVGQRPYEMGYLSVKL 248

                         250
                  ....*....|....*.
gi 1125163609 328 MADKLTNKIHLPPAVH 343
Cdd:cd06314   249 LYKLLKGGKPVPDVID 264
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
15-349 3.59e-34

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


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 128.78  E-value: 3.59e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  15 KKRSGIHLIAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALSfAKASARVGVCIPREIHFFYDQL 94
Cdd:COG1609     1 RKRVTIKDVARLAGVSVATVSRVLNGPPRVSEETRERVLAAAEELGYRPNAAARSLR-TGRTRTIGVVVPDLSNPFFAEL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  95 WSGVLDEARrvgQLGIQFVDRPVQALGEGDTEAFKELVRSGVDGIILTAGNPKDlsPLIDDAEEKGIRVVCVSTDAPESR 174
Cdd:COG1609    80 LRGIEEAAR---ERGYQLLLANSDEDPEREREALRLLLSRRVDGLILAGSRLDD--ARLERLAEAGIPVVLIDRPLPDPG 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 175 RSTIVcvepfLNGSLAGELMGK-LVPSG-SEVAVIAGMLTTEDHRKKTDGFSESFPRHCAGGKIVSVVEGHEEEDESFQK 252
Cdd:COG1609   155 VPSVG-----VDNRAGARLATEhLIELGhRRIAFIGGPADSSSARERLAGYREALAEAGLPPDPELVVEGDFSAESGYEA 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 253 TFALLTRVPGLAGIYV-NTVNCLPVCRALGARGLA--GKVKLIT---TDLFAEMSPyfqkgTITaSIYQQPHRQGQIAVR 326
Cdd:COG1609   230 ARRLLARGPRPTAIFCaNDLMALGALRALREAGLRvpEDVSVVGfddIPLARYLTP-----PLT-TVRQPIEEMGRRAAE 303

                         330       340
                  ....*....|....*....|...
gi 1125163609 327 LMADKLTNKIHLPPAVHLSPGLV 349
Cdd:COG1609   304 LLLDRIEGPDAPPERVLLPPELV 326
PBP1_ABC_sugar_binding-like cd19969
monosaccharide ABC transporter substrate binding protein; Periplasmic sugar-binding domain of ...
 78-348 3.25e-31

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: 119.75  E-value: 3.25e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  78 RVGVCIPREIHFFYDQLWSGVLDEARrvgQLGIQFVDR-PVQALGEGDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDA 156
Cdd:cd19969     1 YYVMVTFKSGHPYWDDVKEGFEDAGA---ELGVKTEYTgPATADVNEQITAIEQAIAKNPDGIAVSAIDPEALTPTINKA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 157 EEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTeDHRKKTDGFSESFPRHcAGGKI 236
Cdd:cd19969    78 VDAGIPVVTFDSDAPESKRISYVGTDNYEAGYAAAEKLAELLGGKGKVAVLTGPGQP-NHEERVEGFKEAFAEY-PGIEV 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 237 VSVVEGHEEEDESFQKTFALLTRVPGLAGIYVNTVNCLP-VCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQ 315
Cdd:cd19969   156 VAVGDDNDDPEKAAQNTSALLQAHPDLVGIFGVDASGGVgAAQAVREAGKTGKVKIVAFDDDPETLDLIKDGVIDASIAQ 235

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1125163609 316 QPHRQGQIAVRLMADKLTNKIHLPPAVHLSPGL 348
Cdd:cd19969   236 RPWMMGYWSLQFLYDLANGLVKDAWQTAGVNPL 268
PBP1_allose_binding cd06320
periplasmic allose-binding domain of bacterial transport systems that function as a primary ...
 97-354 3.34e-27

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: 108.89  E-value: 3.34e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  97 GVLDEARRVGqlgiqfVDRPVQAL-GEGDTE----AFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCV-STDA 170
Cdd:cd06320    20 GIEAEAKKLG------VKVDVQAApSETDTQgqlnLLETMLNKGYDAILVSPISDTNLIPPIEKANKKGIPVINLdDAVD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 171 PESRRSTIVCVEPFL------NGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHcAGGKIVSVVEGHE 244
Cdd:cd06320    94 ADALKKAGGKVTSFIgtdnvaAGALAAEYIAEKLPGGGKVAIIEGLPGNAAAEARTKGFKETFKKA-PGLKLVASQPADW 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 245 EEDESFQKTFALLTRVPGLAGIYV-NTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQI 323
Cdd:cd06320   173 DRTKALDAATAILQAHPDLKGIYAaNDTMALGAVEAVKAAGKTGKVLVVGTDGIPEAKKSIKAGELTATVAQYPYLEGAM 252

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1125163609 324 AVRLMADKLTNKiHLPPAVHLSPGLVMSSNL 354
Cdd:cd06320   253 AVEAALRLLQGQ-KVPAVVATPQALITKDNV 282
PBP1_ABC_sugar_binding-like cd06310
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 88-344 1.54e-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: 380533 [Multi-domain]  Cd Length: 272  Bit Score: 101.26  E-value: 1.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  88 HFFYDQLWSGVLDEARrvgQLGIQFVDRPVQALG--EGDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVC 165
Cdd:cd06310    11 SAFWRTVREGAEAAAK---DLGVKIIFVGPESEEdvAGQNSLLEELINKKPDAIVVAPLDSEDLVDPLKDAKDKGIPVIV 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 166 VSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHCAGGKIVSVVEGHEE 245
Cdd:cd06310    88 IDSGIKGDAYLSYIATDNYAAGRLAAQKLAEALGGKGKVAVLSLTAGNSTTDQREEGFKEYLKKHPGGIKVLASQYAGSD 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 246 EDESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIA 324
Cdd:cd06310   168 YAKAANETEDLLGKYPDIDGIFaTNEITALGAAVAIKSRKLSGQIKIVGFDSQEELLDALKNGKIDALVVQNPYEIGYEG 247

                         250       260
                  ....*....|....*....|
gi 1125163609 325 VRLmADKLTNKIHLPPAVHL 344
Cdd:cd06310   248 IKL-ALKLLKGEEVPKNIDT 266
PBP1_ABC_sugar_binding-like cd20006
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 122-335 2.73e-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: 380661 [Multi-domain]  Cd Length: 274  Bit Score: 100.75  E-value: 2.73e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 122 EGDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSG 201
Cdd:cd20006    46 DGQIELIEEAIAQKPDAIVLAASDYDRLVEAVERAKKAGIPVITIDSPVNSKKADSFVATDNYEAGKKAGEKLASLLGEK 125

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 202 SEVAVIAGMLTTEDHRKKTDGFSESFPRHCAgGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYV-NTVNCLPVCRAL 280
Cdd:cd20006   126 GKVAIVSFVKGSSTAIEREEGFKQALAEYPN-IKIVETEYCDSDEEKAYEITKELLSKYPDINGIVAlNEQSTLGAARAL 204

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1125163609 281 GARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRLMADKLTNK 335
Cdd:cd20006   205 KELGLGGKVKVVGFDSSVEEIQLLEEGIIDALVVQNPFNMGYLSVQAAVDLLNGK 259
PBP1_ABC_sugar_binding-like cd20004
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 95-350 6.72e-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: 380659 [Multi-domain]  Cd Length: 273  Bit Score: 99.61  E-value: 6.72e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  95 WSGVLDEARRVGQ-LGIQFVDRpvQALGEGDTEA----FKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTD 169
Cdd:cd20004    14 WKSVKAGAEKAAQeLGVEIYWR--GPSREDDVEAqiqiIEYFIDQGVDGIVLAPLDRKALVAPVERARAQGIPVVIIDSD 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 170 APESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVI---AGMLTTEDhrkKTDGFSESFPRHCAGGKIVSVVEGHEEE 246
Cdd:cd20004    92 LGGDAVISFVATDNYAAGRLAAKRMAKLLNGKGKVALLrlaKGSASTTD---RERGFLEALKKLAPGLKVVDDQYAGGTV 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 247 DESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAV 325
Cdd:cd20004   169 GEARSSAENLLNQYPDVDGIFtPNESTTIGALRALRRLGLAGKVKFIGFDASDLLLDALRAGEISALVVQDPYRMGYLGV 248

                         250       260
                  ....*....|....*....|....*
gi 1125163609 326 RLMADKLTNKihlPPAVHLSPGLVM 350
Cdd:cd20004   249 KTAVAALRGK---PVPKRIDTGVVL 270
PBP1_LsrB_Quorum_Sensing-like cd06302
periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium ...
 107-325 8.29e-24

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: 99.62  E-value: 8.29e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 107 QLGIQFV-DRPVQALGEGDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTDAPESRRStiVCVEPFL 185
Cdd:cd06302    27 ELGVEVVyTGPTQADAAQQVQIVENLIAQGVDAIAVSPNDADALAPVLKKAKDAGIKVITWDSDAPPSARD--YFVNQAD 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 186 NGSLA---GELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHCAGGKIVSVVEGHEEEDESFQKTFALLTRVPG 262
Cdd:cd06302   105 DEGLGealVDSLAKEIGGKGKVAILSGSLTATNLNAWIKAMKEYLKSKYPDIELVDTYYTDDDQQKAYTQAQNLIQAYPD 184

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1125163609 263 LAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAV 325
Cdd:cd06302   185 LKGIIgVSTTAPPAAAQAVEEAGKTGKVAVTGIGLPNTARPYLKDGSVKEGVLWDPAKLGYLTV 248
PBP1_ABC_sugar_binding-like cd19970
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 129-342 5.11e-23

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: 97.32  E-value: 5.11e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 129 KELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVST----DAPESRRSTIVCVEP--FLNGSLAGELMGKLVPSGS 202
Cdd:cd19970    52 ENLIAQKVDAIVIAPADSKALVPVLKKAVDAGIAVINIDNrldaDALKEGGINVPFVGPdnRQGAYLAGDYLAKKLGKGG 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 203 EVAVIAGMLTTEDHRKKTDGFSESFPRhcAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALG 281
Cdd:cd19970   132 KVAIIEGIPGADNAQQRKAGFLKAFEE--AGMKIVASQSANWEIDEANTVAANLLTAHPDIRGILcANDNMALGAIKAVD 209

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1125163609 282 ARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRlMADKLTNKIHLPPAV 342
Cdd:cd19970   210 AAGKAGKVLVVGFDNIPAVRPLLKDGKMLATIDQHPAKQAVYGIE-YALKMLNGEEVPGWV 269
PBP1_ABC_rhamnose cd20000
rhamnose ABC transporter substrate-binding protein; Rhamnose ABC transporter substrate-binding ...
 82-336 4.42e-22

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: 95.02  E-value: 4.42e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  82 CIPREIHFFYDQLWSGVLDEArrVGQLGIQFVDR-PVQALGEGDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKG 160
Cdd:cd20000     4 FLPKSLGNPYFDAARDGAKEA--AKELGGELIFVgPTTATAEAQIPFINTLIQQGVDAIAISANDPDALAPALKKARAAG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 161 IRVVCVSTDAPESRRStiVCVEPFLNGSLAG---ELMGKLVPSGSEVAVIAGMLTTEDHRK-----KTDGFSESFprhcA 232
Cdd:cd20000    82 IKVVTFDSDVAPEARD--LFVNQADADGIGRaqvDMMAELIGGEGEFAILSATPTATNQNAwidamKKELASPEY----A 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 233 GGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYV-NTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITA 311
Cdd:cd20000   156 GMKLVKVAYGDDDAQKSYQEAEALLQAYPDLKGIIApTTVGIAAAARALEDSGLKGKVKVTGLGLPSEMAKYVKDGTVPA 235

                         250       260
                  ....*....|....*....|....*
gi 1125163609 312 SIYQQPHRQGQIAVRLMADKLTNKI 336
Cdd:cd20000   236 FALWNPIDLGYLAAYAAAALAQGEI 260
PBP1_ABC_sugar_binding-like cd06322
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 79-349 6.94e-21

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: 91.18  E-value: 6.94e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPREIHFFYDQLWSGVLDEArrvGQLGIQfvdrPVQALGEGDTE----AFKELVRSGVDGIILTAGNPKDLSPLID 154
Cdd:cd06322     2 IGVSLLTLQHPFFVDIKDAMKKEA---AELGVK----VVVADANGDLAkqlsQIEDFIQQGVDAIILAPVDSGGIVPAIE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 155 DAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGK-LVPSGSEVAVIaGMLTTEDHRKKTDGFSESFPRHcAG 233
Cdd:cd06322    75 AANEAGIPVFTVDVKADGAKVVTHVGTDNYAGGKLAGEYALKaLLGGGGKIAII-DYPEVESVVLRVNGFKEAIKKY-PN 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 234 GKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAE-MSPYFQKGTITA 311
Cdd:cd06322   153 IEIVAEQPGDGRREEALAATEDMLQANPDLDGIFaIGDPAALGALTAIESAGKEDKIKVIGFDGNPEaIKAIAKGGKIKA 232

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1125163609 312 SIYQQPHRQGQIAVRLMADKLTNKiHLPPAVHLSPGLV 349
Cdd:cd06322   233 DIAQQPDKIGQETVEAIVKYLAGE-TVEKEILIPPKLY 269
PBP1_ABC_sugar_binding-like cd06319
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 90-332 7.43e-21

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: 91.27  E-value: 7.43e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  90 FYDQLWSGVLDEARrvgQLGIQFV------DRPVQALGEGDteafkeLVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRV 163
Cdd:cd06319    13 FWQIMERGVQAAAE---ELGYEFVtydqknSANEQVTNAND------LIAQGVDGIIISPTNSSAAPTVLDLANEAKIPV 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 164 VCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLV----PSGSEVAVIAGMLTTEDHRKKTDGFSESFPRhcAGGKIVSV 239
Cdd:cd06319    84 VIADIGTGGGDYVSYIISDNYDGGYQAGEYLAEALkengWGGGSVGIIAIPQSRVNGQARTAGFEDALEE--AGVEEVAL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 240 -VEGHEEEDESFQKTFALLTRVPGLAGIYV-NTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQP 317
Cdd:cd06319   162 rQTPNSTVEETYSAAQDLLAANPDIKGIFAqNDQMAQGALQAIEEAGRTGDILVVGFDGDPEALDLIKDGKLDGTVAQQP 241

                         250
                  ....*....|....*
gi 1125163609 318 HRQGQIAVRLMADKL 332
Cdd:cd06319   242 FGMGARAVELAIQAL 256
PBP1_LsrB_Quorum_Sensing cd20003
ligand-binding protein LsrB of ABC transporter periplasmic binding protein; Periplasmic ...
 107-336 1.04e-20

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: 91.18  E-value: 1.04e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 107 QLGIQFV-DRPVQALGEGDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTDA-PESRrstivcvEPF 184
Cdd:cd20003    27 ELGVDVTyDGPTEASVSKQVEVINNFINQGYDVIAVSANDPDALAPALKKAMKKGIKVVTWDSDVnPDAR-------DFF 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 185 LN-------GSLAGELMGKLVPSGSEVAVIAGMLTTED------HRKKTdgFSESFPrhcaGGKIVSVVEGHEEEDESFQ 251
Cdd:cd20003   100 VNqatpegiGKTLVDMVAEQTGEKGKVAIVTSSPTATNqnawikAMKAY--IAEKYP----DMKIVTTQYGQEDPAKSLQ 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 252 KTFALLTRVPGLAGIYVNTVNCLP-VCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRLMAD 330
Cdd:cd20003   174 VAENILKAYPDLKAIIAPDSVALPgAAEAVEQLGRTGKVAVTGLSTPNVMRPYVKDGTVKSVVLWDVVDLGYLAVYVARA 253


                  ....*.
gi 1125163609 331 KLTNKI 336
Cdd:cd20003   254 LADGTL 259
PBP1_TorT-like cd06306
TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor ...
 78-350 1.02e-18

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: 84.94  E-value: 1.02e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  78 RVGVCIPreiHFfYDQLWS----GVLDEARRVG-QLGIqfvdrpVQAlGeGDTEA------FKELVRSGVDGIILTAGNP 146
Cdd:cd06306     1 KICVLFP---HL-KDSYWVgvnyGIVDEAKRLGvKLTV------YEA-G-GYTNLskqisqLEDCVASGADAILLGAISF 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 147 KDLSPLIDDAEEKGIRVVC----VSTDAPESRrstiVCVEPFLNGSLAGELMGKLVPSGS-EVAVIAGMLTTEDHRKKTD 221
Cdd:cd06306    69 DGLDPKVAEAAAAGIPVIDlvngIDSPKVAAR----VLVDFYDMGYLAGEYLVEHHPGKPvKVAWFPGPAGAGWAEDREK 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 222 GFSEsfprHCAGGKIVSVVEGHEEEDESFQKTFA--LLTRVPGLAGIYVNTVNCLPVCRALGARGLAGKVKLITTDLFAE 299
Cdd:cd06306   145 GFKE----ALAGSNVEIVATKYGDTGKAVQLNLVedALQAHPDIDYIVGNAVAAEAAVGALREAGLTGKVKVVSTYLTPG 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1125163609 300 MSPYFQKGTITASIYQQPHRQGQIAVRLMADKLTNKihlPPAVHLSPGLVM 350
Cdd:cd06306   221 VYRGIKRGKILAAPSDQPVLQGRIAVDQAVRALEGK---PVPKHVGPPILV 268
PBP1_ABC_sugar_binding-like cd20007
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 90-335 1.06e-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: 380662 [Multi-domain]  Cd Length: 271  Bit Score: 81.90  E-value: 1.06e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  90 FYDQLWSGVLDEARRvgqLGIQFVdrpVQALGEGDTEA----FKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVC 165
Cdd:cd20007    13 FYITMQCGAEAAAKE---LGVELD---VQGPPTFDPTLqtpiVNAVIAKKPDALLIAPTDPQALIAPLKRAADAGIKVVT 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 166 VSTD-APESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIA---GMLTTEDHRKktdGFSESFPRHcaGGKIVSVVE 241
Cdd:cd20007    87 VDTTlGDPSFVLSQIASDNVAGGALAAEALAELIGGKGKVLVINstpGVSTTDARVK---GFAEEMKKY--PGIKVLGVQ 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 242 GHEEE-DESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHR 319
Cdd:cd20007   162 YSENDpAKAASIVAAALQANPDLAGIFgTNTFSAEGAAAALRNAGKTGKVKVVGFDASPAQVEQLKAGTIDALIAQKPAE 241

                         250
                  ....*....|....*.
gi 1125163609 320 QGQIAVRLMADKLTNK 335
Cdd:cd20007   242 IGYLAVEQAVAALTGK 257
PBP1_ABC_sugar_binding-like cd20008
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 122-332 4.57e-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: 380663 [Multi-domain]  Cd Length: 277  Bit Score: 80.35  E-value: 4.57e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 122 EGDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDAEeKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSG 201
Cdd:cd20008    44 AGQVNLVENAISRKPDAIVLAPNDTAALVPAVEAAD-AGIPVVLVDSGANTDDYDAFLATDNVAAGALAADELAELLKAS 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 202 S----EVAVIAGMLTTEDHRKKTDGFSESFPRHCAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIY-VNTVNCLPV 276
Cdd:cd20008   123 GggkgKVAIISFQAGSQTLVDREEGFRDYIKEKYPDIEIVDVQYSDGDIAKALNQTTDLLTANPDLVGIFgANNPSAVGV 202

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1125163609 277 CRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRLMADKL 332
Cdd:cd20008   203 AQALAEAGKAGKIVLVGFDSSPDEVALLKSGVIKALVVQDPYQMGYEGVKTAVKAL 258
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 23-71 6.75e-16

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: 70.90  E-value: 6.75e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1125163609  23 IAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALS 71
Cdd:cd01392     3 IARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNAAARSLR 51
PBP1_ABC_sugar_binding-like cd06317
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 90-358 6.33e-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: 74.33  E-value: 6.33e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  90 FYDQLWSGVLDEARrvgQLGIQFVDRPVQALGEGDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTD 169
Cdd:cd06317    13 FFNQINQGAQAAAK---DLGVDLVVFNANDDPSKQNTAVDNYIARGVDAIILDAIDVNGSIPAIKRASEAGIPVIAYDAV 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 170 APESRRSTIVCVEPFLNGSLAGELMGKLVPSG----SEVAVIaGMLTTEDHRKKTDGFSESFpRHCAGGKIVSVVEGHEE 245
Cdd:cd06317    90 IPSDFQAAQVGVDNLEGGKEIGKYAADYIKAElggqAKIGVV-GALSSLIQNQRQKGFEEAL-KANPGVEIVATVDGQNV 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 246 EDESFQKTFALLTRVPGLAGIYV-NTVNCLPVCRALGARGLAGKVKLITTDLFAEMspYFQK---GTITASIYQQPHRQG 321
Cdd:cd06317   168 QEKALSAAENLLTANPDLDAIYAtGEPALLGAVAAVRSQGRQGKIKVFGWDLTKQA--IFLGideGVLQAVVQQDPEKMG 245

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1125163609 322 QIAVRLmADKLTNKIHLPPAVHLSPGLVMSSNLHLFR 358
Cdd:cd06317   246 YEAVKA-AVKAIKGEDVEKTIDVPPTIVTKENVDQFR 281
PBP1_ABC_sugar_binding-like cd20005
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 134-330 1.00e-14

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: 73.43  E-value: 1.00e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 134 SGVDGIILTAGNPKDLSPLIDDAEEKGIRVVC----VSTDAPESRRSTIvcvepflN---GSLAGELMGKLVPSGSEVAV 206
Cdd:cd20005    56 KKPDAIALAALDTNALLPQLEKAKEKGIPVVTfdsgVPSDLPLATVATD-------NyaaGALAADHLAELIGGKGKVAI 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 207 IAGMLTTEDHRKKTDGFSESFPRHCAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGL 285
Cdd:cd20005   129 VAHDATSETGIDRRDGFKDEIKEKYPDIKVVNVQYGVGDHAKAADIAKAILQANPDLKGIYaTNEGAAIGVANALKEMGK 208

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1125163609 286 AGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRLMAD 330
Cdd:cd20005   209 LGKIKVVGFDSGEAQIDAIKNGVIAGSVTQNPYGMGYKTVKAAVK 253
PBP1_ABC_sugar_binding-like cd19972
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 79-342 6.78e-14

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: 70.93  E-value: 6.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPREIHFFYDQLWSGVLDEARrvgQLGIQFVdrPVQALGEGDTEA--FKELVRSGVDGIILTAGNPKDLSPLIDDA 156
Cdd:cd19972     2 IGLAVANLQADFFNQIKQSVEAEAK---KKGYKVI--TVDAKGDSATQVnqIQDLITQNIDALIYIPAGATAAAVPVKAA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 157 EEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRhCAGGKI 236
Cdd:cd19972    77 RAAGIPVIAVDRNPEDAPGDTFIATDSVAAAKELGEWVIKQTGGKGEIAILHGQLGTTPEVDRTKGFQEALAE-APGIKV 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 237 VSVVEGHEEEDESFQKTFALLTRVPGLAGIYVNTVnclpvCRALGAR------GLAGKVKLITTDLFAEMSPYFQKGTIT 310
Cdd:cd19972   156 VAEQTADWDQDEGFKVAQDMLQANPNITVFFGQSD-----AMALGAAqavkvaGLDHKIWVVGFDGDVAGLKAVKDGVLD 230

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1125163609 311 ASIYQQPHRQGQIAVR----LMADKLTNKIHLPPAV 342
Cdd:cd19972   231 ATMTQQTQKMGRLAVDsaidLLNGKAVPKEQLQDAV 266
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
20-85 1.28e-13

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 65.30  E-value: 1.28e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1125163609   20 IHLIAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALSfAKASARVGVCIPR 85
Cdd:smart00354   3 IKDVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGYIPNRVARSLK-GKKTKTIGLIVPD 67
PBP1_ABC_sugar_binding-like cd06312
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 92-349 5.83e-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: 380535 [Multi-domain]  Cd Length: 272  Bit Score: 68.41  E-value: 5.83e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  92 DQLWSGVLDEARRVGQ-LGIqfvdrPVQALG--EGDTEAFKELVRS----GVDGIILTAGNPKDLSPLIDDAEEKGIRVV 164
Cdd:cd06312    12 DPFWSVVKKGAKDAAKdLGV-----TVQYLGpqNNDIADQARLIEQaiaaKPDGIIVTIPDPDALEPALKRAVAAGIPVI 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 165 CVST--DAPESRRSTIVCV--EPFLNGSLAGElmgKLVPSGSEVAVI----AGMLTTEDhrkKTDGFSESFPrhcAGGKI 236
Cdd:cd06312    87 AINSgdDRSKERLGALTYVgqDEYLAGQAAGE---RALEAGPKNALCvnhePGNPGLEA---RCKGFADAFK---GAGIL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 237 VSVVEGHEEEDESFQKTFALLTRVPGLAGIYVNTVNCL-PVCRALGARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQ 315
Cdd:cd06312   158 VELLDVGGDPTEAQEAIKAYLQADPDTDAVLTLGPVGAdPALKAVKEAGLKGKVKIGTFDLSPETLEAIKDGKILFAIDQ 237

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1125163609 316 QPHRQGQIAVRLMADKLTNKIhLPPAVHLS--PGLV 349
Cdd:cd06312   238 QPYLQGYLAVVFLYLYKRYGT-LPPPEPILtgPGFV 272
PRK10014 PRK10014
DNA-binding transcriptional repressor MalI; Provisional
 16-167 9.14e-13

DNA-binding transcriptional repressor MalI; Provisional


Pssm-ID: 182193 [Multi-domain]  Cd Length: 342  Bit Score: 68.58  E-value: 9.14e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  16 KRSGIHLIAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALSfAKASARVGVcIPREIHF-FYDQL 94
Cdd:PRK10014    5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRNRQASALR-GGQSGVIGL-IVRDLSApFYAEL 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1125163609  95 WSGVLDEARRVGQLgiQFVDRPVQAlGEGDTEAFKELVRSGVDGIILtAGNPKDLSPLIDDAEEKGIRVVCVS 167
Cdd:PRK10014   83 TAGLTEALEAQGRM--VFLLQGGKD-GEQLAQRFSTLLNQGVDGVVI-AGAAGSSDDLREMAEEKGIPVVFAS 151
PBP1_ABC_sugar_binding-like cd19965
monosaccharide ABC transporter substrate binding protein CUT2 family and similar proteins; ...
 132-343 1.18e-12

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: 67.30  E-value: 1.18e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 132 VRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTDAP--ESRRSTIVCVEPFLNG-SLAGELMGKLVPSGSEVAVI- 207
Cdd:cd19965    53 IASGPDGIATTIVDPEAFDEVIKRALDAGIPVVAFNVDAPggENARLAFVGQDLYPAGyVLGKRIAEKFKPGGGHVLLGi 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 208 --AGMLTTEdHRKktDGFSESFPRHCAGGKIVSVVEGHEEEdESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARG 284
Cdd:cd19965   133 stPGQSALE-QRL--DGIKQALKEYGRGITYDVIDTGTDLA-EALSRIEAYYTAHPDIKAIFaTGAFDTAGAGQAIKDLG 208

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1125163609 285 LAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRLMAdkLTNKIHLPPAVH 343
Cdd:cd19965   209 LKGKVLVGGFDLVPEVLQGIKAGYIDFTIDQQPYLQGFYPVMQLF--LYKKFGLSPFDI 265
PBP1_ABC_sugar_binding-like cd06316
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 135-354 1.31e-12

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: 67.65  E-value: 1.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 135 GVDGIILTAGNPKDLSPLIDDAEEKGIRVVcVSTDAPESRR-----STIVCVEPFLNGSLAGELMGKLVPSGSEVAVI-- 207
Cdd:cd06316    56 KPDIIISIPVDPVATAAAYKKVADAGIKLV-FMDNVPDGLEagkdyVSVVSSDNRGNGQIAAELLAEAIGGKGKVGIIyh 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 208 -AGMLTTEDhrkKTDGFSESFPRHCAGGKIVSVVeGHEEEDESFQKTFALLTRVPGLAGIYVN-TVNCLPVCRALGARGL 285
Cdd:cd06316   135 dADFYATNQ---RDKAFKDTLKEKYPDIKIVAEQ-GFADPNDAEEVASAMLTANPDIDGIYVSwDTPALGVISALRAAGR 210

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 286 AgKVKLITTDLFAEMSPYFQKGTITASI-YQQPHRQGQIAVRLMADKLTNKIhLPPAVHLSPGLVMSSNL 354
Cdd:cd06316   211 S-DIKITTVDLGTEIALDMAKGGNVKGIgAQRPYDQGVAEALAAALALLGKE-VPPFIGVPPLAVTKDNL 278
PBP1_ABC_IbpA-like cd19968
periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The ...
 98-335 1.91e-11

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


Pssm-ID: 380623 [Multi-domain]  Cd Length: 271  Bit Score: 63.94  E-value: 1.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  98 VLDEARRVGqLGIQFVDrpVQALGEGDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTDAPESRRST 177
Cdd:cd19968    21 AVDEAAKLG-VKLVVLD--AQNSSSKQASDLENAIAQGVDGIIVSPIDVKALVPAIEAAIKAGIPVVTVDRRAEGAAPVP 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 178 IVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPrhcAGGKIVSVVE--GHEEEDESFQKTFA 255
Cdd:cd19968    98 HVGADNVAGGREVAKFVVDKLPNGAKVIELTGTPGSSPAIDRTKGFHEELA---AGPKIKVVFEqtGNFERDEGLTVMEN 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 256 LLTRVPGL--AGIYVNTVNCLPVCRALGARGL-AGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRLMADKL 332
Cdd:cd19968   175 ILTSLPGPpdAIICANDDMALGAIEAMRAAGLdLKKVKVIGFDAVPDALQAIKDGELYATVEQPPGGQARTALRILVDYL 254


                  ...
gi 1125163609 333 TNK 335
Cdd:cd19968   255 KDK 257
PBP1_ABC_D-talitol-like cd06318
periplasmic D-talitol-binding protein of an ABC transport system and similar proteins; ...
 130-353 4.51e-11

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: 62.81  E-value: 4.51e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 130 ELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCV-STDAPESRRSTIVCVEPFLNGSLAGELMGKLV-PSGSEVAVI 207
Cdd:cd06318    50 DLITRGVDVLILNPVDPEGLTPAVKAAKAAGIPVITVdSALDPSANVATQVGRDNKQNGVLVGKEAAKALgGDPGKIIEL 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 208 AGMLTTEDHRKKTDGFSESF---PRHCAGGKIVSVVE---GHEEEDESFQKTFALLTRVPGLAGIYV-NTVNCLPVCRAL 280
Cdd:cd06318   130 SGDKGNEVSRDRRDGFLAGVneyQLRKYGKSNIKVVAqpyGNWIRSGAVAAMEDLLQAHPDINVVYAeNDDMALGAMKAL 209

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1125163609 281 GARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRLMADKLTNKIHLPPAVHLSPGLVMSSN 353
Cdd:cd06318   210 KAAGMLDKVKVAGADGQKEALKLIKDGKYVATGLNDPDLLGKTAVDTAAKVVKGEESFPEFTYTPTALITKDN 282
PBP1_LsrB_Quorum_Sensing-like cd20002
ligand-binding protein LsrB-like of ABC transporter periplasmic binding protein; ...
 130-321 6.57e-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: 380657  Cd Length: 295  Bit Score: 62.72  E-value: 6.57e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 130 ELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVcvSTDAPESRRSTIVcVEPFLN---GSLAGELMGKLVPSGSEVAV 206
Cdd:cd20002    51 DLIAQGVDAILVVPNDAKVLEPVFKKAREKGIVVI--THESPGQKGADWD-VELIDNekfGEAQMELLAKEMGGKGEYAI 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 207 IAGMLTTEDHRKKTDGFSESFPRHCAGGKIV-SVVEGHEEEDESFQKTFALLTRVPGLAGI-YVNTVNCLPVCRALGARG 284
Cdd:cd20002   128 FVGSLTVPLHNLWADAAVEYQKEKYPNMKQVtDRIPGGEDVDVSRQTTLELLKAYPDLKGIiSFGSLGPIGAGQALREKG 207

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1125163609 285 LAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQG 321
Cdd:cd20002   208 LKGKVAVVGTVIPSQAAAYLKEGSITEGYLWDPADAG 244
PBP1_sensor_kinase-like cd06308
periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic ...
 121-335 9.53e-11

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: 61.79  E-value: 9.53e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 121 GEGDTEAF----KELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGK 196
Cdd:cd06308    38 AQGDAAKQiadiEDLIAQGVDLLIVSPNEADALTPVVKKAYDAGIPVIVLDRKVSGDDYTAFIGADNVEIGRQAGEYIAE 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 197 LVPSGSEVAVIAGMLTTEDHRKKTDGFSESFpRHCAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYV-NTVNCLP 275
Cdd:cd06308   118 LLNGKGNVVEIQGLPGSSPAIDRHKGFLEAI-AKYPGIKIVASQDGDWLRDKAIKVMEDLLQAHPDIDAVYAhNDEMALG 196

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1125163609 276 VCRALGARGLAGKVKLITTD-LFAEMSPYFQKGTITASIYQQPHrqGQIAVRLMADKLTNK 335
Cdd:cd06308   197 AYQALKKAGREKEIKIIGVDgLPEAGEKAVKDGILAATFLYPTG--GKEAIEAALKILNGE 255
PRK09701 PRK09701
D-allose transporter substrate-binding protein;
90-340 1.22e-10

D-allose transporter substrate-binding protein;


Pssm-ID: 182037 [Multi-domain]  Cd Length: 311  Bit Score: 61.81  E-value: 1.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  90 FYDQLWSGVLDEARRvgqLGIQfVDrPVQALGEGDTEA----FKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVC 165
Cdd:PRK09701   38 FWVDMKKGIEDEAKT---LGVS-VD-IFASPSEGDFQSqlqlFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVN 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 166 VSTDAP-ESRRSTIVCVEPFLN-------GSLAGELMGKLVPSGSEVAVI---AGMLTTEDHRKktdGFSESFprhcagg 234
Cdd:PRK09701  113 LDEKIDmDNLKKAGGNVEAFVTtdnvavgAKGASFIIDKLGAEGGEVAIIegkAGNASGEARRN---GATEAF------- 182

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 235 KIVSVVEGHEEEDESFQKTFAL------LTRVPGLAGIYV-NTVNCLPVCRALGARGLAGKVKLITTDLFAEMSPYFQKG 307
Cdd:PRK09701  183 KKASQIKLVASQPADWDRIKALdvatnvLQRNPNIKAIYCaNDTMAMGVAQAVANAGKTGKVLVVGTDGIPEARKMVEAG 262

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1125163609 308 TITASIYQQPHRQGQIAVRLMADKLTNKIHLPP 340
Cdd:PRK09701  263 QMTATVAQNPADIGATGLKLMVDAEKSGKVIPL 295
PBP1_ABC_sugar_binding-like cd19971
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 130-335 6.17e-10

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


Pssm-ID: 380626 [Multi-domain]  Cd Length: 267  Bit Score: 59.13  E-value: 6.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 130 ELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVST--DAPESRRSTIVCvEPFLNGSLAGELMGKLVPSGSEVAVI 207
Cdd:cd19971    50 DMINQGVDAIFLNPVDSEGIRPALEAAKEAGIPVINVDTpvKDTDLVDSTIAS-DNYNAGKLCGEDMVKKLPEGAKIAVL 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 208 agmltteDHRK------KTDGFSESFPRHcAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRAL 280
Cdd:cd19971   129 -------DHPTaescvdRIDGFLDAIKKN-PKFEVVAQQDGKGQLEVAMPIMEDILQAHPDLDAVFaLNDPSALGALAAL 200

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1125163609 281 GARGLAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRLMADKLTNK 335
Cdd:cd19971   201 KAAGKLGDILVYGVDGSPDAKAAIKDGKMTATAAQSPIEIGKKAVETAYKILNGE 255
PBP1_LacI_sugar_binding-like cd06267
ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 ...
 79-349 6.17e-10

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: 59.45  E-value: 6.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPREIHFFYDQLWSGVLDEARRVG-QLGIQFVDRPVqalgEGDTEAFKELVRSGVDGIILTAGNPKDlsPLIDDAE 157
Cdd:cd06267     2 IGLIVPDISNPFFAELLRGIEDAARERGySLLLCNTDEDP----EREREYLRLLLSRRVDGIILAPSSLDD--ELLEELL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 158 EKGIRVVCVSTDAPESRRSTIVCvepflNGSLAGELMGK-LVPSG-SEVAVIAGMLTTEDHRKKTDGFSESFPRHCAGGK 235
Cdd:cd06267    76 AAGIPVVLIDRRLDGLGVDSVVV-----DNYAGAYLATEhLIELGhRRIAFIGGPLDLSTSRERLEGYRDALAEAGLPVD 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 236 IVSVVEGHEEEDESFQKTFALLTRVPGLAGIYV-NTVNCLPVCRALGARGLA--GKVKLIT---TDLFAEMSPyfqkgTI 309
Cdd:cd06267   151 PELVVEGDFSEESGYEAARELLALPPRPTAIFAaNDLMAIGALRALRELGLRvpEDISVVGfddIPLAALLTP-----PL 225

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1125163609 310 TaSIYQQPHRQGQIAVRLMADKLTNKIHLPPAVHLSPGLV 349
Cdd:cd06267   226 T-TVRQPAYEMGRAAAELLLERIEGEEEPPRRIVLPTELV 264
PBP1_ABC_sugar_binding-like cd06300
periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are ...
 126-354 6.37e-10

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: 59.64  E-value: 6.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 126 EAFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVS--TDAPEsrrSTIVCVEPFLNGSLAGELMGKLVPSGSE 203
Cdd:cd06300    51 AQIRNLIDQGVDAIIINPSSPTALNAVIEQAADAGIPVVAFDgaVTSPD---AYNVSNDQVEWGRLGAKWLFEALGGKGN 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 204 VAV---IAGMLTTEDHRKktdGFSESFPRhCAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYVNTVNCLPVCRAL 280
Cdd:cd06300   128 VLVvrgIAGAPASADRHA---GVKEALAE-YPGIKVVGEVFGGWDEATAQTAMLDFLATHPQVDGVWTQGGEDTGVLQAF 203

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1125163609 281 GARGLAgKVKLITTD-----LFAEMSPYFQKGTITASiyqQPHRQGQIAVRLMADKLTNKIHLPPAVHLSPGLVMSSNL 354
Cdd:cd06300   204 QQAGRP-PVPIVGGDengfaKQWWKHPKKGLTGAAVW---PPPAIGAAGLEVALRLLEGQGPKPQSVLLPPPLITNDDA 278
PBP1_LsrB_Quorum_Sensing-like cd20001
ligand-binding protein LsrB-like of ABC transporter periplasmic binding protein; ...
 131-311 7.87e-10

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: 59.21  E-value: 7.87e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 131 LVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVcvSTDAPeSRRSTIVCVEPFLN---GSLAGELMGKLVPSGSEVAVI 207
Cdd:cd20001    52 LIAQGVDAICVVPNDPEALEPVLKKARDAGIVVI--THEAS-NLKNVDYDVEAFDNaayGAFIMDKLAEAMGGKGKYVTF 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 208 AGMLTTEDHRKKTDG----FSESFPrhcaGGKIVS-VVEGHEEEDESFQKTFALLTRVPGLAGIYVNTVNCLP-VCRALG 281
Cdd:cd20001   129 VGSLTSTSHMEWANAavayQKANYP----DMLLVTdRVETNDDSETAYEKAKELLKTYPDLKGIVGCSSSDVPgAARAVE 204

                         170       180       190
                  ....*....|....*....|....*....|
gi 1125163609 282 ARGLAGKVKLITTDLFAEMSPYFQKGTITA 311
Cdd:cd20001   205 ELGLQGKIAVVGTGLPSVAGEYLEDGTIDY 234
PBP1_methylthioribose_binding-like cd06305
similar to methylthioribose-binding protein of ABC-type transport systems that belong to a ...
 78-349 1.05e-09

similar to methylthioribose-binding protein of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily; Proteins similar to methylthioribose-binding protein of 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 transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380528 [Multi-domain]  Cd Length: 273  Bit Score: 58.85  E-value: 1.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  78 RVGVCIPREIHFFYDQLWSGVLDEARRvgqLGIQfvdrpVQAL-GEGDTEAFKE----LVRSGVDGIILTAGNPKDLSPL 152
Cdd:cd06305     1 TIAVVRNGTSGDWDQQALQGAVAEAEK---LGGT-----VIVFdANGDDARMADqiqqAITQKVDAIIISHGDADALDPK 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 153 IDDAEEKGIRVVCVSTDAPESRrstiVCVEPFLNGSLAGELMGKLV---PSGSEVAVI--AGMLTTEDHRKKTDGFSESF 227
Cdd:cd06305    73 LKKALDAGIPVVTFDTDSQVPG----VNNITQDDYALGTLSLGQLVkdlNGEGNIAVFnvFGVPPLDKRYDIYKAVLKAN 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 228 PrhcaGGKIV----SVVEGHEEEDeSFQKTFALLTRVP--GLAGIYVN-TVNCLPVCRALGARGLAgKVKLITTDLFAEM 300
Cdd:cd06305   149 P----GIKKIvaelGDVTPNTAAD-AQTQVEALLKKYPegGIDAIWAAwDEPAKGAVQALEEAGRT-DIKVYGVDISNQD 222

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1125163609 301 SPYFQK--GTITASIYQQPHRQGQIAVRLMADKLtNKIHLPPAVHLSPGLV 349
Cdd:cd06305   223 LELMADegSPWVATAAQDPALIGTVAVRNVARKL-AGEDLPDKYSLVPVLI 272
Periplasmic_Binding_Protein_type1 cd01391
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ...
 90-339 1.22e-09

Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins, the ligands are monosaccharides, including lactose, ribose, fructose, xylose, arabinose, galactose/glucose and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold.


Pssm-ID: 380477 [Multi-domain]  Cd Length: 280  Bit Score: 58.43  E-value: 1.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  90 FYDQLWSGVLDEARRVGqLGIQFVDRPVQalGEGDTEAFKELVRSGVDGIIltaGNPKDLSPLIDDAEEKGIRVVCVSTD 169
Cdd:cd01391    16 FGIQRVEAIFHTADKLG-ASVEIRDSCWH--GSVALEQSIEFIRDNIAGVI---GPGSSSVAIVIQNLAQLFDIPQLALD 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 170 APESRRSTIVCVEPFLNGSLAGELMGKLVPS------GSEVAVIAGMLTTEDhRKKTDGFSESFPRhcAGGKIVSVVEGH 243
Cdd:cd01391    90 ATSQDLSDKTLYKYFLSVVFSDTLGARLGLDivkrknWTYVAAIHGEGLNSG-ELRMAGFKELAKQ--EGICIVASDKAD 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 244 EEEDE-SFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGLAGKVKLITTDLFAEMS--PYFQKGTITASIYQQPHR 319
Cdd:cd01391   167 WNAGEkGFDRALRKLREGLKARVIVcANDMTARGVLSAMRRLGLVGDVSVIGSDGWADRDevGYEVEANGLTTIKQQKMG 246

                         250       260
                  ....*....|....*....|
gi 1125163609 320 QGQIAVRLMADKLTNKIHLP 339
Cdd:cd01391   247 FGITAIKAMADGSQNMHEEV 266
LacI pfam00356
Bacterial regulatory proteins, lacI family;
20-64 2.93e-09

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 52.25  E-value: 2.93e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1125163609  20 IHLIAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPN 64
Cdd:pfam00356   2 IKDVARLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNYIPN 46
PBP1_ABC_sugar_binding-like cd19996
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
 123-281 5.37e-09

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: 56.87  E-value: 5.37e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 123 GDTEA----FKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVcVSTDAPESRRSTI-VCVEPFLNGSLAGELMGKL 197
Cdd:cd19996    42 GDTQKqiadIQDLIAQGVDAIIVSPNSPTALLPAIEKAAAAGIPVV-LFDSGVGSDKYTAfVGVDDAAFGRVGAEWLVKQ 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 198 VPSGSEVAV---IAGMLTTEDHRKktdGFSESFPRHcAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYVN----T 270
Cdd:cd19996   121 LGGKGNIIAlrgIAGVSVSEDRWA---GAKEVFKEY-PGIKIVGEVYADWDYAKAKQAVESLLAAYPDIDGVWSDggamT 196

                         170
                  ....*....|.
gi 1125163609 271 VNCLPVCRALG 281
Cdd:cd19996   197 LGAIEAFEEAG 207
PBP1_rhizopine_binding-like cd06301
periplasmic binding proteins specific to rhizopines; Periplasmic binding proteins specific to ...
 129-327 1.02e-08

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


Pssm-ID: 380524 [Multi-domain]  Cd Length: 272  Bit Score: 55.70  E-value: 1.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 129 KELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTDAPESRRSTIVC-VEPFLNGSLAGELMGKLVPSGSEVAVI 207
Cdd:cd06301    51 ENFIAQGVDAIIVNPVDTDASAPAVDAAADAGIPLVYVNREPDSKPKGVAFVgSDDIESGELQMEYLAKLLGGKGNIAIL 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 208 AGMLTTEDHRKKTDGFSESFPRHcAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYVNtvN---CLPVCRALGARG 284
Cdd:cd06301   131 DGVLGHEAQILRTEGNKDVLAKY-PGMKIVAEQTANWSREKAMDIVENWLQSGDKIDAIVAN--NdemAIGAILALEAAG 207

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1125163609 285 LAGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRL 327
Cdd:cd06301   208 KKDDILVAGIDATPDALKAMKAGRLDATVFQDAAGQGETAVDV 250
PBP1_ribose_binding cd06323
periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose ...
 90-334 1.57e-08

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: 54.99  E-value: 1.57e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  90 FYDQLWSGVLDEARRVGqlgiqfVDRPV------QALGEGDTEafkELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRV 163
Cdd:cd06323    13 FFVSLKDGAQAEAKELG------VELVVldaqndPAKQLSQVE---DLIVRKVDALLINPTDSDAVSPAVEEANEAGIPV 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 164 VCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHcAGGKIVSVVEGH 243
Cdd:cd06323    84 ITVDRSVTGGKVVSHIASDNVAGGEMAAEYIAKKLGGKGKVVELQGIPGTSAARERGKGFHNAIAKY-PKINVVASQTAD 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 244 EEEDESFQKTFALLTRVPGLAGIYV-NTVNCLPVCRALGARGLAgKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQ 322
Cdd:cd06323   163 FDRTKGLNVMENLLQAHPDIDAVFAhNDEMALGAIQALKAAGRK-DVIVVGFDGTPDAVKAVKDGKLAATVAQQPEEMGA 241

                         250
                  ....*....|..
gi 1125163609 323 IAVrLMADKLTN 334
Cdd:cd06323   242 KAV-ETADKYLK 252
PBP1_ABC_sugar_binding-like cd06321
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 129-349 3.50e-08

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: 54.22  E-value: 3.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 129 KELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVstDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIA 208
Cdd:cd06321    51 DDFIAQGVDLILLNAADSAGIEPAIKRAKDAGIIVVAV--DVAAEGADATVTTDNVQAGYLACEYLVEQLGGKGKVAIID 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 209 GMLTTEdHRKKTDGFSESFPRHcAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYvnTVNCLPVCRALGARGLAGK 288
Cdd:cd06321   129 GPPVSA-VIDRVNGCKEALAEY-PGIKLVDDQNGKGSRAGGLSVMTRMLTAHPDVDGVF--AINDPGAIGALLAAQQAGR 204

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1125163609 289 --VKLITTDLFAEMSPYFQK--GTITASIYQQPHRQGQIAVRLMADKLTNKIHLPPAVHLSPGLV 349
Cdd:cd06321   205 ddIVITSVDGSPEAVAALKRegSPFIATAAQDPYDMARKAVELALKILNGQEPAPELVLIPSTLV 269
PBP1_ABC_sugar_binding-like cd19999
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
 131-295 7.56e-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: 53.47  E-value: 7.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 131 LVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVvcVSTDAPESRRSTI-VCVEPFLNGS-----LAGELMGKlvpsGSEV 204
Cdd:cd19999    56 MINEGVDAILIDPVSATALNPVIEKAQAAGILV--VSFDQPVSSPDAInVVIDQYKWAAiqaqwLAEQLGGK----GNIV 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 205 AV--IAGMlTTEDHRKKtdGFSESFPRHcAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYVNTVNCLPVCRALGA 282
Cdd:cd19999   130 AIngVAGN-PANEARVK--AADDVFAKY-PGIKVLASVPGGWDQATAQQVMATLLATYPDIDGVLTQDGMAEGVLRAFQA 205

                         170
                  ....*....|...
gi 1125163609 283 RGLagKVKLITTD 295
Cdd:cd19999   206 AGK--DPPVMTGD 216
lacI PRK09526
lac repressor; Reviewed
 23-337 1.13e-07

lac repressor; Reviewed


Pssm-ID: 181929 [Multi-domain]  Cd Length: 342  Bit Score: 53.07  E-value: 1.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  23 IAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALSfAKASARVG-VCIPREIHfFYDQLWSGVLDE 101
Cdd:PRK09526   11 VARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNRVAQQLA-GKQSLTIGlATTSLALH-APSQIAAAIKSR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 102 ARRVG-QLGIQFVDRPVqalGEGDTEAFKELVRSGVDGIILTAgnpkdlsPLIDDAEEKgIRVVCVST-----DAPESrr 175
Cdd:PRK09526   89 ADQLGySVVISMVERSG---VEACQAAVNELLAQRVSGVIINV-------PLEDADAEK-IVADCADVpclflDVSPQ-- 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 176 STIVCV--EPFLNGSLAGELmgkLVPSG-SEVAVIAGMLTTEDHRKKTDGFSESFPRHcaGGKIVSVVEGHEEEDESFQK 252
Cdd:PRK09526  156 SPVNSVsfDPEDGTRLGVEH---LVELGhQRIALLAGPESSVSARLRLAGWLEYLTDY--QLQPIAVREGDWSAMSGYQQ 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 253 TFALLTRVPGLAGIYV-NTVNCLPVCRALGARGLA--GKVKLITTDLFAEmSPYFQKGTITasIYQQPHRQGQIAVRLMA 329
Cdd:PRK09526  231 TLQMLREGPVPSAILVaNDQMALGVLRALHESGLRvpGQISVIGYDDTED-SSYFIPPLTT--IKQDFRLLGKEAVDRLL 307


                  ....*...
gi 1125163609 330 DKLTNKIH 337
Cdd:PRK09526  308 ALSQGQAV 315
PBP1_LacI-like cd06278
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 79-267 1.70e-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: 380501 [Multi-domain]  Cd Length: 266  Bit Score: 49.07  E-value: 1.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPReihfFYDQLWSGVLDE-ARRVGQLGIQ---FVDRPvqalGEGDTEAFKELVRSGVDGIILTAGNPKdlSPLID 154
Cdd:cd06278     2 VGVVVGD----LSNPFYAELLEElSRALQARGLRpllFNVDD----EDDVDDALRQLLQYRVDGVIVTSATLS--SELAE 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 155 DAEEKGIRVVCVSTDAPESRRSTIVCvepflNGSLAGELMGK-LVPSG-SEVAVIAGMLTTEDHRKKTDGFSESFPRHca 232
Cdd:cd06278    72 ECARRGIPVVLFNRVVEDPGVDSVSC-----DNRAGGRLAADlLLAAGhRRIAFLGGPEGTSTSRERERGFRAALAEL-- 144

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1125163609 233 GGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIY 267
Cdd:cd06278   145 GLPPPAVEAGDYSYEGGYEAARRLLAAPDRPDAIF 179
PBP1_SalR cd01545
ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of ...
 88-182 4.54e-06

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: 47.55  E-value: 4.54e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  88 HFFYDQLWSGVLDEARrvgQLGIQFVDRPVQALGEGDTEAFKELV-RSGVDGIILTAgnP-KDLSPLIDDAEEKGIRVVC 165
Cdd:cd01545    11 ASYVSALQVGALRACR---EAGYHLVVEPCDSDDEDLADRLRRFLsRSRPDGVILTP--PlSDDPALLDALDELGIPYVR 85

                          90
                  ....*....|....*..
gi 1125163609 166 VSTDAPESRRSTIVCVE 182
Cdd:cd01545    86 IAPGTDDDRSPSVRIDD 102
PRK15408 PRK15408
autoinducer 2 ABC transporter substrate-binding protein LsrB;
107-335 1.53e-05

autoinducer 2 ABC transporter substrate-binding protein LsrB;


Pssm-ID: 237961  Cd Length: 336  Bit Score: 46.33  E-value: 1.53e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 107 QLGIQFV-DRPVQALGEGDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTDA-PESRRSTIVCVEPF 184
Cdd:PRK15408   51 ELGVDVTyDGPTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPALKRAMQRGVKVLTWDSDTkPECRSYYINQGTPE 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 185 LNGSLAGELMGKLV-PSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHCAGGKIVSVVEGHEEEDESFQKTFALLTRVPGL 263
Cdd:PRK15408  131 QLGSMLVEMAAKQVgKDKAKVAFFYSSPTVTDQNQWVKEAKAKIAKEHPGWEIVTTQFGYNDATKSLQTAEGILKAYPDL 210

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1125163609 264 AGIYVNTVNCLPVCrALGARGLA-GKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVrLMADKLTNK 335
Cdd:PRK15408  211 DAIIAPDANALPAA-AQAAENLKrDKVAIVGFSTPNVMRPYVKRGTVKEFGLWDVVQQGKISV-YVANELLKK 281
PBP1_ABC_sugar_binding-like cd19966
monosaccharide ABC transporter substrate binding protein CUT2 family and simialr proteins; ...
 126-340 2.87e-05

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: 45.39  E-value: 2.87e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 126 EAFKELVRSGVDGIIlTAGNPKD--LSPLIDDAEEKGIRVVCVSTDAPESRRSTivCVEPFLNGSL--AGELMGK----- 196
Cdd:cd19966    47 EQFKEAIAAKPDGIA-IMGHPGDgaYTPLIEAAKKAGIIVTSFNTDLPKLEYGD--CGLGYVGADLyaAGYTLAKelvkr 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 197 -LVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHcagGKIVSVVEGHEEEDESFQ---KTFALLTRVPGLAGIYVNTVN 272
Cdd:cd19966   124 gGLKTGDRVFVPGLLPGQPYRVLRTKGVIDALKEA---GIKVDYLEISLEPNKPAEgipVMTGYLAANPDVKAIVGDGGG 200

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 273 CL-PVCRALGARGL-AGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRLMAdkLTNKIHLPP 340
Cdd:cd19966   201 LTaNVAKYLKAAGKkPGEIPVAGFDLSPATVQAIKSGYVNATIDQQPYLQGYLPVLQIY--LTKKYGFSG 268
PBP1_ABC_ThpA_XypA cd06313
periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group ...
 121-330 4.45e-05

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: 44.57  E-value: 4.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 121 GEGDTEA----FKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGK 196
Cdd:cd06313    37 GNGDVSTqinqVDTLIAQGVDAIIVVPVDADALAPAVEKAKEAGIPLVGVNALIENEDLTAYVGSDDVVAGELEGQAVAD 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 197 LVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHcAGGKIVSVVEGHEEEDESFQKTFALLTRVPG-LAGIYV-NTVNCL 274
Cdd:cd06313   117 RLGGKGNVVILEGPIGQSAQIDRGKGIENVLKKY-PDIKVLAEQTANWSRDEAMSLMENWLQAYGDeIDGIIAqNDDMAL 195

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1125163609 275 PVCRALGARGLaGKVKLITTDLFAEMSPYFQKGTITASIYQQPHRQGQIAVRLMAD 330
Cdd:cd06313   196 GALQAVKAAGR-DDIPVVGIDGIEDALQAVKSGELIATVLQDAEAQGKGAVEVAVD 250
PBP1_LacI-like cd06285
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 79-285 5.01e-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: 380508 [Multi-domain]  Cd Length: 269  Bit Score: 44.52  E-value: 5.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPREIHFFYDQLWSGVLDEARRVGQLGIQFVDRPVqalGEGDTEAFKELVRSGVDGIILTagNPKDLSPLIDDAEE 158
Cdd:cd06285     2 IGVLVSDLSNPFYAELVEGIEDAARERGYTVLLADTGDD---PERELAALDSLLSRRVDGLIIT--PARDDAPDLQELAA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 159 KGIRVVCVSTDAPESRRSTIVCvEPFLNGSLAGE-LMGKlvpsG-SEVAVIAGMLTTEDHRKKTDGFSESFPRHCAGGKI 236
Cdd:cd06285    77 RGVPVVLVDRRIGDTALPSVTV-DNELGGRLATRhLLEL----GhRRIAVVAGPLNASTGRDRLRGYRRALAEAGLPVPD 151

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1125163609 237 VSVVEGHEEEDESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGL 285
Cdd:cd06285   152 ERIVPGGFTIEAGREAAYRLLSRPERPTAVFaANDLMAIGVLRAARDLGL 201
PBP1_AglR_RafR-like cd06292
Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that ...
 79-349 6.45e-05

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: 44.18  E-value: 6.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIP----REIHFFYDQLWSGVLDEARRVGQLGIQFVdrpvQALGEGDTEAFKELVRS-GVDGIILTAGNPKDlsPLI 153
Cdd:cd06292     2 IGYVVPelpgGFSDPFFDEFLAALGHAAAARGYDVLLFT----ASGDEDEIDYYRDLVRSrRVDGFVLASTRHDD--PRV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 154 DDAEEKGIRVVCVSTDAPESRRSTIVCvepflNGSLA-GELMGKLVPSGSE-VAVIAGMLTTEDHRKKTDGFSESFPRHC 231
Cdd:cd06292    76 RYLHEAGVPFVAFGRANPDLDFPWVDV-----DGAAGmRQAVRHLIALGHRrIGLIGGPEGSVPSDDRLAGYRAALEEAG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 232 AGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIY-VNTVNCLPVCRALGARGLAgkvklITTDL----F--AEMSPYF 304
Cdd:cd06292   151 LPFDPGLVVEGENTEEGGYAAAARLLDLGPPPTAIVcVSDLLALGAMRAARERGLR-----VGRDVsvvgFddSPLAAFT 225

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1125163609 305 QKGTITASiyqQPHRQ-GQIAVRLMADKLtNKIHLPPAVHL-SPGLV 349
Cdd:cd06292   226 HPPLTTVR---QPIDEiGRAVVDLLLAAI-EGNPSEPREILlQPELV 268
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
20-83 1.07e-04

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 44.00  E-value: 1.07e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1125163609  20 IHLIAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALSfAKASARVGVCI 83
Cdd:PRK10401    4 IRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPNANAQALA-TQVSDTIGVVV 66
PBP1_repressor_sugar_binding-like cd01537
Ligand-binding domain of the LacI-GalR family of transcription regulators and the ...
 78-348 1.47e-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: 43.00  E-value: 1.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  78 RVGVCIPR-EIHFFydqlwsGVLDEA--RRVGQLGIQFVDRPVQALGEGDTEAFKELVRSGVDGIILTAgnPKDLSPLID 154
Cdd:cd01537     1 RIGVTIYSyDDNFM------SVIRKAieQDAKQPGVQLLMNDSQNDQEKQNDQIDVLLAKRVKGLAINL--VDPAAAGVA 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 155 DaEEKGIRVVCVSTDAPESRRSTI--VCVEPFLNGSLAGELMGKLvpSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHCA 232
Cdd:cd01537    73 E-KARGQNVPVVFFDKEPSRYDKAyyVITDSKEGGIIQGDLLAKH--GHIQIVLLKGPLGHPDAEARLAGVIKELNDKGI 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 233 GGKIVSVVEGHEEEDESFQKTFALLTR--VPgLAGIYVNTVNCLPVCRALGARGL--AGKVKLITTDLFAEMSPYfqkGT 308
Cdd:cd01537   150 KTEQLQLDTGDWDTASGKDKMDQWLSGpnKP-TAVIANNDAMAMGAVEALKEHGLrvPSDISVFGYDALPEALKS---GP 225

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1125163609 309 ITASIYQQPHRQGQIAVRLMADKLTNKIHLPPAVHLSPGL 348
Cdd:cd01537   226 LLTTILQDANNLGKTTFDLLLNLADNWKIDNKVVRVPYVL 265
PBP1_ABC_sugar_binding-like cd19998
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
 131-354 1.61e-04

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: 380653 [Multi-domain]  Cd Length: 302  Bit Score: 43.05  E-value: 1.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 131 LVRSGVDGIILTAGNPKDLSPLIDDAEEKGIrvVCVSTDAP-ESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAG 209
Cdd:cd19998    55 MIAAGYDAILIYAISPTALNPVIKRACDAGI--VVVAFDNVvDEPCAYNVNTDQAKAGEQTAQWLVDKLGGKGNILMVRG 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 210 MLTTEDHRKKTDGFSESFPRHcAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYVNtVNCLPVCRALGARGLagKV 289
Cdd:cd19998   133 VPGTSVDRDRYEGAKEVFKKY-PDIKVVAEYYGNWDDGTAQKAVADALAAHPDVDGVWTQ-GGETGVIKALQAAGH--PL 208

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1125163609 290 KLITTD-------LFAEMSPYFQKGtitaSIYQQPHRQGQIAVRLMADKLTNKiHLPPAVHLSPGLVMSSNL 354
Cdd:cd19998   209 VPVGGEaengfrkAMLEPLANGLPG----ISAGSPPALSAVALKLAVAVLEGE-KEPKTIELPLPWVTTDDV 275
PBP1_arabinose_binding cd01540
periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose ...
 131-350 1.86e-04

periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily; Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380482 [Multi-domain]  Cd Length: 294  Bit Score: 42.66  E-value: 1.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 131 LVRSGVDGIILTAGNPKdLSP-LIDDAEEKGIRVVCVSTDAPESRRSTIVcvePFLN------GSLAGELMGKLV----- 198
Cdd:cd01540    51 LIAQGAQGIVICTPDQK-LGPaIAAKAKAAGIPVIAVDDQLVDADPMKIV---PFVGidaykiGEAVGEWLAKEMkkrgw 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 199 PSGSEVAVIA-GMLTTEDHRKKTDGFSESFPRhcAGG---KIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYVNTVN-- 272
Cdd:cd01540   127 DDVKEVGVLAiTMDTLSVCVDRTDGAKDALKA--AGFpedQIFQAPYKGTDTEGAFNAANAVITAHPEVKHWLVVGCNde 204

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 273 -CLPVCRALGARGLaGKVKLITTDLFAEMS--PYFQKGT--ITASIYQQPHRQGQIAVRLMADKLTNKIHlPPAVHLSPG 347
Cdd:cd01540   205 gVLGAVRALEQAGF-DAEDIIGVGIGGYLAadEEFKKQPtgFKASLYISPDKHGYIAAEELYNWITDGKP-PPAETLTDG 282


                  ...
gi 1125163609 348 LVM 350
Cdd:cd01540   283 VIV 285
PBP1_ABC_sugar_binding-like cd06324
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 107-313 2.34e-04

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: 42.59  E-value: 2.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 107 QLGIQFVdrpVQAlGEGDTEAFKELVR------SGVDGIILTAgNPKDLSPLIDDAEEKGIRVVCVSTDAPESRRSTIVC 180
Cdd:cd06324    28 DLGIELE---VLY-ANRNRFKMLELAEellarpPKPDYLILVN-EKGVAPELLELAEQAKIPVFLINNDLTDEERALLGK 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 181 VE---PFLNGSL------AGELMGKLV---------PSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHcAGGKIVSVVEG 242
Cdd:cd06324   103 PRekfKYWLGSIvpdneqAGYLLAKALikaarkksdDGKIRVLAISGDKSTPASILREQGLRDALAEH-PDVTLLQIVYA 181

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1125163609 243 HEEEDESFQKTFALLTRVPGLAGIYV-NTVNCLPVCRALGARGL-AGK-VKLITTDLFAEMSPYFQKGTITASI 313
Cdd:cd06324   182 NWSEDEAYQKTEKLLQRYPDIDIVWAaNDAMALGAIDALEEAGLkPGKdVLVGGIDWSPEALQAVKDGELTASV 255
PRK10936 PRK10936
TMAO reductase system periplasmic protein TorT; Provisional
 132-358 3.14e-04

TMAO reductase system periplasmic protein TorT; Provisional


Pssm-ID: 236801 [Multi-domain]  Cd Length: 343  Bit Score: 42.24  E-value: 3.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 132 VRSGVDGIILTAGNPKDLSPLIDDAEeKGIRVVCV----STDAPESRrstiVCVEPFLNGSLAGELMGKLVPSGSEVAVI 207
Cdd:PRK10936  101 VAWGADAILLGAVTPDGLNPDLELQA-ANIPVIALvngiDSPQVTTR----VGVSWYQMGYQAGRYLAQWHPKGSKPLNV 175

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 208 AgMLTTEDHRKKTDGFSESFpRHCAGGKIVSVVE-GHEEEDESFQKTFA--LLTRVPGLAGIYVNTVNCLPVCRALGARG 284
Cdd:PRK10936  176 A-LLPGPEGAGGSKAVEQGF-RAAIAGSDVRIVDiAYGDNDKELQRNLLqeLLERHPDIDYIAGSAVAAEAAIGELRGRN 253

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 285 LAGKVKLITTDLfaemSP--Y--FQKGTITASIYQQPHRQGQIAVRLMADKLTNKihlPPAVHLSPGLVM--SSNLHLFR 358
Cdd:PRK10936  254 LTDKIKLVSFYL----SHqvYrgLKRGKVLAAPSDQMVLQGRLAIDQAVRQLEGA---PVPGDVGPKILVltPKNLDSED 326
PBP1_Qymf-like cd06291
ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing ...
 79-349 4.24e-04

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: 41.74  E-value: 4.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPREIHFFYDQLWSGVLDEARRvgqLGIQFV-----DRPvqalgEGDTEAFKELVRSGVDGIILTAGNPKdlsplI 153
Cdd:cd06291     2 IGLIVPDISNPFFAELAKYIEKELFK---KGYKMIlcnsnEDE-----EKEKEYLEMLKRNKVDGIILGSHSLD-----I 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 154 DDAEEKGIRVVCVSTDAPESrrstIVCVEP--FLNGSLAGElmgKLVPSGSE-VAVIAGMLTTEDHRKKTDGFSESFPRH 230
Cdd:cd06291    69 EEYKKLNIPIVSIDRYLSEG----IPSVSSdnYQGGRLAAE---HLIEKGCKkILHIGGPSNNSPANERYRGFEDALKEA 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 231 CAGGKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIYVNT----VNCLpvcRALGARGLA--GKVKLITTD--LFAEMSP 302
Cdd:cd06291   142 GIEYEIIEIDENDFSEEDAYELAKELLEKYPDIDGIFASNdllaIGVL---KALQKLGIRvpEDVQIIGFDgiEISELLY 218

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1125163609 303 YfqkgTITaSIYQQPHRQGQIAVRLMADKLTNKIHLPPAVHLSPGLV 349
Cdd:cd06291   219 P----ELT-TIRQPIEEMAKEAVELLLKLIEGEEIEESRIVLPVELI 260
PBP1_LacI-like cd06299
ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum ...
 90-334 1.01e-03

ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum produces significant amounts of L-glutamate directly from cheap sugar and ammonia; This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member 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: 380522 [Multi-domain]  Cd Length: 268  Bit Score: 40.34  E-value: 1.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  90 FYDQLWSGVLDEARrvgQLGIQFVDRPVQALGEGDTEAFKELVRSGVDGIIL--TAGNpkdlSPLIDDAEEKGIRVVCVS 167
Cdd:cd06299    13 FFAELASGIEDEAR---AHGYSVILGNSDEDPEREDESLEMLLSQRVDGIIAvpTGEN----SEGLQALIAQGLPVVFVD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 168 TDAPESRRSTIVCVEPFlngSLAGELMGKLVPSG-SEVAVIAGMLTTEDHRKKTDGFSESFPRHCAGGKIVSVVEGHEEE 246
Cdd:cd06299    86 REVEGLGGVPVVTSDNR---PGAREAVEYLVSLGhRRIGYISGPLSTSTGRERLAAFRAALTAAGIPIDEELVAFGDFRQ 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 247 DESFQKTFALLTRVPGLAGIYV-NTVNCLPVCRALGARGL--AGKVKLITTD---LFAEMSPyfqkgTITAsIYQQPHRQ 320
Cdd:cd06299   163 DSGAAAAHRLLSRGDPPTALIAgDSLMALGAIQALRELGLriGDDVSLISFDdvpWFELLSP-----PLTV-IAQPVERI 236

                         250
                  ....*....|....
gi 1125163609 321 GQIAVRLMADKLTN 334
Cdd:cd06299   237 GRRAVELLLALIEN 250
PBP1_galactofuranose_YtfQ-like cd06309
periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ...
 121-330 1.41e-03

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: 39.89  E-value: 1.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 121 GEGDTE----AFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVVCVSTDAPESRRSTIVC--VEPFLN-GSLAGEL 193
Cdd:cd06309    37 ANQDQEkqinDIRDLIAQGVDAILISPIDATGWDPVLKEAKDAGIPVILVDRTIDGEDGSLYVTfiGSDFVEeGRRAAEW 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 194 MGK-LVPSGSEVAVIAGMLTTEDHRKKTDGFSESFPRHCaGGKIVSVVEGHEEEDESFQKTFALLTRVPG-LAGIYvnTV 271
Cdd:cd06309   117 LVKnYKGGKGNVVELQGTAGSSVAIDRSKGFREVIKKHP-NIKIVASQSGNFTREKGQKVMENLLQAGPGdIDVIY--AH 193

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1125163609 272 N---CLPVCRALGARGL--AGKVKLITTDLFAEMSPYFQKGTITASIYQQPhRQGQIAVRLMAD 330
Cdd:cd06309   194 NddmALGAIQALKEAGLkpGKDVLVVGIDGQKDALEAIKAGELNATVECNP-LFGPTAFDTIAK 256
PBP1_LacI-like cd06280
ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus ...
 90-349 1.64e-03

ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus 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: 380503 [Multi-domain]  Cd Length: 266  Bit Score: 39.93  E-value: 1.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  90 FYDQLWSGVLDEARRVG-QLgiqfvdrpVQALGEGDTEAFKELVRS----GVDGIILTAGnpKDLSPLIDDAEEKGIRVV 164
Cdd:cd06280    13 FFTTIARGIEDAAEKHGyQV--------ILANTDEDPEKEKRYLDSllskQVDGIILAPS--AGPSRELKRLLKHGIPIV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 165 CVSTDAPESRRSTIVcVEpflNGSLAGELMGKLVPSG-SEVAVIAGMLTTEDHRKKTDGFSESFPRHcaGGKIVS--VVE 241
Cdd:cd06280    83 LIDREVEGLELDLVA-GD---NREGAYKAVKHLIELGhRRIGLITGPLEISTTRERLAGYREALAEA--GIPVDEslIFE 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 242 GHEEEDESFQKTFALLTRVPGLAGIYV-NTVNCLPVCRALGARGLAgkvklITTDL----FAEMSPY-FQKGTITAsIYQ 315
Cdd:cd06280   157 GDSTIEGGYEAVKALLDLPPRPTAIFAtNNLMAVGALRALRERGLE-----IPQDIsvvgFDDSDWFeIVDPPLTV-VAQ 230

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1125163609 316 QPHRQGQIAVRLMADKLTNKIHLPPAVHLSPGLV 349
Cdd:cd06280   231 PAYEIGRIAAQLLLERIEGQGEEPRRIVLPTELI 264
PBP1_ABC_sugar_binding-like cd06311
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 79-267 2.75e-03

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


Pssm-ID: 380534 [Multi-domain]  Cd Length: 270  Bit Score: 39.27  E-value: 2.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPREIHFfydqlWSGVL-----DEARRVGQLGIQFVdrpVQALGEGDTEAFKELVRSGVDGIILTAGNPKDLSPLI 153
Cdd:cd06311     2 IGISIPSADHG-----WTAGVayyaeKQAKELADLEYKLV---TSSNANEQVSQLEDLIAQKVDAIVILPQDSEELTVAA 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 154 DDAEEKGIRVVCVSTDAPESRRSTIVCVEPFLNGSLAGELMGKLVPSGSEVAVIAGMLTTEDHRKKTDGFSESFpRHCAG 233
Cdd:cd06311    74 QKAKDAGIPVVNFDRGLNVLIYDLYVAGDNPGMGVVSAEYIGKKLGGKGNVVVLEVPSSGSVNEERVAGFKEVI-KGNPG 152

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1125163609 234 GKIVSVVEGHEEEDESFQKTFALLTRVPGLAGIY 267
Cdd:cd06311   153 IKILAMQAGDWTREDGLKVAQDILTKNKKIDAVW 186
PBP1_LacI-like cd06282
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 126-241 3.84e-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: 380505 [Multi-domain]  Cd Length: 267  Bit Score: 38.80  E-value: 3.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 126 EAFKELVRSGVDGIILTAGNPkDLSPLIDDAEEKGIRVVCVSTDAPESRRStIVCVEPFLNGSLAGELMGKLvpSGSEVA 205
Cdd:cd06282    46 DAVETLLEQRVDGLILTVGDA-QGSEALELLEEEGVPYVLLFNQTENSSHP-FVSVDNRLASYDVAEYLIAL--GHRRIA 121

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1125163609 206 VIAGMLTTEDH-RKKTDGFSESFPRHcaGGKIVSVVE 241
Cdd:cd06282   122 MVAGDFSASDRaRLRYQGYRDALKEA--GLKPIPIVE 156
PBP1_ABC_sugar_binding-like cd19973
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 79-330 5.91e-03

monosaccharide ABC transporter substrate-binding protein; 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: 380628 [Multi-domain]  Cd Length: 285  Bit Score: 38.22  E-value: 5.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPREIHFFYDQLWSGVLDEARRvgqLGIQFvdRPVQALGEGDTE----AFKELVRSGVDGIILTAGNPKDLSPLID 154
Cdd:cd19973     2 IGLITKTDTNPFFVKMKEGAQKAAKA---LGIKL--MTAAGKIDGDNAtqvtAIENMIAAGAKGILITPSDTKAIVPAVK 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 155 DAEEKGIRVVCVST-----DAPESRRSTivcvepflNGSLAGELMGKLVPS--GSEVAVIAGMLTTEDH---RKKTDGFS 224
Cdd:cd19973    77 KARDAGVLVIALDTptdpiDAADATFAT--------DNFKAGVLIGEWAKAalGAKDAKIATLDLTPGHtvgVLRHQGFL 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609 225 ESF-----PRHCAGGKIVSVVEGHEE---EDESFQKTFA-LLTRVPGLAGIY-VNTVNCLPVCRALGARGLAGKVKLITT 294
Cdd:cd19973   149 KGFgidekDPESNEDEDDSQVVGSADtngDQAKGQTAMEnLLQKDPDINLVYtINEPAAAGAYQALKAAGKEKGVLIVSV 228

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1125163609 295 DLFAEMSPYFQKGTITASIYQQPHRQGQIAVRLMAD 330
Cdd:cd19973   229 DGGCPGVKDVKDGIIGATSQQYPLRMAALGVEAIAA 264
PBP1_DegA_Like cd19976
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
 79-223 6.23e-03

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: 38.00  E-value: 6.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125163609  79 VGVCIPREIHFFYDQLWSGVLDEARRVGqLGIQFVDrpVQALGEGDTEAFKELVRSGVDGIILTAGNPKDLSpLIDDAEE 158
Cdd:cd19976     2 IGLIVPDISNPFFSELVRGIEDTLNELG-YNIILCN--TYNDFEREKKYIQELKERNVDGIIIASSNISDEA-IIKLLKE 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1125163609 159 KGIRVVCVSTDAPEsRRSTIVCVEPFLNGSLAGELmgkLVPSG-SEVAVIAGMLTTEDHRKKTDGF 223
Cdd:cd19976    78 EKIPVVVLDRYIED-NDSDSVGVDDYRGGYEATKY---LIELGhTRIGCIVGPPSTYNEHERIEGY 139
PBP1_ABC_sugar_binding-like cd06315
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 123-164 8.63e-03

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


Pssm-ID: 380538  Cd Length: 278  Bit Score: 37.71  E-value: 8.63e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1125163609 123 GDTEAFKELVRSGVDGIILTAGNPKDLSPLIDDAEEKGIRVV 164
Cdd:cd06315    44 GRLAALNQALALKPDGIILGGDDAVELQEPLKKAVKAGIPVV 85
PRK10727 PRK10727
HTH-type transcriptional regulator GalR;
23-71 9.30e-03

HTH-type transcriptional regulator GalR;


Pssm-ID: 182681 [Multi-domain]  Cd Length: 343  Bit Score: 37.81  E-value: 9.30e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1125163609  23 IAEMAKVSIGTVDRALHARGGIKDSTRQRILQVARQIGYSPNLAARALS 71
Cdd:PRK10727    7 VARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNANARALA 55
 
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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