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Conserved domains on  [gi|495775830|ref|WP_008500409|]
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MULTISPECIES: arabinose ABC transporter substrate-binding protein AraF [Enterobacterales]

Protein Classification

arabinose ABC transporter substrate-binding protein( domain architecture ID 10107481)

arabinose ABC transporter substrate-binding protein serves as the initial receptor in the high-affinity L-arabinose membrane transport system

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP1_arabinose_binding cd01540
periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose ...
 27-321 3.69e-141

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: 400.90  E-value: 3.69e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVP-DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYD 105
Cdd:cd01540    1 KIGFIVKQPDQPWFQDEWKGAKKAAKELGFEVIKIDAKmDGEKVLSAIDNLIAQGAQGIVICTPDQKLGPAIAAKAKAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 106 MKVIAVDDQFVNakGKPMDSVPLVMMAATKIGERQGQELYKEMQKRGW-DVKETAVMAITADELDTARRRTTGSMDALKA 184
Cdd:cd01540   81 IPVIAVDDQLVD--ADPMKIVPFVGIDAYKIGEAVGEWLAKEMKKRGWdDVKEVGVLAITMDTLSVCVDRTDGAKDALKA 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 185 AGFPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKHWLVVGMNDNTVLGGVRATEGQGFKAPDVIGIGINGVDAVSELS 264
Cdd:cd01540  159 AGFPEDQIFQAPYKGTDTEGAFNAANAVITAHPEVKHWLVVGCNDEGVLGAVRALEQAGFDAEDIIGVGIGGYLAADEEF 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495775830 265 KAQATGFYGSLLPSPDVHGYKSSEMLYNWVTKGAEPPKFTeVTDVVLITRDNFKEEL 321
Cdd:cd01540  239 KKQPTGFKASLYISPDKHGYIAAEELYNWITDGKPPPAET-LTDGVIVTRDNYKEVM 294
 
Name Accession Description Interval E-value
PBP1_arabinose_binding cd01540
periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose ...
 27-321 3.69e-141

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: 400.90  E-value: 3.69e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVP-DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYD 105
Cdd:cd01540    1 KIGFIVKQPDQPWFQDEWKGAKKAAKELGFEVIKIDAKmDGEKVLSAIDNLIAQGAQGIVICTPDQKLGPAIAAKAKAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 106 MKVIAVDDQFVNakGKPMDSVPLVMMAATKIGERQGQELYKEMQKRGW-DVKETAVMAITADELDTARRRTTGSMDALKA 184
Cdd:cd01540   81 IPVIAVDDQLVD--ADPMKIVPFVGIDAYKIGEAVGEWLAKEMKKRGWdDVKEVGVLAITMDTLSVCVDRTDGAKDALKA 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 185 AGFPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKHWLVVGMNDNTVLGGVRATEGQGFKAPDVIGIGINGVDAVSELS 264
Cdd:cd01540  159 AGFPEDQIFQAPYKGTDTEGAFNAANAVITAHPEVKHWLVVGCNDEGVLGAVRALEQAGFDAEDIIGVGIGGYLAADEEF 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495775830 265 KAQATGFYGSLLPSPDVHGYKSSEMLYNWVTKGAEPPKFTeVTDVVLITRDNFKEEL 321
Cdd:cd01540  239 KKQPTGFKASLYISPDKHGYIAAEELYNWITDGKPPPAET-LTDGVIVTRDNYKEVM 294
Peripla_BP_1 pfam00532
Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the ...
 25-320 8.72e-102

Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (pfam00356).


Pssm-ID: 395423 [Multi-domain]  Cd Length: 281  Bit Score: 300.58  E-value: 8.72e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830   25 NLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDGEKTL-NAIDSLAASGAKGFVICTPDPKlGSAIAAKARG 103
Cdd:pfam00532   1 TLKLGALVPQLDEPFFQDLVKGITKAAKDHGFDVFLLAVGDGEDTLtNAIDLLLASGADGIIITTPAPS-GDDITAKAEG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  104 YDMKVIAVDDQFVNAKGkpmdsVPLVMMAATKIGERQGQELYKEMQKRGwdvkeTAVMAITADELdTARRRTTGSMDALK 183
Cdd:pfam00532  80 YGIPVIAADDAFDNPDG-----VPCVMPDDTQAGYESTQYLIAEGHKRP-----IAVMAGPASAL-TARERVQGFMAALA 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  184 AAGFPeKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQG-FKAPDVIGIGINGVDAVSE 262
Cdd:pfam00532 149 AAGRE-VKIYHVATGDNDIPDAALAANAMLVSHPTID--AIVAMNDEAAMGAVRALLKQGrVKIPDIVGIGINSVVGFDG 225

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495775830  263 LSKAQATGFYGSLLPSPDVH----GYKSSEMLYNWVtkgaepPKFTEVTDVVLITRDNFKEE 320
Cdd:pfam00532 226 LSKAQDTGLYLSPLTVIQLPrqllGIKASDMVYQWI------PKFREHPRVLLIPRDFFKET 281
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
 7-316 2.72e-36

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: 132.74  E-value: 2.72e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830   7 ALAAIGLAAVMSQSAIAENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVI-KIAVPDGEKTLNAIDSLAASGAKGFV 85
Cdd:COG1879   15 ALAACGSAAAEAAAAAAKGKTIGFVVKTLGNPFFVAVRKGAEAAAKELGVELIvVDAEGDAAKQISQIEDLIAQGVDAII 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  86 ICTPDPKLGSAIAAKARGYDMKVIAVDDQFvnakgKPMDSVPLVMMAATKIGERQGQELYKEMQKRGwdvkETAVMAITA 165
Cdd:COG1879   95 VSPVDPDALAPALKKAKAAGIPVVTVDSDV-----DGSDRVAYVGSDNYAAGRLAAEYLAKALGGKG----KVAILTGSP 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 166 DeLDTARRRTTGSMDALKAagFPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGfK 245
Cdd:COG1879  166 G-APAANERTDGFKEALKE--YPGIKVVAEQYADWDREKALEVMEDLLQAHPDID--GIFAANDGMALGAAQALKAAG-R 239

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495775830 246 APDVIGIGINGV-DAVSELskaQATGFYGSLLPSPDVHGYKSSEMLYNWVtKGAEPPKFTeVTDVVLITRDN 316
Cdd:COG1879  240 KGDVKVVGFDGSpEALQAI---KDGTIDATVAQDPYLQGYLAVDAALKLL-KGKEVPKEI-LTPPVLVTKEN 306
 
Name Accession Description Interval E-value
PBP1_arabinose_binding cd01540
periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose ...
 27-321 3.69e-141

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: 400.90  E-value: 3.69e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVP-DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYD 105
Cdd:cd01540    1 KIGFIVKQPDQPWFQDEWKGAKKAAKELGFEVIKIDAKmDGEKVLSAIDNLIAQGAQGIVICTPDQKLGPAIAAKAKAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 106 MKVIAVDDQFVNakGKPMDSVPLVMMAATKIGERQGQELYKEMQKRGW-DVKETAVMAITADELDTARRRTTGSMDALKA 184
Cdd:cd01540   81 IPVIAVDDQLVD--ADPMKIVPFVGIDAYKIGEAVGEWLAKEMKKRGWdDVKEVGVLAITMDTLSVCVDRTDGAKDALKA 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 185 AGFPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKHWLVVGMNDNTVLGGVRATEGQGFKAPDVIGIGINGVDAVSELS 264
Cdd:cd01540  159 AGFPEDQIFQAPYKGTDTEGAFNAANAVITAHPEVKHWLVVGCNDEGVLGAVRALEQAGFDAEDIIGVGIGGYLAADEEF 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495775830 265 KAQATGFYGSLLPSPDVHGYKSSEMLYNWVTKGAEPPKFTeVTDVVLITRDNFKEEL 321
Cdd:cd01540  239 KKQPTGFKASLYISPDKHGYIAAEELYNWITDGKPPPAET-LTDGVIVTRDNYKEVM 294
Peripla_BP_1 pfam00532
Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the ...
 25-320 8.72e-102

Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (pfam00356).


Pssm-ID: 395423 [Multi-domain]  Cd Length: 281  Bit Score: 300.58  E-value: 8.72e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830   25 NLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDGEKTL-NAIDSLAASGAKGFVICTPDPKlGSAIAAKARG 103
Cdd:pfam00532   1 TLKLGALVPQLDEPFFQDLVKGITKAAKDHGFDVFLLAVGDGEDTLtNAIDLLLASGADGIIITTPAPS-GDDITAKAEG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  104 YDMKVIAVDDQFVNAKGkpmdsVPLVMMAATKIGERQGQELYKEMQKRGwdvkeTAVMAITADELdTARRRTTGSMDALK 183
Cdd:pfam00532  80 YGIPVIAADDAFDNPDG-----VPCVMPDDTQAGYESTQYLIAEGHKRP-----IAVMAGPASAL-TARERVQGFMAALA 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  184 AAGFPeKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQG-FKAPDVIGIGINGVDAVSE 262
Cdd:pfam00532 149 AAGRE-VKIYHVATGDNDIPDAALAANAMLVSHPTID--AIVAMNDEAAMGAVRALLKQGrVKIPDIVGIGINSVVGFDG 225

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495775830  263 LSKAQATGFYGSLLPSPDVH----GYKSSEMLYNWVtkgaepPKFTEVTDVVLITRDNFKEE 320
Cdd:pfam00532 226 LSKAQDTGLYLSPLTVIQLPrqllGIKASDMVYQWI------PKFREHPRVLLIPRDFFKET 281
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
 7-316 2.72e-36

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: 132.74  E-value: 2.72e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830   7 ALAAIGLAAVMSQSAIAENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVI-KIAVPDGEKTLNAIDSLAASGAKGFV 85
Cdd:COG1879   15 ALAACGSAAAEAAAAAAKGKTIGFVVKTLGNPFFVAVRKGAEAAAKELGVELIvVDAEGDAAKQISQIEDLIAQGVDAII 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  86 ICTPDPKLGSAIAAKARGYDMKVIAVDDQFvnakgKPMDSVPLVMMAATKIGERQGQELYKEMQKRGwdvkETAVMAITA 165
Cdd:COG1879   95 VSPVDPDALAPALKKAKAAGIPVVTVDSDV-----DGSDRVAYVGSDNYAAGRLAAEYLAKALGGKG----KVAILTGSP 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 166 DeLDTARRRTTGSMDALKAagFPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGfK 245
Cdd:COG1879  166 G-APAANERTDGFKEALKE--YPGIKVVAEQYADWDREKALEVMEDLLQAHPDID--GIFAANDGMALGAAQALKAAG-R 239

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495775830 246 APDVIGIGINGV-DAVSELskaQATGFYGSLLPSPDVHGYKSSEMLYNWVtKGAEPPKFTeVTDVVLITRDN 316
Cdd:COG1879  240 KGDVKVVGFDGSpEALQAI---KDGTIDATVAQDPYLQGYLAVDAALKLL-KGKEVPKEI-LTPPVLVTKEN 306
PBP1_ABC_sugar_binding-like cd01536
periplasmic sugar-binding domain of active transport systems that are members of the type 1 ...
 27-310 6.15e-32

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: 119.98  E-value: 6.15e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEV-IKIAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYD 105
Cdd:cd01536    1 KIGVVVKDLTNPFWVAVKKGAEAAAKELGVELvVLDAQGDVAKQISQIEDLIAQGVDAIIIAPVDSEALVPAVKKANAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 106 MKVIAVDDQFvnakGKPMDSVPLVMMAATKIGERQGQELYKEMQKRGwdvketAVMAITADEL-DTARRRTTGSMDALKA 184
Cdd:cd01536   81 IPVVAVDTDI----DGGGDVVAFVGTDNYEAGKLAGEYLAEALGGKG------KVAILEGPPGsSTAIDRTKGFKEALKK 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 185 agFPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGfKAPDVIGIGINGVDAVseLS 264
Cdd:cd01536  151 --YPDIEIVAEQPANWDRAKALTVTENLLQANPDID--AVFAANDDMALGAAEALKAAG-RTGDIKIVGVDGTPEA--LK 223

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 495775830 265 KAQATGFYGSLLPSPDVHGYKSSEMLYNWVtKGAEPPKFTEVTDVV 310
Cdd:cd01536  224 AIKDGELDATVAQDPYLQGYLAVEAAVKLL-NGEKVPKEILTPVTL 268
PBP1_ABC_sugar_binding-like cd06319
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 27-316 1.05e-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: 92.81  E-value: 1.05e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDGEKTL--NAIDsLAASGAKGFVICTPDPKLGSAIAAKARGY 104
Cdd:cd06319    1 KIGYSVYDLDNPFWQIMERGVQAAAEELGYEFVTYDQKNSANEQvtNAND-LIAQGVDGIIISPTNSSAAPTVLDLANEA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 105 DMKVIAVDdqfVNAKGKPMDSVPLVMMAATkiGERQGQELYKEMQKRGWDVKETAVMAITADElDTARRRTTGSMDALKA 184
Cdd:cd06319   80 KIPVVIAD---IGTGGGDYVSYIISDNYDG--GYQAGEYLAEALKENGWGGGSVGIIAIPQSR-VNGQARTAGFEDALEE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 185 AGFPEKQIYKVPTKSNDipGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGfKAPDVIGIGINGVDAVSELS 264
Cdd:cd06319  154 AGVEEVALRQTPNSTVE--ETYSAAQDLLAANPDIK--GIFAQNDQMAQGALQAIEEAG-RTGDILVVGFDGDPEALDLI 228

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 495775830 265 KAQatGFYGSLLPSPDVHGYKSSEMLYNWVtKGAEPPKFTEVTDVVLITRDN 316
Cdd:cd06319  229 KDG--KLDGTVAQQPFGMGARAVELAIQAL-NGDNTVEKEIYLPVLLVTSEN 277
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
 29-292 6.55e-13

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: 67.72  E-value: 6.55e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830   29 GFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKI--AVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYDM 106
Cdd:pfam13407   2 GVVPKSTGNPFFQAAEEGAEEAAKELGGEVIVVgpAEADAAEQVAQIEDAIAQGVDAIIVAPVDPTALAPVLKKAKDAGI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  107 KVIAVDDQFVNAKGkpmdsVPLVMMAATKIGERQGQELYKEMQKRGwdvketAVMAITADELDT-ARRRTTGSMDALKaA 185
Cdd:pfam13407  82 PVVTFDSDAPSSPR-----LAYVGFDNEAAGEAAGELLAEALGGKG------KVAILSGSPGDPnANERIDGFKKVLK-E 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  186 GFPEKQIYKVPTKSNDIPG-AFDAANSMLVQHP-EVKHwlVVGMNDNTVLGGVRATEGQGFKAPDVIGiginGVDAVSEL 263
Cdd:pfam13407 150 KYPGIKVVAEVEGTNWDPEkAQQQMEALLTAYPnPLDG--IISPNDGMAGGAAQALEAAGLAGKVVVT----GFDATPEA 223

                         250       260       270
                  ....*....|....*....|....*....|
gi 495775830  264 SKAQATG-FYGSLLPSPDVHGYKSSEMLYN 292
Cdd:pfam13407 224 LEAIKDGtIDATVLQDPYGQGYAAVELAAA 253
PBP1_ABC_D-talitol-like cd06318
periplasmic D-talitol-binding protein of an ABC transport system and similar proteins; ...
 27-316 4.17e-12

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: 65.51  E-value: 4.17e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKI-AVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYD 105
Cdd:cd06318    1 KIGFSQRTLASPYYAALVAAAKAEAKKLGVELVVTdAQNDLTKQISDVEDLITRGVDVLILNPVDPEGLTPAVKAAKAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 106 MKVIAVDDQfVNAKGKPmdsVPLVMMAATKIGERQGQELYKEMQKrgwdvKETAVMAITADELDT-ARRRTTGSMDA--- 181
Cdd:cd06318   81 IPVITVDSA-LDPSANV---ATQVGRDNKQNGVLVGKEAAKALGG-----DPGKIIELSGDKGNEvSRDRRDGFLAGvne 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 182 --LKAAGFPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGfKAPDVIgigINGVDA 259
Cdd:cd06318  152 yqLRKYGKSNIKVVAQPYGNWIRSGAVAAMEDLLQAHPDIN--VVYAENDDMALGAMKALKAAG-MLDKVK---VAGADG 225

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 495775830 260 VSELSKAQATGFYG-SLLPSPDVHGYKSSEMLYNWVTKGAEPPKFTEVTDvVLITRDN 316
Cdd:cd06318  226 QKEALKLIKDGKYVaTGLNDPDLLGKTAVDTAAKVVKGEESFPEFTYTPT-ALITKDN 282
PBP1_ABC_sugar_binding-like cd20008
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 27-313 5.62e-11

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


Pssm-ID: 380663 [Multi-domain]  Cd Length: 277  Bit Score: 62.25  E-value: 5.62e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVP---DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARG 103
Cdd:cd20008    1 KIAVIVKDTDSEYWQTVLKGAEKAAKELGVEVTFLGPAteaDIAGQVNLVENAISRKPDAIVLAPNDTAALVPAVEAADA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 104 yDMKVIAVDDQfVNAKgkpmDSVPLVMMAATKIGERQGQELYKEMQKRGWDVKETAVMAITADElDTARRRTTGSMDALK 183
Cdd:cd20008   81 -GIPVVLVDSG-ANTD----DYDAFLATDNVAAGALAADELAELLKASGGGKGKVAIISFQAGS-QTLVDREEGFRDYIK 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 184 AAgFPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKHwlVVGMNDNTVLGGVRATEGQGfKAPDVIGIginGVDAVSEL 263
Cdd:cd20008  154 EK-YPDIEIVDVQYSDGDIAKALNQTTDLLTANPDLVG--IFGANNPSAVGVAQALAEAG-KAGKIVLV---GFDSSPDE 226

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495775830 264 SKAQATGF-YGSLLPSPDVHGYKSSEMLYNwVTKGAEPPKFTEVTDVVLIT 313
Cdd:cd20008  227 VALLKSGViKALVVQDPYQMGYEGVKTAVK-ALKGEEIVEKNVDTGVTVVT 276
PBP1_TmRBP-like cd19967
D-ribose ABC transporter substrate-binding protein such as Thermoanaerobacter tengcongensis ...
 32-313 2.17e-09

D-ribose ABC transporter substrate-binding protein such as Thermoanaerobacter tengcongensis ribose binding protein (ttRBP); Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging 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: 380622 [Multi-domain]  Cd Length: 272  Bit Score: 57.33  E-value: 2.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  32 VKQPEEPWFQTEWKFADKAGKDLGFEViKIAVPDGEKTLNA--IDSLAASGAKGfVICTPdPKLGSAIAA--KARGYDMK 107
Cdd:cd19967    6 VSTPNNPFFVVEAEGAKEKAKELGYEV-TVFDHQNDTAKEAelFDTAIASGAKA-IILDP-ADADASIAAvkKAKDAGIP 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 108 VIAVDDQfVNAKGKPMDSVPLVMMAATKIGerqGQELYKEMQKRGwdvKETAVMAITADEldTARRRTTGSMDALKaaGF 187
Cdd:cd19967   83 VFLIDRE-INAEGVAVAQIVSDNYQGAVLL---AQYFVKLMGEKG---LYVELLGKESDT--NAQLRSQGFHSVID--QY 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 188 PEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGfKAPDVIGIGING----VDAVSEl 263
Cdd:cd19967  152 PELKMVAQQSADWDRTEAFEKMESILQANPDIK--GVICGNDEMALGAIAALKAAG-RAGDVIIVGFDGsndvRDAIKE- 227

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 495775830 264 SKAQATGfygslLPSPDVHGYKSSEMLYNWVTKGAEPPKFTEVTDVVLIT 313
Cdd:cd19967  228 GKISATV-----LQPAKLIARLAVEQADQYLKGGSTGKEEKQLFDCVLIT 272
PBP1_repressor_sugar_binding-like cd01537
Ligand-binding domain of the LacI-GalR family of transcription regulators and the ...
 65-306 2.39e-08

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: 54.17  E-value: 2.39e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  65 DGEKTLNAIDSLAASGAKGFVICTPDPKlGSAIAAKARGYDMKVIAVDDQfvNAKGKPMDSvplVMMAATKIGERQGQEL 144
Cdd:cd01537   40 DQEKQNDQIDVLLAKRVKGLAINLVDPA-AAGVAEKARGQNVPVVFFDKE--PSRYDKAYY---VITDSKEGGIIQGDLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 145 YKEMQKRgwdvketavMAITADELD--TARRRTTGSMDALKAAGFPEKQIYKVpTKSNDIPGAFDAANSMLVQhPEVKHW 222
Cdd:cd01537  114 AKHGHIQ---------IVLLKGPLGhpDAEARLAGVIKELNDKGIKTEQLQLD-TGDWDTASGKDKMDQWLSG-PNKPTA 182

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 223 LVVGmNDNTVLGGVRATEGQGFKAPDviGIGINGVDAVSELSKaqATGFYGSLLPSPDVHGYKSSEMLYNWVTKGAEPPK 302
Cdd:cd01537  183 VIAN-NDAMAMGAVEALKEHGLRVPS--DISVFGYDALPEALK--SGPLLTTILQDANNLGKTTFDLLLNLADNWKIDNK 257


                 ....
gi 495775830 303 FTEV 306
Cdd:cd01537  258 VVRV 261
PBP1_ABC_sugar_binding-like cd20004
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 44-314 8.07e-08

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


Pssm-ID: 380659 [Multi-domain]  Cd Length: 273  Bit Score: 52.62  E-value: 8.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  44 WKF----ADKAGKDLGFEVIKIAvPDGEKTLNA----IDSLAASGAKGFVICTPDPKLGSAIAAKARGYDMKVIAVDdqf 115
Cdd:cd20004   14 WKSvkagAEKAAQELGVEIYWRG-PSREDDVEAqiqiIEYFIDQGVDGIVLAPLDRKALVAPVERARAQGIPVVIID--- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 116 vnakgKPMDSVPLVMMAAT---KIGERQGQELYKEMQKRGwdvkeTAVMAITADELDTARRRTTGSMDALKaAGFPEKQI 192
Cdd:cd20004   90 -----SDLGGDAVISFVATdnyAAGRLAAKRMAKLLNGKG-----KVALLRLAKGSASTTDRERGFLEALK-KLAPGLKV 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 193 YKVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGfKAPDVIGIGIngvDAVSELSKA-QATGF 271
Cdd:cd20004  159 VDDQYAGGTVGEARSSAENLLNQYPDVD--GIFTPNESTTIGALRALRRLG-LAGKVKFIGF---DASDLLLDAlRAGEI 232

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 495775830 272 YGSLLPSPDVHGYKSSEMLYNwVTKGAEPPKFTeVTDVVLITR 314
Cdd:cd20004  233 SALVVQDPYRMGYLGVKTAVA-ALRGKPVPKRI-DTGVVLVTK 273
PBP1_ABC_sugar_binding-like cd20005
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 47-315 1.98e-07

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: 51.47  E-value: 1.98e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  47 ADKAGKDLGFEVIKIAvPDGE----KTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYDMKVIAVDdqfvnaKGKP 122
Cdd:cd20005   21 AEQAAKELGVKITFEG-PDTEsdvdKQIEMLDNAIAKKPDAIALAALDTNALLPQLEKAKEKGIPVVTFD------SGVP 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 123 MDSVplVMMAAT---KIGERQGQELYKEMQKRGwdvkETAVMAITADELdTARRRTTGSMDALKAAgFPEKQIYKVPTKS 199
Cdd:cd20005   94 SDLP--LATVATdnyAAGALAADHLAELIGGKG----KVAIVAHDATSE-TGIDRRDGFKDEIKEK-YPDIKVVNVQYGV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 200 NDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGfKAPDVIGIginGVDAVSELSKAQATG-FYGSLLPS 278
Cdd:cd20005  166 GDHAKAADIAKAILQANPDLK--GIYATNEGAAIGVANALKEMG-KLGKIKVV---GFDSGEAQIDAIKNGvIAGSVTQN 239

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 495775830 279 PDVHGYKSSEMLYNwVTKGAEPPKFTEvTDVVLITRD 315
Cdd:cd20005  240 PYGMGYKTVKAAVK-ALKGEEVEKLID-TGAKWYDKD 274
PBP1_galactofuranose_YtfQ-like cd06309
periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ...
 27-323 2.19e-07

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: 51.45  E-value: 2.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKI-AVPDGEKTLNAIDSLAASGAKGFVIctpDPKLGSAIAA---KAR 102
Cdd:cd06309    1 TVGFSQAGSESPWRVANTKSIKEAAKKRGYELVYTdANQDQEKQINDIRDLIAQGVDAILI---SPIDATGWDPvlkEAK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 103 GYDMKVIAVDDQfVNAKGKPmDSVPLVMMAATKIGERQGQELYKEMQKrgwdvKETAVMAITADE-LDTARRRTTGSMDA 181
Cdd:cd06309   78 DAGIPVILVDRT-IDGEDGS-LYVTFIGSDFVEEGRRAAEWLVKNYKG-----GKGNVVELQGTAgSSVAIDRSKGFREV 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 182 LKAAGfpekQIYKVPTKSNDI--PGAFDAANSMLVQHPEvKHWLVVGMNDNTVLGGVRATEGQGFKAP-DVIGIGINGV- 257
Cdd:cd06309  151 IKKHP----NIKIVASQSGNFtrEKGQKVMENLLQAGPG-DIDVIYAHNDDMALGAIQALKEAGLKPGkDVLVVGIDGQk 225

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 495775830 258 DAVSEL--SKAQATGFYgsllpSPDvHGYKSSEMLYNWVtKGAEPPKFTEVTDVVlITRDNFKEELAK 323
Cdd:cd06309  226 DALEAIkaGELNATVEC-----NPL-FGPTAFDTIAKLL-AGEKVPKLIIVEERL-FDKDNAAEELEP 285
PBP1_ABC_xylose_binding-like cd19992
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ...
 27-268 3.03e-07

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


Pssm-ID: 380647 [Multi-domain]  Cd Length: 284  Bit Score: 51.05  E-value: 3.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVI-KIAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYD 105
Cdd:cd19992    1 KIGVSFPTQQEERWQKDKEYMEEEAKELGVELIfQVADNDAKTQASQVENLLAQGIDVLIIAPVDAGAAANIVDKAKAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 106 MKVIAVDDQFVNAKgkpmdsVPL-VMMAATKIGERQGQELYKEmqkrgwdVKETAVMAITADELDT-ARRRTTGSMDALK 183
Cdd:cd19992   81 VPVISYDRLILNAD------VDLyVGRDNYKVGQLQAEYALEA-------VPKGNYVILSGDPGDNnAQLITAGAMDVLQ 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 184 AAGFPE--KQIYKVPTKsndipgAFDAANSMlvqhPEVKHWL---------VVGMNDNTVLGGVRATEGQGFkAPDVIgi 252
Cdd:cd19992  148 PAIDSGdiKIVLDQYVK------GWSPDEAM----KLVENALtannnnidaVLAPNDGMAGGAIQALKAQGL-AGKVF-- 214

                        250
                 ....*....|....*.
gi 495775830 253 gINGVDAvsELSKAQA 268
Cdd:cd19992  215 -VTGQDA--ELAALKR 227
PBP1_ribose_binding cd06323
periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose ...
 27-313 6.48e-07

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: 49.99  E-value: 6.48e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKI-AVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYD 105
Cdd:cd06323    1 TIGLSVSTLNNPFFVSLKDGAQAEAKELGVELVVLdAQNDPAKQLSQVEDLIVRKVDALLINPTDSDAVSPAVEEANEAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 106 MKVIAVDDQFvnAKGKpmdSVPLVMMAATKIGERQGQELYKEMQKRGWDVKETAVMAITAdeldtARRRTTGSMDALKAa 185
Cdd:cd06323   81 IPVITVDRSV--TGGK---VVSHIASDNVAGGEMAAEYIAKKLGGKGKVVELQGIPGTSA-----ARERGKGFHNAIAK- 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 186 gFPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKHwlVVGMNDNTVLGGVRATEGQGFKapDVIGIGINGV-DAVSELS 264
Cdd:cd06323  150 -YPKINVVASQTADFDRTKGLNVMENLLQAHPDIDA--VFAHNDEMALGAIQALKAAGRK--DVIVVGFDGTpDAVKAVK 224

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 495775830 265 KAQatgFYGSLLPSPDVHGYKSSEMLYNWVtKGAEPPKFTEVtDVVLIT 313
Cdd:cd06323  225 DGK---LAATVAQQPEEMGAKAVETADKYL-KGEKVPKKIPV-PLKLVT 268
PBP1_allose_binding cd06320
periplasmic allose-binding domain of bacterial transport systems that function as a primary ...
 27-316 9.90e-07

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


Pssm-ID: 380543 [Multi-domain]  Cd Length: 283  Bit Score: 49.57  E-value: 9.90e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVP---DGEKTLNAIDSLAASGAKGFVIcTP--DPKLGSAIA-AK 100
Cdd:cd06320    1 KIGVVLKTLSNPFWVAMKDGIEAEAKKLGVKVDVQAAPsetDTQGQLNLLETMLNKGYDAILV-SPisDTNLIPPIEkAN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 101 ARGydMKVIAVDDQFVNAKGKPMDSVPLVMMA--ATKIGERQGQELYKEMQKRGwdvkETAVMAITADElDTARRRTTGS 178
Cdd:cd06320   80 KKG--IPVINLDDAVDADALKKAGGKVTSFIGtdNVAAGALAAEYIAEKLPGGG----KVAIIEGLPGN-AAAEARTKGF 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 179 MDALKAAgfPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKhwlvvGM---NDNTVLGGVRATEGQGfKAPDVIGIGIN 255
Cdd:cd06320  153 KETFKKA--PGLKLVASQPADWDRTKALDAATAILQAHPDLK-----GIyaaNDTMALGAVEAVKAAG-KTGKVLVVGTD 224

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495775830 256 GV-DAVSELSKAQATgfyGSLLPSPDVHGYKSSEMLYnWVTKGAEPPKFTeVTDVVLITRDN 316
Cdd:cd06320  225 GIpEAKKSIKAGELT---ATVAQYPYLEGAMAVEAAL-RLLQGQKVPAVV-ATPQALITKDN 281
PBP1_tmGBP cd06314
periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and ...
 27-313 2.04e-06

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: 48.35  E-value: 2.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVP--DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGY 104
Cdd:cd06314    1 TFALVPKGLNNPFWDLAEAGAEKAAKELGVNVEFVGPQksDAAEQVQLIEDLIARGVDGIAISPNDPEAVTPVINKAADK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 105 DMKVIAVDDQFVNAKGKpmdsvplvmmaaTKIG---ERQGQELYKEMQKRGWDVKETAVMAITADElDTARRRTTGSMDA 181
Cdd:cd06314   81 GIPVITFDSDAPDSKRL------------AYIGtdnYEAGREAGELMKKALPGGGKVAIITGGLGA-DNLNERIQGFKDA 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 182 LKAAgfpeKQIYKVPTKSN--DIPGAFDAANSMLVQHPEVKHWlvVGMNDNTVLGGVRATEGQGfKAPDVIGIGINGVDA 259
Cdd:cd06314  148 LKGS----PGIEIVDPLSDndDIAKAVQNVEDILKANPDLDAI--FGVGAYNGPAIAAALKDAG-KVGKVKIVGFDTLPE 220

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495775830 260 VSELSKAQATgfYGSLLPSPDVHGYKSSEMLYNWVTKGAEPPKFTEvTDVVLIT 313
Cdd:cd06314  221 TLQGIKDGVI--AATVGQRPYEMGYLSVKLLYKLLKGGKPVPDVID-TGVDVVT 271
PBP1_ABC_ThpA_XypA cd06313
periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group ...
 27-316 6.53e-06

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


Pssm-ID: 380536 [Multi-domain]  Cd Length: 277  Bit Score: 46.88  E-value: 6.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVK-QPEEpwFQTEWKFADKA-GKDLGFEVIKI-AVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARG 103
Cdd:cd06313    1 KIGFTVYgLSSE--FITNLVEAMKAvAKELNVDLVVLdGNGDVSTQINQVDTLIAQGVDAIIVVPVDADALAPAVEKAKE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 104 YDMKVIAVddqfvNAKGKPMDSVPLVMMAATKIGERQGQELYKEMQKRGWDVKETAVMAITAdELDtarrRTTGSMDALK 183
Cdd:cd06313   79 AGIPLVGV-----NALIENEDLTAYVGSDDVVAGELEGQAVADRLGGKGNVVILEGPIGQSA-QID----RGKGIENVLK 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 184 AAgfPEkqiYKVPTKSndiPGAFDAANSMLVqhpeVKHWL---------VVGMNDNTVLGGVRATEGQGFKapDVIGIGI 254
Cdd:cd06313  149 KY--PD---IKVLAEQ---TANWSRDEAMSL----MENWLqaygdeidgIIAQNDDMALGALQAVKAAGRD--DIPVVGI 214

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495775830 255 NGVDAVseLSKAQATGFYGSLLPSPDVHGYKSSEMLYNwVTKGAEPPKFTEVtDVVLITRDN 316
Cdd:cd06313  215 DGIEDA--LQAVKSGELIATVLQDAEAQGKGAVEVAVD-AVKGEGVEKKYYI-PFVLVTKDN 272
PBP1_ABC_sugar_binding-like cd06322
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 49-307 9.37e-06

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


Pssm-ID: 380545 [Multi-domain]  Cd Length: 270  Bit Score: 46.50  E-value: 9.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  49 KAGKDLGFEVIkIAVPDGE--KTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYDMKVIAVDdqfVNAKGKPMDsv 126
Cdd:cd06322   23 KEAAELGVKVV-VADANGDlaKQLSQIEDFIQQGVDAIILAPVDSGGIVPAIEAANEAGIPVFTVD---VKADGAKVV-- 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 127 plvmmaaTKIGERQ---GQELYKEMQKRGWDVKETAVMaITADELDTARRRTTGSMDALKAAgfPEKQIYKVPTKSNDIP 203
Cdd:cd06322   97 -------THVGTDNyagGKLAGEYALKALLGGGGKIAI-IDYPEVESVVLRVNGFKEAIKKY--PNIEIVAEQPGDGRRE 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 204 GAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGfKAPDVIGIGINGVDavsELSKAQATG--FYGSLLPSPDV 281
Cdd:cd06322  167 EALAATEDMLQANPDLD--GIFAIGDPAALGALTAIESAG-KEDKIKVIGFDGNP---EAIKAIAKGgkIKADIAQQPDK 240

                        250       260
                 ....*....|....*....|....*.
gi 495775830 282 HGYKSSEMLYNwVTKGAEPPKFTEVT 307
Cdd:cd06322  241 IGQETVEAIVK-YLAGETVEKEILIP 265
PBP1_ABC_xylose_binding-like cd19995
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ...
 65-245 2.11e-05

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


Pssm-ID: 380650 [Multi-domain]  Cd Length: 294  Bit Score: 45.36  E-value: 2.11e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  65 DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYDMKVIAVDDQFVNAKGKPMDSVPLVmmaatKIGERQGQEL 144
Cdd:cd19995   43 DASTQQQQAEAAITQGAKVLVVDPVDSNAAAGIVAKAAQAGVPVIAYDRLILGGPADYYVSFDNV-----AVGEAQAQSL 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 145 YKEMqkRGWDVKETAVMAITADELDT-ARRRTTGSMDALKAAGFPE--KQIYKVPTKSNDIPGAFDAANSMLVQHPEvKH 221
Cdd:cd19995  118 VDHL--KAIGKKGVNIVMINGSPTDNnAGLFKKGAHEVLDPLGDSGelKLVCEYDTPDWDPANAQTAMEQALTKLGN-NI 194

                        170       180
                 ....*....|....*....|....
gi 495775830 222 WLVVGMNDNTVLGGVRATEGQGFK 245
Cdd:cd19995  195 DGVLSANDGLAGGAIAALKAQGLA 218
PBP1_ABC_sugar_binding-like cd06324
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 35-262 3.58e-05

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which 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: 44.90  E-value: 3.58e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  35 PEEPWFQTEWKFADKAGKDLGFEV-IKIAVPDGEKTLNAIDSLAASGAK-GFVICTPDPKLGSAIAAKARGYDMKVIAVD 112
Cdd:cd06324   10 EDEPFWQNVTRFMQAAAKDLGIELeVLYANRNRFKMLELAEELLARPPKpDYLILVNEKGVAPELLELAEQAKIPVFLIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 113 DQFVNAK----GKPMDS--------VPlvmmAATKIGERQGQELYKEMQKRGwDVKETAVMAITADELDTA-RRRTTGSM 179
Cdd:cd06324   90 NDLTDEErallGKPREKfkywlgsiVP----DNEQAGYLLAKALIKAARKKS-DDGKIRVLAISGDKSTPAsILREQGLR 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 180 DALKAAgfPEKQIYKVptksndIPG------AFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGFKA-PDVIgi 252
Cdd:cd06324  165 DALAEH--PDVTLLQI------VYAnwsedeAYQKTEKLLQRYPDID--IVWAANDAMALGAIDALEEAGLKPgKDVL-- 232

                        250
                 ....*....|
gi 495775830 253 gINGVDAVSE 262
Cdd:cd06324  233 -VGGIDWSPE 241
PBP1_ABC_sugar_binding-like cd19971
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 65-292 3.99e-05

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: 44.50  E-value: 3.99e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  65 DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYDMKVIAVDDQFVNAkgKPMDSVplVMMAATKIGERQGQEL 144
Cdd:cd19971   40 DQNKQNEQIEDMINQGVDAIFLNPVDSEGIRPALEAAKEAGIPVINVDTPVKDT--DLVDST--IASDNYNAGKLCGEDM 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 145 YKEMQKRGwdvketAVMAITADELDTARRRTTGSMDALKA-AGFpeKQIYKVPTKSnDIPGAFDAANSMLVQHPEVKhwL 223
Cdd:cd19971  116 VKKLPEGA------KIAVLDHPTAESCVDRIDGFLDAIKKnPKF--EVVAQQDGKG-QLEVAMPIMEDILQAHPDLD--A 184

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 224 VVGMNDNTVLGGVRATEGqgfkAPDVIGIGINGVDAVSELSKA-QATGFYGSLLPSPDVHGYKSSEMLYN 292
Cdd:cd19971  185 VFALNDPSALGALAALKA----AGKLGDILVYGVDGSPDAKAAiKDGKMTATAAQSPIEIGKKAVETAYK 250
PBP1_LacI-like cd06279
ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium ...
 169-251 4.84e-05

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


Pssm-ID: 380502 [Multi-domain]  Cd Length: 284  Bit Score: 44.12  E-value: 4.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 169 DTARRRTTGSMDALKAAGFPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGFKAPD 248
Cdd:cd06279  146 SVARERLAGYRDALEEAGLDLDDVPVVEAPGNTEEAGRAAARALLALDPRPT--AILCMSDVLALGALRAARERGLRVPE 223


                 ....*.
gi 495775830 249 ---VIG 251
Cdd:cd06279  224 dlsVTG 229
PBP1_ABC_sugar_binding-like cd06310
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 47-313 9.23e-05

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: 43.48  E-value: 9.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  47 ADKAGKDLGFEVIKIAVP---DGEKTLNAIDSLAASGAKGFVICTPDPK--LGSAIAAKARGydMKVIAVDdqfvnAKGK 121
Cdd:cd06310   21 AEAAAKDLGVKIIFVGPEseeDVAGQNSLLEELINKKPDAIVVAPLDSEdlVDPLKDAKDKG--IPVIVID-----SGIK 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 122 PMDSVPLVMMAATKIGERQGQELYKEMQKRGwdvkETAVMAITADElDTARRRTTGSMDALKAAGfPEKQIYKVPTKSND 201
Cdd:cd06310   94 GDAYLSYIATDNYAAGRLAAQKLAEALGGKG----KVAVLSLTAGN-STTDQREEGFKEYLKKHP-GGIKVLASQYAGSD 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 202 IPGAFDAANSMLVQHPEVKHwlVVGMNDNTVLGGVRATEGQGFKAPdvigIGINGVDAVSELSKAQATG-FYGSLLPSPD 280
Cdd:cd06310  168 YAKAANETEDLLGKYPDIDG--IFATNEITALGAAVAIKSRKLSGQ----IKIVGFDSQEELLDALKNGkIDALVVQNPY 241

                        250       260       270
                 ....*....|....*....|....*....|...
gi 495775830 281 VHGYKSSEMLYNwVTKGAEPPKFTEvTDVVLIT 313
Cdd:cd06310  242 EIGYEGIKLALK-LLKGEEVPKNID-TGAELIT 272
PBP1_ABC_sugar_binding-like cd19965
monosaccharide ABC transporter substrate binding protein CUT2 family and similar proteins; ...
 36-234 1.14e-04

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: 43.03  E-value: 1.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  36 EEPWFQTEWKFADKAGKDLGFEVIKIAVPDG--EKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYDMKVIAVDd 113
Cdd:cd19965   10 TNPFFQPVKKGMDDACELLGAECQFTGPQTFdvAEQVSLLEAAIASGPDGIATTIVDPEAFDEVIKRALDAGIPVVAFN- 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 114 qfVNAKGKPMDSVPLVMMAATKIGERQGQELYKEMQKRGWDVketaVMAITADELDTARRRTTGSMDALKAAGFPEKqiY 193
Cdd:cd19965   89 --VDAPGGENARLAFVGQDLYPAGYVLGKRIAEKFKPGGGHV----LLGISTPGQSALEQRLDGIKQALKEYGRGIT--Y 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 495775830 194 KVPTKSNDIPGAFDAANSMLVQHPEVKHWLVVGMNDNTVLG 234
Cdd:cd19965  161 DVIDTGTDLAEALSRIEAYYTAHPDIKAIFATGAFDTAGAG 201
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
47-251 1.27e-04

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


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 43.26  E-value: 1.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  47 ADKAGKDLgfeVIKIAVPDGEKTLNAIDSLAASGAKGFVICTPDpkLGSAIAAKARGYDMKVIAVDDQFvnakgkPMDSV 126
Cdd:COG1609   87 ARERGYQL---LLANSDEDPEREREALRLLLSRRVDGLILAGSR--LDDARLERLAEAGIPVVLIDRPL------PDPGV 155

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 127 PLVMMAATKIGERQGQELYKemqkRGWdvkeTAVMAITADE-LDTARRRTTGSMDALKAAGFPEKQIYkVPTKSNDIPGA 205
Cdd:COG1609  156 PSVGVDNRAGARLATEHLIE----LGH----RRIAFIGGPAdSSSARERLAGYREALAEAGLPPDPEL-VVEGDFSAESG 226

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 495775830 206 FDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGFKAPD---VIG 251
Cdd:COG1609  227 YEAARRLLARGPRPT--AIFCANDLMALGALRALREAGLRVPEdvsVVG 273
PBP1_ABC_unchar_transporter cd06325
type 1 periplasmic ligand-binding domain of uncharacterized ABC-type transport systems ...
 27-118 1.55e-04

type 1 periplasmic ligand-binding domain of uncharacterized ABC-type transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions; This group includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.


Pssm-ID: 380548  Cd Length: 282  Bit Score: 42.88  E-value: 1.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVkQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDGEKTLNAIDSLAASGAKGFVIcTPDPKLGSA---IAAKARG 103
Cdd:cd06325  133 RVGVLY-NPGEPNSVAQLEELEAAAKKLGLELVEVPVSSPADIEQAFASLAGKVADALYV-PTDNTVASArprIAALALK 210

                         90
                 ....*....|....*
gi 495775830 104 YDMKVIAVDDQFVNA 118
Cdd:cd06325  211 ARIPVIYSDREFVEA 225
PBP1_LsrB_Quorum_Sensing-like cd06302
periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium ...
 27-315 3.10e-04

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: 41.84  E-value: 3.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIA--VPDGEKTLNAIDSLAASGAKGFVICTPDPklgSAIAA---KA 101
Cdd:cd06302    1 KIAFVPKVVGIPYFDAAEEGAKKAAKELGVEVVYTGptQADAAQQVQIVENLIAQGVDAIAVSPNDA---DALAPvlkKA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 102 RGYDMKVIAVDDQfVNAKGKPMDsvplVMMAATKIgerQGQELYKEMQKRgwdVKETAVMAITADELDTARRRT-TGSMD 180
Cdd:cd06302   78 KDAGIKVITWDSD-APPSARDYF----VNQADDEG---LGEALVDSLAKE---IGGKGKVAILSGSLTATNLNAwIKAMK 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 181 ALKAAGFPEKQIYKVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGfKAPDVIGIGINGVDAV 260
Cdd:cd06302  147 EYLKSKYPDIELVDTYYTDDDQQKAYTQAQNLIQAYPDLK--GIIGVSTTAPPAAAQAVEEAG-KTGKVAVTGIGLPNTA 223

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 495775830 261 SELSKAQATGFygSLLPSPDVHGYKSSEMLYNWVTKGAEPPKFTEVTDVVLITRD 315
Cdd:cd06302  224 RPYLKDGSVKE--GVLWDPAKLGYLTVYAAYQLLKGKGFTEDSDDVGTGGKVKVD 276
PBP1_ABC_sugar_binding-like cd19970
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 27-269 3.35e-04

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


Pssm-ID: 380625 [Multi-domain]  Cd Length: 275  Bit Score: 41.85  E-value: 3.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGK-DLGFEVIKIAVP---DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKAR 102
Cdd:cd19970    1 KVALVMKSLANEFFIEMEKGARKHAKeANGYELLVKGIKqetDIEQQIAIVENLIAQKVDAIVIAPADSKALVPVLKKAV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 103 GYDMKVI----AVDDQFVNAKGKPmdsVPLVMMAATKIGERQGQELYKEMQKRGwdvkETAVM-AITadELDTARRRTTG 177
Cdd:cd19970   81 DAGIAVInidnRLDADALKEGGIN---VPFVGPDNRQGAYLAGDYLAKKLGKGG----KVAIIeGIP--GADNAQQRKAG 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 178 SMDALKAAGFpekQIYKVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGfKAPDVIGIGINGV 257
Cdd:cd19970  152 FLKAFEEAGM---KIVASQSANWEIDEANTVAANLLTAHPDIR--GILCANDNMALGAIKAVDAAG-KAGKVLVVGFDNI 225

                        250
                 ....*....|....*
gi 495775830 258 DAVSELSKA---QAT 269
Cdd:cd19970  226 PAVRPLLKDgkmLAT 240
PBP1_GGBP cd01539
periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and ...
 65-301 3.79e-04

periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species; Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member 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. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380481 [Multi-domain]  Cd Length: 302  Bit Score: 41.80  E-value: 3.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  65 DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYDMKVIavddqFVNAkgKPMDSvplVMMAATKI-------- 136
Cdd:cd01539   42 DQSTQNDQIDTMIAKGVDLLVVNLVDRTAAQTIIDKAKAANIPVI-----FFNR--EPSRE---DLKSYDKAyyvgtdae 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 137 --GERQGQELYKEMQK-RGWD-----VKETAVMAITADELDTArRRTTGSMDALKAAGFPEKQIYKVpTKSNDIPGAFDA 208
Cdd:cd01539  112 esGIMQGEIIADYWKAnPEIDkngdgKIQYVMLKGEPGHQDAI-ARTKYSVKTLNDAGIKTEQLAED-TANWDRAQAKDK 189

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 209 ANSMLVQHP---EVkhwlVVGMNDNTVLGGVRATEGQGFKAPDVI-GIGINGVDAVSELSKAQATGF-YGSLLPSPDVHG 283
Cdd:cd01539  190 MDAWLSKYGdkiEL----VIANNDDMALGAIEALKAAGYNTGDGDkYIPVFGVDATPEALEAIKEGKmLGTVLNDAKAQA 265

                        250
                 ....*....|....*...
gi 495775830 284 YKSSEMLYNwVTKGAEPP 301
Cdd:cd01539  266 KAIYELAKN-LANGKEPL 282
PBP1_ABC_sugar_binding-like cd19966
monosaccharide ABC transporter substrate binding protein CUT2 family and simialr proteins; ...
 35-262 4.13e-04

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: 41.54  E-value: 4.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  35 PEEPWFQTEWKFADKAGKDLGFEViKIAVPDG--EKTLNAIDSLAASGAKGFVICT--PDPKLGSAI-AAKARGydMKVI 109
Cdd:cd19966   10 PGDPFWTVVYNGAKDAAADLGVDL-DYVFSSWdpEKMVEQFKEAIAAKPDGIAIMGhpGDGAYTPLIeAAKKAG--IIVT 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 110 AVD-DQFVNAKGKPMDSVplvmmaatkIG---ERQGQELYKEMQKRGwDVKE--TAVMAITADELDTARRRTTGSMDALK 183
Cdd:cd19966   87 SFNtDLPKLEYGDCGLGY---------VGadlYAAGYTLAKELVKRG-GLKTgdRVFVPGLLPGQPYRVLRTKGVIDALK 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 184 AAGFpekqIYKVPTKSNDIPGAFDAANSM---LVQHPEVKhwLVVGMNDNTVLGGVRATEGQGFKAPDVIGIGI----NG 256
Cdd:cd19966  157 EAGI----KVDYLEISLEPNKPAEGIPVMtgyLAANPDVK--AIVGDGGGLTANVAKYLKAAGKKPGEIPVAGFdlspAT 230


                 ....*.
gi 495775830 257 VDAVSE 262
Cdd:cd19966  231 VQAIKS 236
PBP1_ABC_sugar_binding-like cd19973
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 29-126 5.50e-04

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: 40.91  E-value: 5.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  29 GFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVP---DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYD 105
Cdd:cd19973    3 GLITKTDTNPFFVKMKEGAQKAAKALGIKLMTAAGKidgDNATQVTAIENMIAAGAKGILITPSDTKAIVPAVKKARDAG 82

                         90       100
                 ....*....|....*....|.
gi 495775830 106 MKVIAVDDQFvnakgKPMDSV 126
Cdd:cd19973   83 VLVIALDTPT-----DPIDAA 98
PBP1_LacI-like cd06280
ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus ...
 167-252 8.14e-04

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: 40.32  E-value: 8.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 167 ELDTARRRTTGSMDALKAAGFPEKQIYkVPTKSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGFKA 246
Cdd:cd06280  127 EISTTRERLAGYREALAEAGIPVDESL-IFEGDSTIEGGYEAVKALLDLPPRPT--AIFATNNLMAVGALRALRERGLEI 203


                 ....*.
gi 495775830 247 PDVIGI 252
Cdd:cd06280  204 PQDISV 209
PBP1_ABC_rhamnose cd20000
rhamnose ABC transporter substrate-binding protein; Rhamnose ABC transporter substrate-binding ...
 27-113 2.68e-03

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: 39.16  E-value: 2.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIA--VPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGY 104
Cdd:cd20000    1 RIAFLPKSLGNPYFDAARDGAKEAAKELGGELIFVGptTATAEAQIPFINTLIQQGVDAIAISANDPDALAPALKKARAA 80


                 ....*....
gi 495775830 105 DMKVIAVDD 113
Cdd:cd20000   81 GIKVVTFDS 89
PBP1_ChvE cd19994
periplasmic sugar binding protein ChvE that interacts with a bacterial two-component signaling ...
 34-112 4.10e-03

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


Pssm-ID: 380649 [Multi-domain]  Cd Length: 304  Bit Score: 38.38  E-value: 4.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  34 QPEEPWFQTEwKFADKAGKDLGFEV-IKIAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYDMKVIAVD 112
Cdd:cd19994    9 KSEERWIKDG-ENLKSELEEAGYTVdLQYADDDVATQNSQIENMINKGAKVLVIAPVDGSALGDVLEEAKDAGIPVIAYD 87
PBP1_LacI-like cd06273
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 169-315 4.56e-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: 380497 [Multi-domain]  Cd Length: 268  Bit Score: 38.26  E-value: 4.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 169 DTARRRTTGSMDALKAAG--FPEKQIYKVPTksnDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGFKA 246
Cdd:cd06273  130 DRARARLAGIRDALAERGleLPEERVVEAPY---SIEEGREALRRLLARPPRPT--AIICGNDVLALGALAECRRLGISV 204

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495775830 247 PDVIGI-GINGVDAVSELSKAQATgfygsllpspdVH------GYKSSEMLYNWVtKGAEPPKFTEVtDVVLITRD 315
Cdd:cd06273  205 PEDLSItGFDDLELAAHLSPPLTT-----------VRvpareiGELAARYLLALL-EGGPPPKSVEL-ETELIVRE 267
XylF COG4213
ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism] ...
 49-152 4.82e-03

ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism];


Pssm-ID: 443359 [Multi-domain]  Cd Length: 310  Bit Score: 38.19  E-value: 4.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  49 KAGKDLGFEV-IKIAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGYDMKVIAVD--------DQFVNak 119
Cdd:COG4213   26 AALKELGYEVdVQNANGDVATQLSQIENMITKGADVLVIAPIDGTALAAVLEKAKAAGIPVIAYDrlilnsdvDYYVS-- 103

                         90       100       110
                 ....*....|....*....|....*....|...
gi 495775830 120 gkpMDSVplvmmaatKIGERQGQELYKEMQKRG 152
Cdd:COG4213  104 ---FDNV--------KVGELQGQYLVDGLPLKG 125
PBP1_AglR-like cd20010
Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and ...
 166-312 5.51e-03

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


Pssm-ID: 380665 [Multi-domain]  Cd Length: 269  Bit Score: 37.92  E-value: 5.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 166 DELDTARRRTTGSMDALKAAGFPEKQIYKVPTkSNDIPGAFDAANSMLVQHPEVKhwLVVGMNDNTVLGGVRATEGQGFK 245
Cdd:cd20010  130 EELNFAHQRRDGYRAALAEAGLPVDPALVREG-PLTEEGGYQAARRLLALPPPPT--AIVCGSDLLALGAYRALREAGLS 206

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830 246 AP-DVIGIGINGVDAVSELSKAQATGFygsllpSPDVH--GYKSSEMLYNWVtKGAEPPKFTEVTDVVLI 312
Cdd:cd20010  207 PGkDVSVIGHDDLLPALEYFSPPLTTT------RSSLRdaGRRLAEMLLALI-DGEPAAELQELWPPELI 269
PBP1_LsrB_Quorum_Sensing-like cd20002
ligand-binding protein LsrB-like of ABC transporter periplasmic binding protein; ...
 27-152 9.82e-03

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: 37.30  E-value: 9.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775830  27 KLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDGE--KTLNAIDSLAASGAKGFVICTPDPKLGSAIAAKARGY 104
Cdd:cd20002    1 TIVTVVKLAGIPWFNRMEQGVKKAGKEFGVNAYQVGPADADpaQQVRIIEDLIAQGVDAILVVPNDAKVLEPVFKKAREK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 495775830 105 DMKVIAVDDQfvNAKGKPMDsvpLVMMAATKIGERQGQELYKEMQKRG 152
Cdd:cd20002   81 GIVVITHESP--GQKGADWD---VELIDNEKFGEAQMELLAKEMGGKG 123
 
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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