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Conserved domains on  [gi|493171821|ref|WP_006174322|]
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MULTISPECIES: arginine ABC transporter substrate-binding protein ArtI [Enterobacter]

Protein Classification

PRK15007 family protein( domain architecture ID 11487562)

PRK15007 family protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PRK15007 PRK15007
arginine ABC transporter substrate-binding protein;
1-243 0e+00

arginine ABC transporter substrate-binding protein;


:

Pssm-ID: 184969 [Multi-domain]  Cd Length: 243  Bit Score: 509.19  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   1 MKKVLIAALLASVSLSATAAQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRR 80
Cdd:PRK15007   1 MKKVLIAALIAGFSLSATAAETIRFATEASYPPFESIDANNQIVGFDVDLAQALCKEIDATCTFSNQAFDSLIPSLKFRR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  81 IDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAK 160
Cdd:PRK15007  81 VEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQGKYTSVDQLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAK 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 161 LDLQNGRIDAVFGDTAVVTEWLKANDKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:PRK15007 161 LDLQNGRIDAVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKW 240

                 ...
gi 493171821 241 FQK 243
Cdd:PRK15007 241 FQK 243
 
Name Accession Description Interval E-value
PRK15007 PRK15007
arginine ABC transporter substrate-binding protein;
1-243 0e+00

arginine ABC transporter substrate-binding protein;


Pssm-ID: 184969 [Multi-domain]  Cd Length: 243  Bit Score: 509.19  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   1 MKKVLIAALLASVSLSATAAQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRR 80
Cdd:PRK15007   1 MKKVLIAALIAGFSLSATAAETIRFATEASYPPFESIDANNQIVGFDVDLAQALCKEIDATCTFSNQAFDSLIPSLKFRR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  81 IDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAK 160
Cdd:PRK15007  81 VEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQGKYTSVDQLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAK 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 161 LDLQNGRIDAVFGDTAVVTEWLKANDKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:PRK15007 161 LDLQNGRIDAVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKW 240

                 ...
gi 493171821 241 FQK 243
Cdd:PRK15007 241 FQK 243
PBP2_Arg_STM4351 cd13700
Substrate binding domain of arginine-specific ABC transporter; type 2 periplasmic-binding ...
20-241 5.56e-139

Substrate binding domain of arginine-specific ABC transporter; type 2 periplasmic-binding protein fold; This group includes domains similar to Escherichia coli arginine third transport system. STM4351 is the high arginine specific periplasmic-binding protein of ABC transport system. STM4351 belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270418 [Multi-domain]  Cd Length: 222  Bit Score: 388.73  E-value: 5.56e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  20 AQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVL 99
Cdd:cd13700    1 AETIHFGTEATYPPFESIGAKGEIVGFDIDLANALCKQMQAECTFTNQAFDSLIPSLKFKKFDAVISGMDITPEREKQVS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FTTPYYDNSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVT 179
Cdd:cd13700   81 FSTPYYENSAVVIAKKDTYKTFADLKGKKIGVQNGTTHQKYLQDKHKEITTVSYDSYQNAFLDLKNGRIDGVFGDTAVVA 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 493171821 180 EWLKANDKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13700  161 EWLKTNPDLAFVGEKVTDPNYFGTGLGIAVRKDNQALLEKLNAALAAIKANGEYQKIYDKWF 222
3A0103s03R TIGR01096
lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino ...
2-241 3.24e-114

lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino acids, peptides and amines]


Pssm-ID: 273440 [Multi-domain]  Cd Length: 250  Bit Score: 327.39  E-value: 3.24e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821    2 KKVLIAALLASVSLSATAA----QTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLK 77
Cdd:TIGR01096   1 KSVLLAALVAGASSAATAAaakeGSVRIGTETGYPPFESKDANGKLVGFDVDLAKALCKRMKAKCKFVEQNFDGLIPSLK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   78 FRRIDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGK--YASVDLLKGKKVGVQNGTTHQKFIMDKHP-EITTVPYD 154
Cdd:TIGR01096  81 AKKVDAIMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSdlAKTLEDLDGKTVGVQSGTTHEQYLKDYFKpGVDIVEYD 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  155 SYQNAKLDLQNGRIDAVFGDTAVVTEWLKANDK---LAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDG 231
Cdd:TIGR01096 161 SYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNgkdFKFVGPSVTDEKYFGDGYGIGLRKGDTELKAAFNKALAAIRADG 240
                         250
                  ....*....|
gi 493171821  232 TYETIYKKWF 241
Cdd:TIGR01096 241 TYQKISKKWF 250
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
23-241 1.04e-80

ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms];


Pssm-ID: 440596 [Multi-domain]  Cd Length: 223  Bit Score: 241.42  E-value: 1.04e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  23 IRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTT 102
Cdd:COG0834    1 LRVGVDPDYPPFSFRDEDGKLVGFDVDLARAIAKRLGLKVEFVPVPWDRLIPALQSGKVDLIIAGMTITPEREKQVDFSD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 103 PYYDNSALFIGQKG--KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTE 180
Cdd:COG0834   81 PYYTSGQVLLVRKDnsGIKSLADLKGKTVGVQAGTTYEEYLKKLGPNAEIVEFDSYAEALQALASGRVDAVVTDEPVAAY 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 493171821 181 WLKANDKLAAvgdKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:COG0834  161 LLAKNPGDDL---KIVGEPLSGEPYGIAVRKGDPELLEAVNKALAALKADGTLDKILEKWF 218
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
23-241 6.75e-78

Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognizes Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 425719 [Multi-domain]  Cd Length: 221  Bit Score: 234.11  E-value: 6.75e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   23 IRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTT 102
Cdd:pfam00497   1 LRVGTDGDYPPFEYVDENGKLVGFDVDLAKAIAKRLGVKVEFVPVSWDGLIPALQSGKVDLIIAGMTITPERAKQVDFSD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  103 PYYDNSALFIGQKG----KYASVDLLKGKKVGVQNGTTHQKFI-MDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAV 177
Cdd:pfam00497  81 PYYYSGQVILVRKKdsskSIKSLADLKGKTVGVQKGSTAEELLkNLKLPGAEIVEYDDDAEALQALANGRVDAVVADSPV 160
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493171821  178 VTEWLKANDKLaavGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:pfam00497 161 AAYLIKKNPGL---NLVVVGEPLSPEPYGIAVRKGDPELLAAVNKALAELKADGTLAKIYEKWF 221
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
22-241 9.62e-76

Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 228.37  E-value: 9.62e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821    22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:smart00062   1 TLRVGTNGDYPPFSFADEDGELTGFDVDLAKAIAKELGLKVEFVEVSFDSLLTALKSGKIDVVAAGMTITPERAKQVDFS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   102 TPYYDNSALFIGQKGK-YASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTE 180
Cdd:smart00062  81 DPYYRSGQVILVRKDSpIKSLEDLKGKKVAVVAGTTAEELLKKLYPEAKIVSYDSNAEALAALKAGRADAAVADAPLLAA 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821   181 WLK--ANDKLAAVGDKVTDKDyfgtGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:smart00062 161 LVKqhGLPELKIVPDPLDTPE----GYAIAVRKGDPELLDKINKALKELKADGTLKKISEKWF 219
 
Name Accession Description Interval E-value
PRK15007 PRK15007
arginine ABC transporter substrate-binding protein;
1-243 0e+00

arginine ABC transporter substrate-binding protein;


Pssm-ID: 184969 [Multi-domain]  Cd Length: 243  Bit Score: 509.19  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   1 MKKVLIAALLASVSLSATAAQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRR 80
Cdd:PRK15007   1 MKKVLIAALIAGFSLSATAAETIRFATEASYPPFESIDANNQIVGFDVDLAQALCKEIDATCTFSNQAFDSLIPSLKFRR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  81 IDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAK 160
Cdd:PRK15007  81 VEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQGKYTSVDQLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAK 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 161 LDLQNGRIDAVFGDTAVVTEWLKANDKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:PRK15007 161 LDLQNGRIDAVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKW 240

                 ...
gi 493171821 241 FQK 243
Cdd:PRK15007 241 FQK 243
PBP2_Arg_STM4351 cd13700
Substrate binding domain of arginine-specific ABC transporter; type 2 periplasmic-binding ...
20-241 5.56e-139

Substrate binding domain of arginine-specific ABC transporter; type 2 periplasmic-binding protein fold; This group includes domains similar to Escherichia coli arginine third transport system. STM4351 is the high arginine specific periplasmic-binding protein of ABC transport system. STM4351 belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270418 [Multi-domain]  Cd Length: 222  Bit Score: 388.73  E-value: 5.56e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  20 AQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVL 99
Cdd:cd13700    1 AETIHFGTEATYPPFESIGAKGEIVGFDIDLANALCKQMQAECTFTNQAFDSLIPSLKFKKFDAVISGMDITPEREKQVS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FTTPYYDNSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVT 179
Cdd:cd13700   81 FSTPYYENSAVVIAKKDTYKTFADLKGKKIGVQNGTTHQKYLQDKHKEITTVSYDSYQNAFLDLKNGRIDGVFGDTAVVA 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 493171821 180 EWLKANDKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13700  161 EWLKTNPDLAFVGEKVTDPNYFGTGLGIAVRKDNQALLEKLNAALAAIKANGEYQKIYDKWF 222
3A0103s03R TIGR01096
lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino ...
2-241 3.24e-114

lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino acids, peptides and amines]


Pssm-ID: 273440 [Multi-domain]  Cd Length: 250  Bit Score: 327.39  E-value: 3.24e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821    2 KKVLIAALLASVSLSATAA----QTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLK 77
Cdd:TIGR01096   1 KSVLLAALVAGASSAATAAaakeGSVRIGTETGYPPFESKDANGKLVGFDVDLAKALCKRMKAKCKFVEQNFDGLIPSLK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   78 FRRIDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGK--YASVDLLKGKKVGVQNGTTHQKFIMDKHP-EITTVPYD 154
Cdd:TIGR01096  81 AKKVDAIMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSdlAKTLEDLDGKTVGVQSGTTHEQYLKDYFKpGVDIVEYD 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  155 SYQNAKLDLQNGRIDAVFGDTAVVTEWLKANDK---LAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDG 231
Cdd:TIGR01096 161 SYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNgkdFKFVGPSVTDEKYFGDGYGIGLRKGDTELKAAFNKALAAIRADG 240
                         250
                  ....*....|
gi 493171821  232 TYETIYKKWF 241
Cdd:TIGR01096 241 TYQKISKKWF 250
PBP2_HisJ_LAO_like cd01001
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and ...
20-241 8.28e-100

Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and related proteins; the type 2 periplasmic-binding protein fold; This family comprises the periplasmic substrate-binding proteins, including the lysine-, arginine-, ornithine-binding protein (LAO) and the histidine-binding protein (HisJ), which serve as initial receptors for active transport. HisJ and LAO proteins belong to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270222 [Multi-domain]  Cd Length: 228  Bit Score: 289.96  E-value: 8.28e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  20 AQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVL 99
Cdd:cd01001    1 ADTLRIGTEGDYPPFNFLDADGKLVGFDIDLANALCKRMKVKCEIVTQPWDGLIPALKAGKYDAIIASMSITDKRRQQID 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FTTPYYDNSALFIGQKGK---YASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTA 176
Cdd:cd01001   81 FTDPYYRTPSRFVARKDSpitDTTPAKLKGKRVGVQAGTTHEAYLRDRFPEADLVEYDTPEEAYKDLAAGRLDAVFGDKV 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 493171821 177 VVTEWLK---ANDKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd01001  161 ALSEWLKktkSGGCCKFVGPAVPDPKYFGDGVGIAVRKDDDALRAKLDKALAALKADGTYAEISKKYF 228
PBP2_HisJ_LAO cd13703
Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; ...
20-241 2.05e-88

Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; the type 2 periplasmic-binding protein fold; This subgroup includes the periplasmic-binding proteins, HisJ and LAO, that serve as initial receptors in the ABC transport of histidine and lysine-arginine-ornithine amino acids. They are belong to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270421 [Multi-domain]  Cd Length: 229  Bit Score: 261.03  E-value: 2.05e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  20 AQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVL 99
Cdd:cd13703    1 WKTLRIGTDATYPPFESKDADGELTGFDIDLGNALCAEMKVKCTWVEQDFDGLIPGLLARKFDAIISSMSITEERKKVVD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FTTPYYDNSALFIGQKGKYA--SVDLLKGKKVGVQNGTTHQKFIMDKHPE--ITTVPYDSYQNAKLDLQNGRIDAVFGDT 175
Cdd:cd13703   81 FTDKYYHTPSRLVARKGSGIdpTPASLKGKRVGVQRGTTQEAYATDNWAPkgVDIKRYATQDEAYLDLVSGRVDAALQDA 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 493171821 176 AVVTEWL---KANDKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13703  161 VAAEEGFlkkPAGKDFAFVGPSVTDKKYFGEGVGIALRKDDTELKAKLNKAIAAIRADGTYDKIQKKYF 229
PBP2_mlr5654_like cd13702
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
20-241 1.87e-86

Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the type 2 periplasmic-binding protein fold; This group includes uncharacterized periplasmic substrate-binding protein similar to HisJ and LAO proteins which serve as initial receptors in the ABC transport of histidine-, arginine, and lysine-arginine-ornithine amino acids. This group belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270420 [Multi-domain]  Cd Length: 223  Bit Score: 255.71  E-value: 1.87e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  20 AQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVL 99
Cdd:cd13702    1 AKKIRIGTEGAYPPFNYVDADGKLGGFDVDIANALCAEMKAKCEIVAQDWDGIIPALQAKKFDAIIASMSITPERKKQVD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FTTPYYDNSALFIGQKG---KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTA 176
Cdd:cd13702   81 FTDPYYTNPLVFVAPKDstiTDVTPDDLKGKVIGAQRSTTAAKYLEENYPDAEVKLYDTQEEAYLDLASGRLDAVLSDKF 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 493171821 177 VVTEWLK--ANDKLAAVGDKVTDkdyfGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13702  161 PLLDWLKspAGKCCELKGEPIAD----DDGIGIAVRKGDTELREKFNKALAAIRADGTYKKINAKYF 223
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
23-241 1.04e-80

ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms];


Pssm-ID: 440596 [Multi-domain]  Cd Length: 223  Bit Score: 241.42  E-value: 1.04e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  23 IRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTT 102
Cdd:COG0834    1 LRVGVDPDYPPFSFRDEDGKLVGFDVDLARAIAKRLGLKVEFVPVPWDRLIPALQSGKVDLIIAGMTITPEREKQVDFSD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 103 PYYDNSALFIGQKG--KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTE 180
Cdd:COG0834   81 PYYTSGQVLLVRKDnsGIKSLADLKGKTVGVQAGTTYEEYLKKLGPNAEIVEFDSYAEALQALASGRVDAVVTDEPVAAY 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 493171821 181 WLKANDKLAAvgdKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:COG0834  161 LLAKNPGDDL---KIVGEPLSGEPYGIAVRKGDPELLEAVNKALAALKADGTLDKILEKWF 218
PBP2_Arg_Lys_His cd13624
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ...
22-241 1.18e-79

Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 periplasmic binding protein fold; This group includes the periplasmic substrate-binding protein ArtJ of the ATP-binding cassette (ABC) transport system from the thermophilic bacterium Geobacillus stearothermophilus, which is specific for arginine, lysine, and histidine. ArtJ belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270342 [Multi-domain]  Cd Length: 219  Bit Score: 238.55  E-value: 1.18e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd13624    1 TLVVGTDATFPPFEFVDENGKIVGFDIDLIKAIAKEAGFEVEFKNMAFDGLIPALQSGKIDIIISGMTITEERKKSVDFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNSALFIGQKGK--YASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVT 179
Cdd:cd13624   81 DPYYEAGQAIVVRKDStiIKSLDDLKGKKVGVQIGTTGAEAAEKILKGAKVKRFDTIPLAFLELKNGGVDAVVNDNPVAA 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493171821 180 EWLKAN--DKLAAVGDKVTDKDYfgtglGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13624  161 YYVKQNpdKKLKIVGDPLTSEYY-----GIAVRKGNKELLDKINKALKKIKENGTYDKIYKKWF 219
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
22-240 2.00e-79

Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1, but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 270248 [Multi-domain]  Cd Length: 217  Bit Score: 237.92  E-value: 2.00e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd13530    1 TLRVGTDADYPPFEYIDKNGKLVGFDVDLANAIAKRLGVKVEFVDTDFDGLIPALQSGKIDVAISGMTITPERAKVVDFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNSALFIGQKG--KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVT 179
Cdd:cd13530   81 DPYYYTGQVLVVKKDskITKTVADLKGKKVGVQAGTTGEDYAKKNLPNAEVVTYDNYPEALQALKAGRIDAVITDAPVAK 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 493171821 180 EWLKANDKLAAVGDKVTDKDYFgtglGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:cd13530  161 YYVKKNGPDLKVVGEPLTPEPY----GIAVRKGNPELLDAINKALAELKADGTLDKLLEKW 217
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
23-241 6.75e-78

Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognizes Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 425719 [Multi-domain]  Cd Length: 221  Bit Score: 234.11  E-value: 6.75e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   23 IRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTT 102
Cdd:pfam00497   1 LRVGTDGDYPPFEYVDENGKLVGFDVDLAKAIAKRLGVKVEFVPVSWDGLIPALQSGKVDLIIAGMTITPERAKQVDFSD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  103 PYYDNSALFIGQKG----KYASVDLLKGKKVGVQNGTTHQKFI-MDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAV 177
Cdd:pfam00497  81 PYYYSGQVILVRKKdsskSIKSLADLKGKTVGVQKGSTAEELLkNLKLPGAEIVEYDDDAEALQALANGRVDAVVADSPV 160
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493171821  178 VTEWLKANDKLaavGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:pfam00497 161 AAYLIKKNPGL---NLVVVGEPLSPEPYGIAVRKGDPELLAAVNKALAELKADGTLAKIYEKWF 221
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
22-241 9.62e-76

Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 228.37  E-value: 9.62e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821    22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:smart00062   1 TLRVGTNGDYPPFSFADEDGELTGFDVDLAKAIAKELGLKVEFVEVSFDSLLTALKSGKIDVVAAGMTITPERAKQVDFS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   102 TPYYDNSALFIGQKGK-YASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTE 180
Cdd:smart00062  81 DPYYRSGQVILVRKDSpIKSLEDLKGKKVAVVAGTTAEELLKKLYPEAKIVSYDSNAEALAALKAGRADAAVADAPLLAA 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821   181 WLK--ANDKLAAVGDKVTDKDyfgtGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:smart00062 161 LVKqhGLPELKIVPDPLDTPE----GYAIAVRKGDPELLDKINKALKELKADGTLKKISEKWF 219
PBP2_OccT_like cd13699
Substrate binding domain of ABC-type octopine transporter-like; the type 2 periplasmic-binding ...
22-241 1.08e-58

Substrate binding domain of ABC-type octopine transporter-like; the type 2 periplasmic-binding protein fold; This group includes periplasmic octopine-binding protein and related proteins. This group belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270417 [Multi-domain]  Cd Length: 211  Bit Score: 184.88  E-value: 1.08e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd13699    3 TLTIATEGAYAPWNLTDPDGKLGGFEIDLANVLCERMKVKCTFVVQDWDGMIPALNAGKFDVIMDAMSITAERKKVIDFS 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNSALFigqkgkyASVdllkgkKVGVQNGTTHQKFIMDKHPEITTV-PYDSYQNAKLDLQNGRIDAVFGDTAVVTE 180
Cdd:cd13699   83 TPYAATPNSF-------AVV------TIGVQSGTTYAKFIEKYFKGVADIrEYKTTAERDLDLAAGRVDAVFADATYLAA 149
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821 181 WLKA--NDKLAAVGDKVTDKDYfGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13699  150 FLAKpdNADLTLVGPKLSGDIW-GEGEGVGLRKGDTELKAKFDSAIKAAVADGTVKKLSEKWF 211
PRK15010 PRK15010
lysine/arginine/ornithine ABC transporter substrate-binding protein ArgT;
1-241 2.23e-57

lysine/arginine/ornithine ABC transporter substrate-binding protein ArgT;


Pssm-ID: 184972 [Multi-domain]  Cd Length: 260  Bit Score: 183.28  E-value: 2.23e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   1 MKKVLIAALLAsVSLSATAA------QTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIP 74
Cdd:PRK15010   1 MKKSILALSLL-VGLSAAASsyaalpETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMCKRMQVKCTWVASDFDALIP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  75 SLKFRRIDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGK--YASVDLLKGKKVGVQNGTTHQKFIMDKHPEiTTVP 152
Cdd:PRK15010  80 SLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSpiQPTLDSLKGKHVGVLQGSTQEAYANETWRS-KGVD 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 153 YDSYQNAKL---DLQNGRIDAVFGDTAVVTE-WLK--ANDKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEK 226
Cdd:PRK15010 159 VVAYANQDLvysDLAAGRLDAALQDEVAASEgFLKqpAGKDFAFAGPSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGE 238
                        250
                 ....*....|....*
gi 493171821 227 VKKDGTYETIYKKWF 241
Cdd:PRK15010 239 LRQDGTYDKMAKKYF 253
PBP2_GlnH cd00994
Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; ...
22-241 3.01e-57

Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; This periplasmic substrate-binding component serves as an initial receptor in the ABC transport of glutamine in bacteria and eukaryota. GlnH belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270216 [Multi-domain]  Cd Length: 218  Bit Score: 181.32  E-value: 3.01e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDaNNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd00994    1 TLTVATDTTFVPFEFKQ-DGKYVGFDIDLWEAIAKEAGFKYELQPMDFKGIIPALQTGRIDIAIAGITITEERKKVVDFS 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDnSALFIGQKGK---YASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVV 178
Cdd:cd00994   80 DPYYD-SGLAVMVKADnnsIKSIDDLAGKTVAVKTGTTSVDYLKENFPDAQLVEFPNIDNAYMELETGRADAVVHDTPNV 158
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 493171821 179 TEWLK--ANDKLAAVGDKVTDKDYfgtglGIAVRQGNtELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd00994  159 LYYAKtaGKGKVKVVGEPLTGEQY-----GIAFPKGS-ELREKVNAALKTLKADGTYDEIYKKWF 217
PBP2_ml15202_like cd13701
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
20-241 3.80e-57

Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the type 2 periplasmic-binding protein fold; This group includes uncharacterized periplasmic substrate-binding protein similar to HisJ and LAO proteins which are involved in the ABC transport of histidine-, arginine, and lysine-arginine-ornithine amino acids. This group belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270419 [Multi-domain]  Cd Length: 227  Bit Score: 181.51  E-value: 3.80e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  20 AQTIRFATEA-SYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQV 98
Cdd:cd13701    1 ADPLKIGISAePYPPFTSKDASGKWSGWEIDLIDALCARLDARCEITPVAWDGIIPALQSGKIDMIWNSMSITDERKKVI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  99 LFTTPYYDNSALFIGQKGK--YASVDLLKGKKVGVQNGTTHQKFiMDKH--PEITTVPYDSYQNAKLDLQNGRIDAVFGD 174
Cdd:cd13701   81 DFSDPYYETPTAIVGAKSDdrRVTPEDLKGKVIGVQGSTNNATF-ARKHfaDDAELKVYDTQDEALADLVAGRVDAVLAD 159
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 493171821 175 TAVVTEWLKANDKlAAVGDK--VTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13701  160 SLAFTEFLKSDGG-ADFEVKgtAADDPEFGLGIGAGLRQGDTALREKLNTAIASLRADGTYDEISARYF 227
PRK15437 PRK15437
histidine ABC transporter substrate-binding protein HisJ; Provisional
1-241 1.25e-56

histidine ABC transporter substrate-binding protein HisJ; Provisional


Pssm-ID: 185334 [Multi-domain]  Cd Length: 259  Bit Score: 181.38  E-value: 1.25e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   1 MKKVLIAALLASVSLSATAA-----QTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPS 75
Cdd:PRK15437   1 MKKLVLSLSLVLAFSSATAAfaaipQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDALIPS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  76 LKFRRIDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGK--YASVDLLKGKKVGVQNGTTHQKFiMDKH--PE-ITT 150
Cdd:PRK15437  81 LKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSdiQPTVESLKGKRVGVLQGTTQETF-GNEHwaPKgIEI 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 151 VPYDSYQNAKLDLQNGRIDAVFGDTAVVTE-WLK--ANDKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKV 227
Cdd:PRK15437 160 VSYQGQDNIYSDLTAGRIDAAFQDEVAASEgFLKqpVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEM 239
                        250
                 ....*....|....
gi 493171821 228 KKDGTYETIYKKWF 241
Cdd:PRK15437 240 RADGTYEKLAKKYF 253
PBP2_MidA_like cd01004
Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 ...
20-240 2.60e-55

Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 periplasmic binding protein fold; This subgroup includes the periplasmic binding component of ABC transporter involved in uptake of mimosine MidA and its similar proteins. This periplasmic binding domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270225 [Multi-domain]  Cd Length: 230  Bit Score: 176.66  E-value: 2.60e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  20 AQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVL 99
Cdd:cd01004    1 AGTLTVGTNPTYPPYEFVDEDGKLIGFDVDLAKAIAKRLGLKVEIVNVSFDGLIPALQSGRYDIIMSGITDTPERAKQVD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FTTPYYDNSAlFIGQKG---KYASVDLLKGKKVGVQNGTTHQKFIMD--------KHPEITTVPYDSYQNAKLDLQNGRI 168
Cdd:cd01004   81 FVDYMKDGLG-VLVAKGnpkKIKSPEDLCGKTVAVQTGTTQEQLLQAankkckaaGKPAIEIQTFPDQADALQALRSGRA 159
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821 169 DAVFGDTAVVTEWLK-ANDKLAAVGDKVTDKdyfgTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:cd01004  160 DAYLSDSPTAAYAVKqSPGKLELVGEVFGSP----APIGIAVKKDDPALADAVQAALNALIADGTYKKILKKW 228
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
20-241 4.46e-55

The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding fold protein; This subfamily includes the periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space through their function as an initial high-affinity binding component. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270422 [Multi-domain]  Cd Length: 220  Bit Score: 175.85  E-value: 4.46e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  20 AQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVmAGMDITPEREKQVL 99
Cdd:cd13704    1 ARTVIVGGDKNYPPYEFLDENGNPTGFNVDLLRAIAEEMGLKVEIRLGPWSEVLQALENGEIDVL-IGMAYSEERAKLFD 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FTTPYYDNSALFIGQKG--KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAV 177
Cdd:cd13704   80 FSDPYLEVSVSIFVRKGssIINSLEDLKGKKVAVQRGDIMHEYLKERGLGINLVLVDSPEEALRLLASGKVDAAVVDRLV 159
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 493171821 178 VTEWLKAN--DKLAAVGDKVtdkdyFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13704  160 GLYLIKELglTNVKIVGPPL-----LPLKYCFAVRKGNPELLAKLNEGLAILKASGEYDEIYEKWF 220
PBP2_Cystine_like cd13626
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ...
22-241 2.09e-54

Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein fold; Cystine-binding domain of periplasmic receptor-dependent ATP-binding cassette (ABC) transporters. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Also, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270344 [Multi-domain]  Cd Length: 219  Bit Score: 174.04  E-value: 2.09e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd13626    1 KLTVGTEGTYPPFTFKDEDGKLTGFDVEVGREIAKRLGLKVEFKATEWDGLLPGLNSGKFDVIANQVTITPEREEKYLFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNSALFIGQKG--KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVT 179
Cdd:cd13626   81 DPYLVSGAQIIVKKDntIIKSLEDLKGKVVGVSLGSNYEEVARDLANGAEVKAYGGANDALQDLANGRADATLNDRLAAL 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821 180 EWLKA-NDKLAAVGDKVTdkdyfGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13626  161 YALKNsNLPLKIVGDIVS-----TAKVGFAFRKDNPELRKKVNKALAEMKADGTLKKLSEKWF 218
PBP2_Cystine_like_1 cd13713
Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ...
22-241 2.76e-54

Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold; This group contains uncharacterized periplasmic cystine-binding domain of ATP-binding cassette (ABC) transporters. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270431 [Multi-domain]  Cd Length: 218  Bit Score: 174.01  E-value: 2.76e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd13713    1 ELRFAMSGQYPPFNFLDEDNQLVGFDVDVAKAIAKRLGVKVEPVTTAWDGIIAGLWAGRYDIIIGSMTITEERLKVVDFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNSA-LFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTE 180
Cdd:cd13713   81 NPYYYSGAqIFVRKDSTITSLADLKGKKVGVVTGTTYEAYARKYLPGAEIKTYDSDVLALQDLALGRLDAVITDRVTGLN 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 493171821 181 WLKAND-KLAAVGDkvtdkDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13713  161 AIKEGGlPIKIVGK-----PLYYEPMAIAIRKGDPELRAAVNKALAEMKADGTLEKISKKWF 217
PBP2_Arg_3 cd13622
Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding ...
20-241 6.02e-54

Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding fold; This subgroup is similar to the HisJ-like family that comprises the periplasmic substrate-binding proteins, including the lysine-, arginine-, ornithine-binding protein (LAO) and the histidine-binding protein (HisJ), which serve as initial receptors for active transport. HisJ and LAO proteins belong to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270340 [Multi-domain]  Cd Length: 222  Bit Score: 173.26  E-value: 6.02e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  20 AQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVL 99
Cdd:cd13622    1 SKPLIVGVGKFNPPFEMQGTNNELFGFDIDLMNEICKRIQRTCQYKPMRFDDLLAALNNGKVDVAISSISITPERSKNFI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FTTPYYDNSALFIGQK--GKYASVDLLKGKKVGVQNGT-THQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTA 176
Cdd:cd13622   81 FSLPYLLSYSQFLTNKdnNISSFLEDLKGKRIGILKGTiYKDYLLQMFVINPKIIEYDRLVDLLEALNNNEIDAILLDNP 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 493171821 177 VVTEWL-KANDKLAAVGDKVtdkdYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13622  161 IAKYWAsNSSDKFKLIGKPI----PIGNGLGIAVNKDNAALLTKINKALLEIENDGTYLKIYNKYF 222
PBP2_ArtJ cd00999
The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold ...
22-240 1.53e-52

The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold protein superfamily; An arginine-binding protein found in Chlamydiae trachomatis (CT-ArtJ) and pneumoniae (CPn-ArtJ) and its closely related proteins. CT- and CPn-ArtJ are shown to have different immunogenic properties despite a high sequence similarity. The ArtJ proteins display the type 2 periplasmic binding fold organized in two alpha-beta domains with arginine-binding region at their interface.


Pssm-ID: 270220 [Multi-domain]  Cd Length: 223  Bit Score: 169.43  E-value: 1.53e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd00999    5 VIIVGTESTYPPFEFRDEKGELVGFDIDLAEAISEKLGKKLEWRDMAFDALIPNLLTGKIDAIAAGMSATPERAKRVAFS 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDN-SALFIGQKGKY-ASVDLLKGKKVGVQNGTTHQKFImDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVT 179
Cdd:cd00999   85 PPYGESvSAFVTVSDNPIkPSLEDLKGKSVAVQTGTIQEVFL-RSLPGVEVKSFQKTDDCLREVVLGRSDAAVMDPTVAK 163
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 493171821 180 EWLKANDkLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:cd00999  164 VYLKSKD-FPGKLATAFTLPEWGLGKALAVAKDDPALKEAVNKALDELKKEGELAALRKKW 223
PBP2_Dsm1740 cd13629
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ...
22-241 8.48e-52

Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily includes the periplasmic binding protein type II (BPBII). This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBPII proteins share the same architecture as periplasmic binding proteins type I (PBPI), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBPII proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 270347 [Multi-domain]  Cd Length: 221  Bit Score: 167.36  E-value: 8.48e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd13629    1 VLRVGMEAGYPPFEMTDKKGELIGFDVDLAKALAKDLGVKVEFVNTAWDGLIPALQTGKFDLIISGMTITPERNLKVNFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNSALFIGQKGKYASV----DL-LKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTA 176
Cdd:cd13629   81 NPYLVSGQTLLVNKKSAAGIksleDLnKPGVTIAVKLGTTGDQAARKLFPKATILVFDDEAAAVLEVVNGKADAFIYDQP 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 493171821 177 VVTEWLKANDKLAavgdKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13629  161 TPARFAKKNDPTL----VALLEPFTYEPLGFAIRKGDPDLLNWLNNFLKQIKGDGTLDELYDKWF 221
PBP2_AatB_like cd00996
Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong ...
30-241 1.40e-51

Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong to the type 2 periplasmic binding fold protein superfamily; This subfamily includes periplasmic binding domain of ATP-binding cassette transporter-like systems that serve as initial receptors in the ABC transport of amino acids and their derivatives in eubacteria. After binding their ligand with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The Abp proteins belong to the PBPI superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270217 [Multi-domain]  Cd Length: 227  Bit Score: 167.37  E-value: 1.40e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  30 SYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTTPYYDNSA 109
Cdd:cd00996   13 TFAPMGFRDENGEIVGFDIDLAKEVAKRLGVEVEFQPIDWDMKETELNSGNIDLIWNGLTITDERKKKVAFSKPYLENRQ 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 110 LFIGQKGK-YASVDLLKGKKVGVQNGTTHQKFIMdKHPEITT-----VPYDSYQNAKLDLQNGRIDAVFGDTAVVTEWL- 182
Cdd:cd00996   93 IIVVKKDSpINSKADLKGKTVGVQSGSSGEDALN-ADPNLLKknkevKLYDDNNDAFMDLEAGRIDAVVVDEVYARYYIk 171
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 183 -KANDKLAAVGDKVTDKDYfgtglGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd00996  172 kKPLDDYKILDESFGSEEY-----GVGFRKEDTELKEKINKALDEMKADGTAAKISQKWF 226
PBP2_Cys_DEBP_like cd01000
Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ...
22-241 1.06e-49

Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 periplasmic-binding protein fold; This family comprises of the periplasmic-binding protein component of ABC transporters specific for cysteine and carboxylic amino acids, as well as their closely related proteins. The cysteine and aspartate-glutamate binding domains belong to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270221 [Multi-domain]  Cd Length: 228  Bit Score: 162.48  E-value: 1.06e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEI---DATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQV 98
Cdd:cd01000    9 VLIVGVKPDLPPFGARDANGKIQGFDVDVAKALAKDLlgdPVKVKFVPVTSANRIPALQSGKVDLIIATMTITPERAKEV 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  99 LFTTPYY-DNSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAV 177
Cdd:cd01000   89 DFSVPYYaDGQGLLVRKDSKIKSLEDLKGKTILVLQGSTAEAALRKAAPEAQLLEFDDYAEAFQALESGRVDAMATDNSL 168
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493171821 178 VTEWLKANDKLAAVGDKVTDKDYfgtgLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd01000  169 LAGWAAENPDDYVILPKPFSQEP----YGIAVRKGDTELLKAVNATIAKLKADGELAEIYKKWL 228
PBP2_GlnP cd13619
Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold ...
22-240 7.04e-49

Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily; Periplasmic glutamine binding domain GlnP serves as an initial receptor in the ABC transport of glutamine in eubacteria. GlnP belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270337 [Multi-domain]  Cd Length: 220  Bit Score: 160.17  E-value: 7.04e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd13619    1 TYTIATDSTFAPFEFQNDDGKYVGIDVDLLNAIAKDQGFKVELKPMGFDAAIQAVQSGQADGVIAGMSITDERKKTFDFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDnSALFIGQK---GKYASVDLLKGKKVGVQNGTTHQKFiMDKHPE---ITTVPYDSYQNAKLDLQNGRIDAVFGDT 175
Cdd:cd13619   81 DPYYD-SGLVIAVKkdnTSIKSYEDLKGKTVAVKNGTAGATF-AESNKEkygYTIKYFDDSDSMYQAVENGNADAAMDDY 158
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 493171821 176 AVVTEWLKANDKLAAVGDKVTDKDYfgtglGIAVRQG-NTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:cd13619  159 PVIAYAIKQGQKLKIVGDKETGGSY-----GFAVKKGqNPELLEKFNKGLKNLKANGEYDKILNKY 219
PBP2_BsGlnH cd13689
Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ...
22-241 4.21e-47

Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 periplasmic-bindig protein fold; This group includes periplasmic glutamine-binding domain GlnP from Bacillus subtilis and its related proteins. The GlnP domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270407 [Multi-domain]  Cd Length: 229  Bit Score: 155.85  E-value: 4.21e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDA-NNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLF 100
Cdd:cd13689    9 VLRCGVFDDVPPFGFIDPkTREIVGFDVDLCKAIAKKLGVKLELKPVNPAARIPELQNGRVDLVAANLTYTPERAEQIDF 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 101 TTPYYDNSALFIGQKG-KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVT 179
Cdd:cd13689   89 SDPYFVTGQKLLVKKGsGIKSLKDLAGKRVGAVKGSTSEAAIREKLPKASVVTFDDTAQAFLALQQGKVDAITTDETILA 168
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 493171821 180 EWL---KANDKLAAVGDKVTDKDYfgtglGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13689  169 GLLakaPDPGNYEILGEALSYEPY-----GIGVPKGESALRDFVNETLADLEKDGEADKIYDKWF 228
glnH PRK09495
glutamine ABC transporter periplasmic protein; Reviewed
2-241 3.45e-44

glutamine ABC transporter periplasmic protein; Reviewed


Pssm-ID: 236540 [Multi-domain]  Cd Length: 247  Bit Score: 148.74  E-value: 3.45e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   2 KKVLIAALLASVSLSATAAQTIRFATEASYPPFEsIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRI 81
Cdd:PRK09495   6 KVSLAALTLAFAVSSHAADKKLVVATDTAFVPFE-FKQGDKYVGFDIDLWAAIAKELKLDYTLKPMDFSGIIPALQTKNV 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  82 DAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKG--KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNA 159
Cdd:PRK09495  85 DLALAGITITDERKKAIDFSDGYYKSGLLVMVKANnnDIKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNA 164
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 160 KLDLQNGRIDAVFGDTAVVTEWLK--ANDKLAAVGDKVTDKDYfgtglGIAVRQGNtELQQKFNAALEKVKKDGTYETIY 237
Cdd:PRK09495 165 YLELGTGRADAVLHDTPNILYFIKtaGNGQFKAVGDSLEAQQY-----GIAFPKGS-ELREKVNGALKTLKENGTYAEIY 238

                 ....
gi 493171821 238 KKWF 241
Cdd:PRK09495 239 KKWF 242
PRK11260 PRK11260
cystine ABC transporter substrate-binding protein;
4-241 1.31e-43

cystine ABC transporter substrate-binding protein;


Pssm-ID: 183061 [Multi-domain]  Cd Length: 266  Bit Score: 147.95  E-value: 1.31e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   4 VLIAALLASVSLSATAAQ----------TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLI 73
Cdd:PRK11260  14 VMAVALVAGMSVKSFADEgllnkvkergTLLVGLEGTYPPFSFQGEDGKLTGFEVEFAEALAKHLGVKASLKPTKWDGML 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  74 PSLKFRRIDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGKYASV---DLLKGKKVGVQNGTTHQKFIMDKHPEITT 150
Cdd:PRK11260  94 ASLDSKRIDVVINQVTISDERKKKYDFSTPYTVSGIQALVKKGNEGTIktaADLKGKKVGVGLGTNYEQWLRQNVQGVDV 173
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 151 VPYD----SYQnaklDLQNGRIDAVFGDTAVVTEWL-KANDKLAAVGDKVTDKdyfgtGLGIAVRQGNTELQQKFNAALE 225
Cdd:PRK11260 174 RTYDddptKYQ----DLRVGRIDAILVDRLAALDLVkKTNDTLAVAGEAFSRQ-----ESGVALRKGNPDLLKAVNQAIA 244
                        250
                 ....*....|....*.
gi 493171821 226 KVKKDGTYETIYKKWF 241
Cdd:PRK11260 245 EMQKDGTLKALSEKWF 260
PBP2_FliY cd13712
Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ...
22-241 1.78e-43

Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic binding protein fold; This group contains cystine binding domain FliY and its related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270430 [Multi-domain]  Cd Length: 219  Bit Score: 145.99  E-value: 1.78e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd13712    1 TLRIGLEGTYPPFNFKDETGQLTGFEVDVAKALAAKLGVKPEFVTTEWSGILAGLQAGKYDVIINQVGITPERQKKFDFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNSALFIGQKGK---YASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVV 178
Cdd:cd13712   81 QPYTYSGIQLIVRKNDtrtFKSLADLKGKKVGVGLGTNYEQWLKSNVPGIDVRTYPGDPEKLQDLAAGRIDAALNDRLAA 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821 179 TEWLKANDKLAAVGDKVTDKDyfgtgLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13712  161 NYLVKTSLELPPTGGAFARQK-----SGIPFRKGNPKLKAAINKAIEDLRADGTLAKLSEKWF 218
PBP2_BvgS_HisK_like cd01007
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
21-241 3.59e-41

The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine kinase receptors, and related proteins; This family comprises the periplasmic sensor domain of the two-component sensor-kinase systems, such as the sensor protein BvgS of Bordetella pertussis and histidine kinase receptors (HisK), and uncharacterized related proteins. Typically, the two-component system consists of a membrane spanning sensor-kinase and a cytoplasmic response regulator. It serves as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. The N-terminal sensing domain of the sensor kinase detects extracellular signals, such as small molecule ligands and ions, which then modulate the catalytic activity of the cytoplasmic kinase domain through a phosphorylation cascade. The periplasmic sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270228 [Multi-domain]  Cd Length: 220  Bit Score: 140.36  E-value: 3.59e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  21 QTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQA-FDSLIPSLKFRRIDaVMAGMDITPEREKQVL 99
Cdd:cd01007    2 PVIRVGVDPDWPPFEFIDEGGEPQGIAADYLKLIAKKLGLKFEYVPGDsWSELLEALKAGEID-LLSSVSKTPEREKYLL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FTTPYYDNSALFIGQKGK--YASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAV 177
Cdd:cd01007   81 FTKPYLSSPLVIVTRKDApfINSLSDLAGKRVAVVKGYALEELLRERYPNINLVEVDSTEEALEAVASGEADAYIGNLAV 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 493171821 178 VTEWLKAN--DKLAAVGDkvTDKDYfgtGLGIAVRQGNTELQQKFNAALEKVKKDgTYETIYKKWF 241
Cdd:cd01007  161 ASYLIQKYglSNLKIAGL--TDYPQ---DLSFAVRKDWPELLSILNKALASISPE-ERQAIRNKWL 220
PBP2_AA_binding_like_1 cd13625
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
19-240 1.62e-40

Substrate-binding domain of putative amino acid-binding protein; the type 2 periplasmic-binding protein fold; This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270343 [Multi-domain]  Cd Length: 230  Bit Score: 139.05  E-value: 1.62e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  19 AAQTIRFATEASYPPFESIDaNNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQV 98
Cdd:cd13625    3 KRGTITVATEADYAPFEFVE-NGKIVGFDRDLLDEMAKKLGVKVEQQDLPWSGILPGLLAGKFDMVATSVTITKERAKRF 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  99 LFTTPYYDNSALFIGQKG--KYASVDLLKGKKVGVQNGTTHQ-------KFIMDKHPE--ITTVPYDSYQNAKLDLQNGR 167
Cdd:cd13625   82 AFTLPIAEATAALLKRAGddSIKTIEDLAGKVVGVQAGSAQLaqlkefnETLKKKGGNgfGEIKEYVSYPQAYADLANGR 161
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821 168 IDAVFGDTAVVTEWLKANDKLAAVGDKVTDKDYFgtglGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:cd13625  162 VDAVANSLTNLAYLIKQRPGVFALVGPVGGPTYF----AWVIRKGDAELRKAINDALLALKKSGKLAALQQKW 230
PBP2_Atu4678_like cd13696
The substrate binding domain of putative amino acid transporter; the type 2 periplasmic ...
22-241 1.93e-40

The substrate binding domain of putative amino acid transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Agrobacterium tumefaciens and its related proteins. The putative Atu4678-like domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270414 [Multi-domain]  Cd Length: 227  Bit Score: 138.66  E-value: 1.93e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd13696    9 KLRCGVCLDFPPFGFRDAAGNPVGYDVDYAKDLAKALGVKPEIVETPSPNRIPALVSGRVDVVVANTTRTLERAKTVAFS 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNS-ALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTE 180
Cdd:cd13696   89 IPYVVAGmVVLTRKDSGIKSFDDLKGKTVGVVKGSTNEAAVRALLPDAKIQEYDTSADAILALKQGQADAMVEDNTVANY 168
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821 181 WLKAN--DKLAAVGDKVTDKDYfgtgLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13696  169 KASSGqfPSLEIAGEAPYPLDY----VAIGVRKGDYDWLRYLNLFVFQQNASGRYAELYQKWF 227
PBP2_Ala cd13628
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ...
22-240 4.44e-40

Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 periplasmic binding protein; This periplasmic substrate component serves as an initial receptor in the ABC transport of glutamine in eubacteria and archaea. After binding the alanine with high affinity, this domain Interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. This alanine specific domain belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270346 [Multi-domain]  Cd Length: 219  Bit Score: 137.60  E-value: 4.44e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFE-SIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLF 100
Cdd:cd13628    1 TLNMGTSPDYPPFEfKIGDRGKIVGFDIELAKTIAKKLGLKLQIQEYDFNGLIPALASGQADLALAGITPTPERKKVVDF 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 101 TTPYYDNSALFIGQKG-KYASVDLLKGKKVGVQNGTTHQ---KFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDtA 176
Cdd:cd13628   81 SEPYYEASDTIVS*KDrKIKQLQDLNGKSLGVQLGTIQEqliKELSQPYPGLKTKLYNRVNELVQALKSGRVDAAIVE-D 159
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493171821 177 VVTEWLKANDKLAAVGDKVTDKDyfgTGLGIAVRQGnTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:cd13628  160 IVAETFAQKKN*LLESRYIPKEA---DGSAIAFPKG-SPLRDDFNRWLKEMGDSGELELMVRRW 219
PBP2_GltS cd13620
Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 ...
26-239 5.54e-40

Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily; This family comprises of the periplasmic-binding protein component (GltS) of an ABC transporter specific for glutamate or arginine from Lactococcus lactis, as well as its closely related proteins. The GltS domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis


Pssm-ID: 270338 [Multi-domain]  Cd Length: 227  Bit Score: 137.47  E-value: 5.54e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  26 ATEASYPPFE---SIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTT 102
Cdd:cd13620    9 GTSADYAPFEfqkMKDGKNQVVGADIDIAKAIAKELGVKLEIKSMDFDNLLASLQSGKVDMAISGMTPTPERKKSVDFSD 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 103 PYYDNSALFIGQKG---KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVT 179
Cdd:cd13620   89 VYYEAKQSLLVKKAdldKYKSLDDLKGKKIGAQKGSTQETIAKDQLKNAKLKSLTKVGDLILELKSGKVDGVIMEEPVAK 168
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 180 EWLKANDKLAAVGDKVTDKDyfGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKK 239
Cdd:cd13620  169 GYANNNSDLAIADVNLENKP--DDGSAVAIKKGSKDLLDAVNKTIKKLKDSGQIDKFVED 226
PBP2_Cysteine cd13694
Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein ...
22-242 3.28e-38

Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein fold; This subfamily comprises of the periplasmic-binding protein component of ABC transporter specific for cysteine and its closely related proteins. The cysteine-binding domains belong to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270412 [Multi-domain]  Cd Length: 229  Bit Score: 132.86  E-value: 3.28e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEI---DATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQV 98
Cdd:cd13694    9 VIRIGVFGDKPPFGYVDENGKFQGFDIDLAKQIAKDLfgsGVKVEFVLVEAANRVPYLTSGKVDLILANFTVTPERAEVV 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  99 LFTTPYYDNSALFIGQKG-KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAV 177
Cdd:cd13694   89 DFANPYMKVALGVVSPKDsNITSVAQLDGKTLLVNKGTTAEKYFTKNHPEIKLLKYDQNAEAFQALKDGRADAYAHDNIL 168
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 493171821 178 VTEWLKANDKLAAVGDKVTDKDYfgtgLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWFQ 242
Cdd:cd13694  169 VLAWAKSNPGFKVGIKNLGDTDF----IAPGVQKGNKELLEFINAEIKKLGKENFFKKAYEKTLE 229
PBP2_HisGluGlnArgOpine cd13698
Substrate binding domain of ABC-type histidine/glutamate/glutamine/arginine/opine transporter; ...
20-241 3.84e-37

Substrate binding domain of ABC-type histidine/glutamate/glutamine/arginine/opine transporter; the type 2 periplasmic-binding protein fold; This group includes periplasmic-binding component of His/Glu/Gln/Arg/Opine ATP-binding cassette transport system. This substrate-binding domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270416 [Multi-domain]  Cd Length: 214  Bit Score: 129.72  E-value: 3.84e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  20 AQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVL 99
Cdd:cd13698    1 GKTIRMGTEGAYPPYNFINDAGEVDGFERELGDELCKRAELTCEWVTNEWDSIIPNLVSGNYDTIIAGMSITDERDEVID 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FTTPYYDNSA-LFIgqkGKYASVDLLKGkKVGVQNGTTHQKFIMDKHPeiTTVPYDSYQNAKLDLQNGRIDAVFGDTAVV 178
Cdd:cd13698   81 FTQNYIPPTAsAYV---ALSDDADDIGG-VVAAQTSTIQAGHVAESGA--TLLEFATPDETVAAVRNGEADAVFADKDYL 154
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493171821 179 TEWL-KANDKLAAVGDKVTdkdyFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13698  155 VPIVeESGGELMFVGDDVP----LGGGIGMGLRESDGELREKFDAAITSMKEDGSLNTLLKKWF 214
PBP2_SMa0082_like cd01072
The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic ...
22-241 4.15e-37

The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Sinorhizobium meliloti and its related proteins. The putative SMa0082-like domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270233 [Multi-domain]  Cd Length: 238  Bit Score: 130.46  E-value: 4.15e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd01072   14 KLKVGVLVDAPPFGFVDASMQPQGYDVDVAKLLAKDLGVKLELVPVTGANRIPYLQTGKVDMLIASLGITPERAKVVDFS 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNSALFIGQKG-KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITT-VPYDSYQNAKLDLQNGRIDAVFGDTAVVT 179
Cdd:cd01072   94 QPYAAFYLGVYGPKDaKVKSPADLKGKTVGVTRGSTQDIALTKAAPKGATiKRFDDDASTIQALLSGQVDAIATGNAIAA 173
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821 180 EWLKANDklaavGDKVTDKDYFGTG-LGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd01072  174 QIAKANP-----DKKYELKFVLRTSpNGIGVRKGEPELLKWVNTFIAKNKANGELNALSQKWF 231
PBP2_AA_binding_like_2 cd13627
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
22-230 5.06e-36

Substrate-binding domain of putative amino acid-binding protein; the type 2 periplasmic-binding protein fold; This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270345 [Multi-domain]  Cd Length: 243  Bit Score: 127.52  E-value: 5.06e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFE---SIDANNKIV----------GFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGM 88
Cdd:cd13627    1 VLRVGMEAAYAPFNwtqETASEYAIPiingqggyadGYDVQIAKKLAEKLDMKLVIKKIEWNGLIPALNSGDIDLIIAGM 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  89 DITPEREKQVLFTTPYY-DNSALFIGQKGKYA---SVDLLKGKKVGVQNGTTHQKfIMDKHPEIT-TVPYDSYQNAKLDL 163
Cdd:cd13627   81 SKTPEREKTIDFSDPYYiSNIVMVVKKDSAYAnatNLSDFKGATITGQLGTMYDD-VIDQIPDVVhTTPYDTFPTMVAAL 159
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821 164 QNGRIDAVFGDTAVVTEWLKANDKLAAV------GDKVTDKDyfgTGLGIAVRQGNTELQQKFNAALEKVKKD 230
Cdd:cd13627  160 QAGTIDGFTVELPSAISALETNPDLVIIkfeqgkGFMQDKED---TNVAIGCRKGNDKLKDKINEALKGISSE 229
PBP2_Ngo0372_TcyA cd13711
Substrate binding domain of ABC transporters involved in cystine import; the type 2 ...
22-243 5.41e-36

Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold; This subgroup includes cystine-binding domain of periplasmic receptor-dependent ATP-binding cassette transporters from Neisseria gonorrhoeae and Bacillus subtilis and their related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270429 [Multi-domain]  Cd Length: 222  Bit Score: 127.03  E-value: 5.41e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd13711    2 VLTIGTEGTYAPFTYHDKSGKLTGFDVEVARAVAKKLGVKVEFVETQWDSMIAGLDAGRFDVVANQVGITDERKKKYDFS 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNSALFIGQKGKYA--SVDLLKGKKVgVQNGTTHQKFIMDKH-PEIttVPYDSYQNAKLDLQNGRIDAVFGDTAVV 178
Cdd:cd13711   82 TPYIYSRAVLIVRKDNSDikSFADLKGKKS-AQSLTSNWGKIAKKYgAQV--VGVDGFAQAVELITQGRADATINDSLAF 158
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 493171821 179 TEWLK----ANDKLAAVGDKVtdkdyfgTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWFQK 243
Cdd:cd13711  159 LDYKKqhpdAPVKIAAETDDA-------SESAFLVRKGNDELVAAINKALKELKADGTLKKISEKYFGK 220
PBP2_GluB cd13690
Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein ...
16-241 2.25e-34

Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein fold; This group includes periplasmic glutamate-binding domain GluB from Corynebacterium efficiens and its related proteins. The GluB domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270408 [Multi-domain]  Cd Length: 231  Bit Score: 123.15  E-value: 2.25e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  16 SATAAQTIRFATEASYPPFESID-ANNKIVGFDVDLANALCKEI---DATCTFSNQAFDSLIPSLKFRRIDAVMAGMDIT 91
Cdd:cd13690    3 KIRKRGRLRVGVKFDQPGFSLRNpTTGEFEGFDVDIARAVARAIggdEPKVEFREVTSAEREALLQNGTVDLVVATYSIT 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  92 PEREKQVLFTTPYYDNSALFIGQKG--KYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRID 169
Cdd:cd13690   83 PERRKQVDFAGPYYTAGQRLLVRAGskIITSPEDLNGKTVCTAAGSTSADNLKKNAPGATIVTRDNYSDCLVALQQGRVD 162
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821 170 AVFGDTAVVTEWLKAN-DKLAAVGDKVTDKDYfgtglGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13690  163 AVSTDDAILAGFAAQDpPGLKLVGEPFTDEPY-----GIGLPKGDDELVAFVNGALEDMRADGTWQALFDRWL 230
PBP2_YxeM cd13709
Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein ...
22-241 2.51e-32

Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein fold; This group contains cystine-binding domain (YxeM) of a periplasmic receptor-dependent ATP-binding cassette transporter and its closely related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270427 [Multi-domain]  Cd Length: 227  Bit Score: 117.45  E-value: 2.51e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDaNNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd13709    2 VIKVGSSGSSYPFTFKE-NGKLKGFEVDVWNAIGKRTGYKVEFVTADFSGLFGMLDSGKVDTIANQITITPERQEKYDFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNSALFIGQKGKYA--SVDLLKGKKVGVQNGTTHQKFI--MDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGD-TA 176
Cdd:cd13709   81 EPYVYDGAQIVVKKDNNSikSLEDLKGKTVAVNLGSNYEKILkaVDKDNKITIKTYDDDEGALQDVALGRVDAYVNDrVS 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 493171821 177 VVTEWLKANDKLAAVGDKV--TDKDYFgtglgIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13709  161 LLAKIKKRGLPLKLAGEPLveEEIAFP-----FVKNEKGKKLLEKVNKALEEMRKDGTLKKISEKWF 222
PBP2_Ehub_like cd01002
Substrate binding domain of ectoine/hydroxyectoine specific ABC transport system; the type 2 ...
22-240 6.20e-31

Substrate binding domain of ectoine/hydroxyectoine specific ABC transport system; the type 2 periplasmic binding protein fold; This family represents the periplasmic substrate-binding component of ABC transport systems that involved in uptake of osmoprotectants (also termed compatible solutes) such as ectoine and hydroxyectoine. To counteract the efflux of water, bacteria and archaea accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270223 [Multi-domain]  Cd Length: 242  Bit Score: 114.30  E-value: 6.20e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEasyPPFESIDANNKIVGFDVDLANALCK-----EIDATCTfsnqAFDSLIPSLKFRRIDAVMAGMDITPEREK 96
Cdd:cd01002   13 RIGYANE---PPYAYIDADGEVTGESPEVARAVLKrlgvdDVEGVLT----EFGSLIPGLQAGRFDVIAAGMFITPERCE 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  97 QVLFTTPYYDNSALFIGQKG------KYASVDLLKGKKVGVQNGTTHQKFIMD-KHPEITTVPYDSYQNAKLDLQNGRID 169
Cdd:cd01002   86 QVAFSEPTYQVGEAFLVPKGnpkglhSYADVAKNPDARLAVMAGAVEVDYAKAsGVPAEQIVIVPDQQSGLAAVRAGRAD 165
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 493171821 170 AVFGdTAVVTEWLKANDK-----LAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:cd01002  166 AFAL-TALSLRDLAAKAGspdveVAEPFQPVIDGKPQIGYGAFAFRKDDTDLRDAFNAELAKFKGSGEHLEILEPF 240
PBP2_GluR0 cd00997
Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ...
19-241 6.47e-30

Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate receptor domain GluR0. These domains are found in the GluR0 proteins that have been shown to function as prokaryotic L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. The GluR0 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270218 [Multi-domain]  Cd Length: 218  Bit Score: 110.89  E-value: 6.47e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  19 AAQTIRFATeASYPPFeSIDANNKIVGFDVDLANALCKEIDATCTFSNQ-AFDSLIPSLKFRRIDAVMAGMDITPEREKQ 97
Cdd:cd00997    1 SAQTLTVAT-VPRPPF-VFYNDGELTGFSIDLWRAIAERLGWETEYVRVdSVSALLAAVAEGEADIAIAAISITAEREAE 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  98 VLFTTPYYDNS-ALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHpeITTVPYDSYQNAKLDLQNGRIDAVFGDTA 176
Cdd:cd00997   79 FDFSQPIFESGlQILVPNTPLINSVNDLYGKRVATVAGSTAADYLRRHD--IDVVEVPNLEAAYTALQDKDADAVVFDAP 156
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 493171821 177 VVTEWLK--ANDKLAAVGDKVTDKDYfgtglGIAVRQGNTeLQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd00997  157 VLRYYAAhdGNGKAEVTGSVFLEENY-----GIVFPTGSP-LRKPINQALLNLREDGTYDELYEKWF 217
PBP2_YfhD_N cd01009
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ...
22-241 3.07e-29

The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold protein superfamily; This subfamily includes the solute binding domain YfhD_N. These domains are found in the YfhD proteins that are predicted to function as lytic transglycosylases that cleave the glycosidic bond between N-acetylmuramic acid and N-acetylglucosamin in peptidoglycan, while the YfhD_N domain might act as an auxiliary or regulatory subunit. In addition to periplasmic solute binding domain, they have an SLT domain, typically found in soluble lytic transglycosylases, and a C-terminal low complexity domain. The YfhD proteins might have been recruited to create localized cell wall openings required for transport of large substrates such as DNA. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270230 [Multi-domain]  Cd Length: 223  Bit Score: 109.22  E-value: 3.07e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATE---ASYppFEsidANNKIVGFDVDLANALCKEIDATCTFSN-QAFDSLIPSLKFRRIDAVMAGMDITPEREKQ 97
Cdd:cd01009    2 ELRVLTRnspTTY--YI---DRGGPRGFEYELAKAFADYLGVELEIVPaDNLEELLEALEEGKGDLAAAGLTITPERKKK 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  98 VLFTTPYYDNSALFIGQKG--KYASVDLLKGKKVGVQNGTTHQKFIM---DKHPEITTVPYDSYQNAKL--DLQNGRIDA 170
Cdd:cd01009   77 VDFSFPYYYVVQVLVYRKGspRPRSLEDLSGKTIAVRKGSSYAETLQklnKGGPPLTWEEVDEALTEELleMVAAGEIDY 156
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821 171 VFGDTAVVTEWLKANDKLAAVGDkvtdkdyFGTGLGI--AVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd01009  157 TVADSNIAALWRRYYPELRVAFD-------LSEPQPLawAVRKNSPSLLAALNRFLAQIKKDGTLARLYERYY 222
ectoine_ehuB TIGR02995
ectoine/hydroxyectoine ABC transporter solute-binding protein; Members of this family are the ...
7-240 4.73e-28

ectoine/hydroxyectoine ABC transporter solute-binding protein; Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes. [Transport and binding proteins, Amino acids, peptides and amines]


Pssm-ID: 132040 [Multi-domain]  Cd Length: 275  Bit Score: 107.70  E-value: 4.73e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821    7 AALLASVSLSATAAQT---------IRFATeASYPPFESIDANNKIVGFDVDLANALCK-----EIDATCTfsnqAFDSL 72
Cdd:TIGR02995  10 LMAIAAATPAAADANTleelkeqgfARIAI-ANEPPFTYVGADGKVSGAAPDVARAIFKrlgiaDVNASIT----EYGAL 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   73 IPSLKFRRIDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGK------YASVDLLKGKKVGVQNGTTHQKFIMD--- 143
Cdd:TIGR02995  85 IPGLQAGRFDAIAAGLFIKPERCKQVAFTQPILCDAEALLVKKGNpkglksYKDIAKNPDAKIAAPGGGTEEKLAREagv 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  144 KHPEITTVPydSYQNAKLDLQNGRIDAVFGDTAVVTEWL-KANDKLAAVGDKVTDKDYFGTGlGIAVRQGNTELQQKFNA 222
Cdd:TIGR02995 165 KREQIIVVP--DGQSGLKMVQDGRADAYSLTVLTINDLAsKAGDPNVEVLAPFKDAPVRYYG-GAAFRPEDKELRDAFNV 241
                         250
                  ....*....|....*...
gi 493171821  223 ALEKVKKDGTYETIYKKW 240
Cdd:TIGR02995 242 ELAKLKESGEFAKIIAPY 259
PBP2_GltI_DEBP cd13688
Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic ...
32-241 9.87e-28

Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic binding protein fold; This subfamily represents the periplasmic-binding protein component of ABC transporter specific for carboxylic amino acids, including GtlI from Escherichia coli. The aspartate-glutamate binding domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270406 [Multi-domain]  Cd Length: 238  Bit Score: 105.80  E-value: 9.87e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  32 PPFESIDANNKIVGFDVDLANALCKEIDA------------TCTFSNQafdslIPSLKFRRIDAVMAGMDITPEREKQVL 99
Cdd:cd13688   19 VPFSYLDDNGKPVGYSVDLCNAIADALKKklalpdlkvryvPVTPQDR-----IPALTSGTIDLECGATTNTLERRKLVD 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FTTPYY-DNSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHPE----ITTVPYDSYQNAKLDLQNGRIDAVFGD 174
Cdd:cd13688   94 FSIPIFvAGTRLLVRKDSGLNSLEDLAGKTVGVTAGTTTEDALRTVNPLaglqASVVPVKDHAEGFAALETGKADAFAGD 173
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 493171821 175 TAvvteWLKANDKLAAVGD--KVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13688  174 DI----LLAGLAARSKNPDdlALIPRPLSYEPYGLMLRKDDPDFRLLVDRALAQLYQSGEIEKLYDKWF 238
PBP2_TcyK cd13710
Substrate binding domain of an ABC transporter TcyJKLMN; the type 2 periplasmic binding ...
21-241 1.93e-27

Substrate binding domain of an ABC transporter TcyJKLMN; the type 2 periplasmic binding protein fold; This group contains periplasmic cystine-binding domain (TcyK) of an ATP-binding cassette transporter from Bacillus subtilus and its closely related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270428 [Multi-domain]  Cd Length: 233  Bit Score: 105.07  E-value: 1.93e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  21 QTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDA-TCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVL 99
Cdd:cd13710    1 KTVKVATGADTPPFSYEDKKGELTGYDIEVLKAIDKKLPQyKFKFKVTEFSSILTGLDSGKYDMAANNFSKTKERAKKFL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 100 FT-TPY-YDNSALFIGQK-GKYASVDLLKGKKVGVQNGTTHQKFIMD---KHP----EITTVPYDSYQNAKlDLQNGRID 169
Cdd:cd13710   81 FSkVPYgYSPLVLVVKKDsNDINSLDDLAGKTTIVVAGTNYAKVLEAwnkKNPdnpiKIKYSGEGINDRLK-QVESGRYD 159
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493171821 170 AVFGDTAVVTEWLK-ANDKLAAVGDKVTDKDYfgtgLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13710  160 ALILDKFSVDTIIKtQGDNLKVVDLPPVKKPY----VYFLFNKDQQKLQKDIDKALKELKKDGTLKKLSKKYF 228
PBP2_ArtJ_like cd13697
Putative substrate-binding domain of ABC arginine transporter; the type 2 periplasmic-binding ...
19-241 4.14e-26

Putative substrate-binding domain of ABC arginine transporter; the type 2 periplasmic-binding protein fold; The ArtJ domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270415 [Multi-domain]  Cd Length: 228  Bit Score: 101.45  E-value: 4.14e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  19 AAQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQV 98
Cdd:cd13697    6 ASKKLVVGVNPNLPPLGAYDDKNVIEGFDVDVAKKLADRLGVKLELVPVSSADRVPFLMAGKIDAVLGGLTRTPDRAKVI 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  99 LFTTPYYDNS-ALFIGQKGKYAS-VDLLKGKKVGVQ-NGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDT 175
Cdd:cd13697   86 DFSDPVNTEVlGILTTAVKPYKDlDDLADPRVRLVQvRGTTPVKFIQDHLPKAQLLLLDNYPDAVRAIAQGRGDALVDVL 165
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 493171821 176 AVVTEWLKA-NDKLAAVGDKVTDKDYFGtglgIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13697  166 DYMGRYTKNyPAKWRVVDDPAIEVDYDC----IGVAQGNTALLEVVNGELADLHKDGFIQASYKRWF 228
PBP2_Peb1a_like cd13691
Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 ...
42-240 6.52e-26

Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 periplasmic-binding protein fold; This group includes periplasmic aspartate/glutamate binding domain Peb1a and its closely related protein. The Peb1a is an important virulence factor in the food-borne human pathogen Campylobacter jejuni, which has a major role in adherence and host colonization. The Peb1a domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270409 [Multi-domain]  Cd Length: 228  Bit Score: 100.99  E-value: 6.52e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  42 KIVGFDVDLANALCKEIDAT-CTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTTPYY-DNSALFIGQKGKYA 119
Cdd:cd13691   30 KYEGMEVDLARKLAKKGDGVkVEFTPVTAKTRGPLLDNGDVDAVIATFTITPERKKSYDFSTPYYtDAIGVLVEKSSGIK 109
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 120 SVDLLKGKKVGVQNGTTHQKFI---MDKHPE-ITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTEWLkaNDKLAAVGDKV 195
Cdd:cd13691  110 SLADLKGKTVGVASGATTKKALeaaAKKIGIgVSFVEYADYPEIKTALDSGRVDAFSVDKSILAGYV--DDSREFLDDEF 187
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 493171821 196 TDKDYfgtglGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:cd13691  188 APQEY-----GVATKKGSTDLSKYVDDAVKKWLADGTLEALIKKW 227
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
6-241 1.50e-25

Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, Signal transduction mechanisms];


Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 103.22  E-value: 1.50e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   6 IAALLASVSLSAT------AAQTIRFATEASyPPFESIDaNNKIVGFDVDLANALCKEIDATCT-FSNQAFDSLIPSLKF 78
Cdd:COG4623    1 LLLLLPACSSEPGdleqikERGVLRVLTRNS-PTTYFIY-RGGPMGFEYELAKAFADYLGVKLEiIVPDNLDELLPALNA 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  79 RRIDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKG--KYASVDLLKGKKVGVQNGTTHQ---KFIMDKHPEITTVPY 153
Cdd:COG4623   79 GEGDIAAAGLTITPERKKQVRFSPPYYSVSQVLVYRKGspRPKSLEDLAGKTVHVRAGSSYAerlKQLNQEGPPLKWEED 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 154 DSYQNAKL--DLQNGRIDAVFGDTAVVTEWLKANDKLaAVGDKVTDKDYfgtgLGIAVRQGNTELQQKFNAALEKVKKDG 231
Cdd:COG4623  159 EDLETEDLleMVAAGEIDYTVADSNIAALNQRYYPNL-RVAFDLSEPQP----IAWAVRKNDPSLLAALNEFFAKIKKGG 233
                        250
                 ....*....|
gi 493171821 232 TYETIYKKWF 241
Cdd:COG4623  234 TLARLYERYF 243
PBP2_HisK_like_1 cd13706
Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein; This ...
21-241 4.87e-24

Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein; This group includes periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space through their function as an initial high-affinity binding component. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270424 [Multi-domain]  Cd Length: 219  Bit Score: 95.71  E-value: 4.87e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  21 QTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDaVMAGMDITPEREKQVLF 100
Cdd:cd13706    2 QPLVVAMDKDYPPFSFLDEDGEPQGILVDLWRLWSEKTGIPVEFVLLDWNESLEAVRQGEAD-VHDGLFKSPEREKYLDF 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 101 TTPYYD-NSALFIGQK-GKYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSY----QNAKldlqNGRIDAVFGD 174
Cdd:cd13706   81 SQPIATiDTYLYFHKDlSGITNLSDLKGFRVGVVKGDAEEEFLRAHGPILSLVYYDNYeamiEAAK----AGEIDVFVAD 156
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 493171821 175 TAVVTEWLkanDKLAAVGDKVTDKD-YFGTgLGIAVRQGNTELQQKFNAALEKVKKDgTYETIYKKWF 241
Cdd:cd13706  157 EPVANYYL---YKYGLPDEFRPAFRlYSGQ-LHPAVAKGNSALLDLINRGFALISPE-ELARIERKWL 219
PBP2_polar_AA cd13693
Substrate binding domain of polar amino-acid uptake ABC transporter; the type 2 periplasmic ...
22-240 4.77e-21

Substrate binding domain of polar amino-acid uptake ABC transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of putative polar amino acid ABC transporter. The polar amino-acid binding domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270411 [Multi-domain]  Cd Length: 228  Bit Score: 87.76  E-value: 4.77e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDA-----TCTFSNQafdslIPSLKFRRIDAVMAGMDITPEREK 96
Cdd:cd13693    9 KLIVGVKNDYPPFGFLDPSGEIVGFEVDLAKDIAKRLGVklelvPVTPSNR-----IQFLQQGKVDLLIATMGDTPERRK 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  97 QVLFTTPYYDNS--ALFIGQKGKYASVDLLKGKKV-GVQNGTTHQKFIMDKHPEIttVPYDSYQNAKLDLQNGRIDA-VF 172
Cdd:cd13693   84 VVDFVEPYYYRSggALLAAKDSGINDWEDLKGKPVcGSQGSYYNKPLIEKYGAQL--VAFKGTPEALLALRDGRCVAfVY 161
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 493171821 173 GDTAVvtewlkaNDKLAAVGDKvtdKDYFG-------TGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:cd13693  162 DDSTL-------QLLLQEDGEW---KDYEIplptiepSPWVIAVRKGETAFQNALDEIIKDWHRTGKLIELEKKW 226
PBP2_PheC cd01069
Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein ...
22-241 3.59e-20

Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein superfamily; This subfamily includes cyclohexadienyl dehydratase PheC. These proteins catalyze the decarboxylation of prephenate to phenylpyruvate in the alternative phenylalanine biosynthesis pathway in some proteobacteria and archaea. The PheC proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Since they the PheC proteins are so similar to periplasmic binding proteins, (PBP), it is evolutionarily plausible that several pre-existing PBP proteins might have been recruited to perform the enzymatic function.


Pssm-ID: 270231 [Multi-domain]  Cd Length: 232  Bit Score: 85.85  E-value: 3.59e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFT 101
Cdd:cd01069   11 VLRVGTTGDYKPFTYRDNQGQYEGYDIDMAEALAKSLGVKVEFVPTSWPTLMDDLAADKFDIAMGGISITLERQRQAFFS 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 102 TPYYDNSALFI---GQKGKYASVDLL--KGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTA 176
Cdd:cd01069   91 APYLRFGKTPLvrcADVDRFQTLEAInrPGVRVIVNPGGTNEKFVRANLKQATITVHPDNLTIFQAIADGKADVMITDAV 170
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 493171821 177 VVTEWLKANDKLAAVgdkVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd01069  171 EARYYQKLDPRLCAV---HPDKPFTFSEKAYMIPRDDQALKRYVDQWLHIMEGSGLLDQLSNKWL 232
PBP2_Mlr3796_like cd13695
The substrate-binding domain of putative amino aicd transporter; the type 2 periplasmic ...
27-224 8.17e-19

The substrate-binding domain of putative amino aicd transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Mesorhizobium loti and its related proteins. The putative Mlr3796-like domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270413 [Multi-domain]  Cd Length: 232  Bit Score: 82.22  E-value: 8.17e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  27 TEASYPPFESIDANNKIVGFDVDLANALCKEI--DAT-CTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTTP 103
Cdd:cd13695   14 TGSTNAPWHFKSADGELQGFDIDMGRIIAKALfgDPQkVEFVNQSSDARIPNLTTDKVDITCQFMTVTAERAQQVAFTIP 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 104 YYDNS-ALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMD----KHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVV 178
Cdd:cd13695   94 YYREGvALLTKADSKYKDYDALKAAGASVTIAVLQNVYAEDlvhaALPNAKVAQYDTVDLMYQALESGRADAAAVDQSSI 173
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 493171821 179 TEWLKANDKLAAVGDKVtdkDYFGTgLGIAVRQGNTELQQKFNAAL 224
Cdd:cd13695  174 GWLMGQNPGKYRDAGYG---WNPQT-YGCAVKRGDLDWLNFVNTAL 215
PBP2_BvgS_D2 cd13707
The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
21-225 2.30e-18

The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 peripasmic-binding fold protein; This group contains the second domain of the periplasmic solute-binding domains of BvgS and related proteins. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a receiver and a Histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270425 [Multi-domain]  Cd Length: 221  Bit Score: 80.73  E-value: 2.30e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  21 QTIRFATEASYPPFESIDANNKIVGFDVDLANALCK----EIDATCTFSNQAfdsLIPSLKFRRIDaVMAGMDITPEREK 96
Cdd:cd13707    2 PVVRVVVNPDLAPLSFFDSNGQFRGISADLLELISLrtglRFEVVRASSPAE---MIEALRSGEAD-MIAALTPSPERED 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  97 QVLFTTPYYDNSALFIGQKGKYASVDL--LKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFgD 174
Cdd:cd13707   78 FLLFTRPYLTSPFVLVTRKDAAAPSSLedLAGKRVAIPAGSALEDLLRRRYPQIELVEVDNTAEALALVASGKADATV-A 156
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 493171821 175 TAVVTEWLKAN---DKLAAVGdkvtDKDYFGTGLGIAVRQGNTELQQKFNAALE 225
Cdd:cd13707  157 SLISARYLINHyfrDRLKIAG----ILGEPPAPIAFAVRRDQPELLSILDKALL 206
PBP2_BvgS_like_1 cd13708
Putative sensor domain similar to BvgS; the type 2 periplasmic binding protein domain; BvgS is ...
21-240 3.05e-18

Putative sensor domain similar to BvgS; the type 2 periplasmic binding protein domain; BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a receiver and a Histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270426 [Multi-domain]  Cd Length: 220  Bit Score: 80.25  E-value: 3.05e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  21 QTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTfsnqafdsLIP------SLKF---RRIDAVMAGMDiT 91
Cdd:cd13708    2 KEITMCVDPDWMPYEGIDEGGKHVGIAADYLKLIAERLGIPIE--------LVPtkswseSLEAakeGKCDILSLLNQ-T 72
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  92 PEREKQVLFTTPYYDNSALFIGQKGK--YASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRID 169
Cdd:cd13708   73 PEREEYLNFTKPYLSDPNVLVTREDHpfIADLSDLGDKTIGVVKGYAIEEILRQKYPNLNIVEVDSEEEGLKKVSNGELF 152
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 493171821 170 AvFGDTAVVTEWLKANDKLAAVgdKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDgTYETIYKKW 240
Cdd:cd13708  153 G-FIDSLPVAAYTIQKEGLFNL--KISGKLDEDNELRIGVRKDEPLLLSILNKAIASITPE-ERQEILNKW 219
PBP2_YckB cd01003
Substrate binding domain of an ABC cystine transporter; the type 2 periplasmic binding protein ...
22-243 2.92e-17

Substrate binding domain of an ABC cystine transporter; the type 2 periplasmic binding protein fold; Periplasmic cystine-binding domain (YckB) of an ATP-binding cassette (ABC) transporter from Bacillus subtilis and its related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270224 [Multi-domain]  Cd Length: 229  Bit Score: 77.69  E-value: 2.92e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEAS-YPPFESIDANNKIVGFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLF 100
Cdd:cd01003    2 SIVVATSGTlYPTSYHDTDSDKLTGYEVEVVREAGKRLGLKIEFKEMGIDGMLTAVNSGQVDAAANDIEVTKDREKKFAF 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 101 TTPYYDNSALFIGQKGKYA---SVDLLKGKKVGVQNGTTHQKFIMDKHPEIttVPYDSYQNAKL--DLQNGRIDAVFGDT 175
Cdd:cd01003   82 STPYKYSYGTAVVRKDDLSgisSLKDLKGKKAAGAATTVYMEIARKYGAEE--VIYDNATNEVYlkDVANGRTDVILNDY 159
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 493171821 176 AVVTEWLKANDKLaavGDKV-TDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKKWFQK 243
Cdd:cd01003  160 YLQTMAVAAFPDL---NITIhPDIKYYPNKQALVMKKSNAALQEKVNKALKEMSKDGTLTKISEQFFNG 225
PRK10859 PRK10859
membrane-bound lytic murein transglycosylase MltF;
40-241 2.46e-13

membrane-bound lytic murein transglycosylase MltF;


Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 68.75  E-value: 2.46e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  40 NNKIVGFDVDLANALCKEIDATC---TFSNQafDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKG 116
Cdd:PRK10859  60 NDGPTGFEYELAKRFADYLGVKLeikVRDNI--SQLFDALDKGKADLAAAGLTYTPERLKQFRFGPPYYSVSQQLVYRKG 137
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 117 KYASVDL--LKGKKVGVQNGTTHQ---KFIMDKHPEITTVPYDSYQNAKLDLQ--NGRIDAVFGDTAVVTewlkANDKL- 188
Cdd:PRK10859 138 QPRPRSLgdLKGGTLTVAAGSSHVetlQELKKKYPELSWEESDDKDSEELLEQvaEGKIDYTIADSVEIS----LNQRYh 213
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 493171821 189 --AAVGDKVTDKDyfgtGLGIAVRQGN-TELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:PRK10859 214 peLAVAFDLTDEQ----PVAWALPPSGdDSLYAALLDFFNQIKEDGTLARLEEKYF 265
PBP2_iGluR_non_NMDA_like cd13685
The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate ...
32-241 2.87e-12

The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This subfamily represents the ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors including AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) receptors (GluR1-4), kainate receptors (GluR5-7 and KA1/2), and orphan receptors delta 1/2. iGluRs form tetrameric ligand-gated ion channels, which are concentrated at postsynaptic sites in excitatory synapses where they fulfill a variety of different functions. While this ligand-binding domain of iGluRs is structurally homologous to the periplasmic binding fold type II superfamily, the N-terminal leucine/isoleucine/valine#binding protein (LIVBP)-like domain belongs to the periplasmic-binding fold type I.


Pssm-ID: 270403 [Multi-domain]  Cd Length: 252  Bit Score: 64.51  E-value: 2.87e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  32 PPF-----ESIDANNKIVGFDVDLANALCKEIDATCTFS------------NQAFDSLIPSLKFRRIDAVMAGMDITPER 94
Cdd:cd13685   12 PPFvmkkrDSLSGNPRFEGYCIDLLEELAKILGFDYEIYlvpdgkygsrdeNGNWNGMIGELVRGEADIAVAPLTITAER 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  95 EKQVLFTTPYYDNSALFIGQKGK-YASV-DLLKGKKV--GVQNGT-THQKFIMDKHPEITTVPYDSYQNAK------LDL 163
Cdd:cd13685   92 EEVVDFTKPFMDTGISILMRKPTpIESLeDLAKQSKIeyGTLKGSsTFTFFKNSKNPEYRRYEYTKIMSAMspsvlvASA 171
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 164 QNG--RID------AVFGDTAVVtEWLKAND-KLAAVGDKVTDKDYfgtglGIAVRQGNtELQQKFNAALEKVKKDGTYE 234
Cdd:cd13685  172 AEGvqRVResnggyAFIGEATSI-DYEVLRNcDLTKVGEVFSEKGY-----GIAVQQGS-PLRDELSLAILELQESGELE 244

                 ....*..
gi 493171821 235 TIYKKWF 241
Cdd:cd13685  245 KLKEKWW 251
PBP2_AA_hypothetical cd13623
Substrate-binding domain of putative amino-acid transport system; the type 2 periplasmic ...
22-239 1.31e-11

Substrate-binding domain of putative amino-acid transport system; the type 2 periplasmic binding protein fold; This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270341 [Multi-domain]  Cd Length: 220  Bit Score: 61.92  E-value: 1.31e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  22 TIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDATCTFsnqafdslipsLKFRRIDAVMAGMD----------IT 91
Cdd:cd13623    5 TLRVAINLGNPVLAVEDATGGPRGVSVDLAKELAKRLGVPVEL-----------VVFPAAGAVVDAASdgewdvaflaID 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  92 PEREKQVLFTTPYYDNSALFIGQKG----KYASVDlLKGKKVGVQNGTTHQKFIMD--KHPEITTVPydSYQNAKLDLQN 165
Cdd:cd13623   74 PARAETIDFTPPYVEIEGTYLVRADspirSVEDVD-RPGVKIAVGKGSAYDLFLTRelQHAELVRAP--TSDEAIALFKA 150
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493171821 166 GRIDAVFGDTAVVTEWLKANDklaavGDKVTDKDYFGTGLGIAVRQGNTELQQKFNAALEKVKKDGTYETIYKK 239
Cdd:cd13623  151 GEIDVAAGVRQQLEAMAKQHP-----GSRVLDGRFTAIHQAIAIPKGRPAALEYLNEFVEEAKASGLLERALQR 219
PRK11917 PRK11917
bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
32-240 2.50e-11

bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed


Pssm-ID: 183381 [Multi-domain]  Cd Length: 259  Bit Score: 61.86  E-value: 2.50e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  32 PPFESID-ANNKIVGFDVDLANALCKEI---DATCTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTTPYY-D 106
Cdd:PRK11917  49 PHYALLDqATGEIKGFEIDVAKLLAKSIlgdDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRIYNFSEPYYqD 128
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 107 NSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHP----EITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTEWL 182
Cdd:PRK11917 129 AIGLLVLKEKNYKSLADMKGANIGVAQAATTKKAIGEAAKkigiDVKFSEFPDYPSIKAALDAKRVDAFSVDKSILLGYV 208
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 493171821 183 kaNDKLAAVGDKVTDKDYfgtglGIAVRQGNTELQQKFNAALEKVKKDgtYETIYKKW 240
Cdd:PRK11917 209 --DDKSEILPDSFEPQSY-----GIVTKKDDPAFAKYVDDFVKEHKNE--IDALAKKW 257
Periplasmic_Binding_Protein_Type_2 cd00648
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
45-211 4.68e-10

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


Pssm-ID: 270214 [Multi-domain]  Cd Length: 196  Bit Score: 57.20  E-value: 4.68e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  45 GFDVDLANALCKE--IDATCTFsNQAFDSLIPSLKFRRIDAVMAGMDITPE------REKQVLFTTPYYDNSALFIGQKG 116
Cdd:cd00648   14 GFAEDAAKQLAKEtgIKVELVP-GSSIGTLIEALAAGDADVAVGPIAPALEaaadklAPGGLYIVPELYVGGYVLVVRKG 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 117 ----KYASVDLLKGKKVGVQNGTTHQKFIM----------DKHPEIttVPYDSYQNAKLDLQNGRIDAVFGDTAVVTEWL 182
Cdd:cd00648   93 ssikGLLAVADLDGKRVGVGDPGSTAVRQArlalgayglkKKDPEV--VPVPGTSGALAAVANGAVDAAIVWVPAAERAQ 170
                        170       180
                 ....*....|....*....|....*....
gi 493171821 183 KANDKLAAVGDkvtDKDYFGTGLGIAVRQ 211
Cdd:cd00648  171 LGNVQLEVLPD---DLGPLVTTFGVAVRK 196
PBP2_iGluR_ligand_binding cd00998
The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic ...
32-241 1.15e-09

The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic binding protein type II superfamily; This subfamily represents the ligand binding of ionotropic glutamate receptors. iGluRs are heterotetrameric ion channels that comprises of three functionally distinct subtypes based on their pharmacology and structural similarities: AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid), NMDA (N-methyl-D-aspartate), and kainate receptors. All three types of channels are also activated by the physiological neurotransmitter, glutamate. iGluRs are concentrated at postsynaptic sites, where they exert a variety of different functions. While this ligand-binding domain of iGluRs is structurally homologous to the periplasmic binding fold type II superfamily, the N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain belongs to the periplasmic-binding fold type I.


Pssm-ID: 270219 [Multi-domain]  Cd Length: 243  Bit Score: 57.00  E-value: 1.15e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  32 PPF-------ESIDANNKIVGFDVDLANALCKEIDATCTF-----------SNQAFDSLIPSLKFRRIDAVMAGMDITPE 93
Cdd:cd00998   11 PPFvmfvtgsNAVTGNGRFEGYCIDLLKELSQSLGFTYEYylvpdgkfgapVNGSWNGMVGEVVRGEADLAVGPITITSE 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  94 REKQVLFTTPYYDnsaLFIGQKGKYASVDLLKGKK----VGVQNGTTHQKFI---------MDKHPEITTVPYDSYQNAK 160
Cdd:cd00998   91 RSVVIDFTQPFMT---SGIGIMIPIRSIDDLKRQTdiefGTVENSFTETFLRssgiypfykTWMYSEARVVFVNNIAEGI 167
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 161 LDLQNGRIDAVFGDTAVVtEWLKANDKLaavgDKVTDKDYFGT-GLGIAVrQGNTELQQKFNAALEKVKKDGTYETIYKK 239
Cdd:cd00998  168 ERVRKGKVYAFIWDRPYL-EYYARQDPC----KLIKTGGGFGSiGYGFAL-PKNSPLTNDLSTAILKLVESGVLQKLKNK 241

                 ..
gi 493171821 240 WF 241
Cdd:cd00998  242 WL 243
PBP2_BztA cd13692
Substrate bindng domain of ABC glutamate/glutamine/aspartate/asparagine transporter; the type ...
29-174 1.79e-09

Substrate bindng domain of ABC glutamate/glutamine/aspartate/asparagine transporter; the type 2 periplasmic binding protein fold; BztA is the periplamic-binding protein component of ABC transporter specific for carboxylic amino acids, glutamine and asparagine. The BZtA domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270410 [Multi-domain]  Cd Length: 236  Bit Score: 56.10  E-value: 1.79e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  29 ASYPPFESIDANNKIVGFDVDLANALckeidATCTFSNQAFDSLIPSLKFRRIDAVMAG-MDI-------TPEREKQ--V 98
Cdd:cd13692   16 EGLPGFSAVDDDGVWRGFDVDLCRAV-----AAAVLGDATAVEFVPLSASDRFTALASGeVDVlsrnttwTLSRDTElgV 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  99 LFTTP-YYDNSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDK----HPEITTVPYDSYQNAKLDLQNGRIDAVFG 173
Cdd:cd13692   91 DFAPVyLYDGQGFLVRKDSGITSAKDLDGATICVQAGTTTETNLADYfkarGLKFTPVPFDSQDEARAAYFSGECDAYTG 170

                 .
gi 493171821 174 D 174
Cdd:cd13692  171 D 171
PBP2_AA_binding_like_3 cd13621
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
45-241 3.00e-09

Substrate-binding domain of putative amino acid-binding protein; the type 2 periplasmic-binding protein fold; This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270339 [Multi-domain]  Cd Length: 229  Bit Score: 55.52  E-value: 3.00e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  45 GFDVDLANALCKEIDATCTFSNQAFDSLIPSLKFRRIDaVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGKYASV--D 122
Cdd:cd13621   33 GFGIDMAEDIAKDLGVKVEPVETTWGNAVLDLQAGKID-VAFALDATPERALAIDFSTPLLYYSFGVLAKDGLAAKSweD 111
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 123 LLKGK-KVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAvFGDTAVVTewLKANDKLAAVGDKVTDKDYF 201
Cdd:cd13621  112 LNKPEvRIGVDLGSATDRIATRRLPNAKIERFKNRDEAVAAFMTGRADA-NVLTHPLL--VPILSKIPTLGEVQVPQPVL 188
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 493171821 202 GTGLGIAVRQGNTELQQKF-NAALEKVKKDGTYETIYKKWF 241
Cdd:cd13621  189 ALPTSIGVRREEDKVFKSFlSAWIQKLRRSGQTQKIILKYL 229
PBP2_BvgS_D1 cd13705
The first of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
21-240 8.52e-09

The first of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 peripasmic-binding fold protein; This group contains the first domain of the periplasmic solute-binding domains of BvgS and related proteins. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a histidine-kinase (HK), a receiver and a histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270423 [Multi-domain]  Cd Length: 221  Bit Score: 54.14  E-value: 8.52e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  21 QTIRFATEAS-YPPFESIDANNKIVGFDVD----LANALCKEIDATcTFSNQafDSLIPSLKFRRIDavMAGMDITPERE 95
Cdd:cd13705    2 RTLRVGVSAPdYPPFDITSSGGRYEGITADylglIADALGVRVEVR-RYPDR--EAALEALRNGEID--LLGTANGSEAG 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  96 KQVL-FTTPYYDNSALFIGQKGKYASV-DLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFG 173
Cdd:cd13705   77 DGGLlLSQPYLPDQPVLVTRIGDSRQPpPDLAGKRVAVVPGYLPAEEIKQAYPDARIVLYPSPLQALAAVAFGQADYFLG 156
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 174 DtAVVTEWLKANDKLaavgDKVTDKDYF---GTGLGIAVRQGNTELQQKFNAALEKVkKDGTYETIYKKW 240
Cdd:cd13705  157 D-AISANYLISRNYL----NNLRIVRFAplpSRGFGFAVRPDNTRLLRLLNRALAAI-PDEQRDEILRRW 220
PBP2_iGluR_delta_2 cd13731
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the ...
69-241 3.51e-06

The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the type 2 periplasmic-binding fold protein superfamily; This group contains the ligand-binding domain of the delta-2 receptor of an orphan glutamate receptor family. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of delta receptors belongs to the periplasmic-binding fold type I. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRalpha2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans.


Pssm-ID: 270449 [Multi-domain]  Cd Length: 257  Bit Score: 46.95  E-value: 3.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  69 FDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGKyaSVDLLK--GKKVGVQNGTTHQKFIMDKHP 146
Cdd:cd13731   66 WNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRRAE--SIQSLQdlSKQTDIPYGTVLDSAVYEHVR 143
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 147 EITTVPYD----------------SYQNAKLDLQNGRIDAVFGD-----TAVVTEWLKAND---KLAAVGDKVTDKDYfg 202
Cdd:cd13731  144 MKGLNPFErdsmysqmwrminrsnGSENNVLESQAGIQKVKYGNyafvwDAAVLEYVAINDpdcSFYTVGNTVADRGY-- 221
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 493171821 203 tglGIAVRQGnTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13731  222 ---GIALQHG-SPYRDVFSQRILELQQNGDMDILKHKWW 256
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
4-226 9.88e-06

ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion transport and metabolism];


Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 45.77  E-value: 9.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   4 VLIAALLASVSLSATAAQ--TIRFA--TEASYPPF-----------ESIDANNKIVGFDVDLANAL-CKEIDATCTFSNQ 67
Cdd:COG0715    3 ALAALALAACSAAAAAAEkvTLRLGwlPNTDHAPLyvakekgyfkkEGLDVELVEFAGGAAALEALaAGQADFGVAGAPP 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  68 AfdslipslkfrrIDAVMAGMDITperekqVLFTTPYYDNSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFI---MDK 144
Cdd:COG0715   83 A------------LAARAKGAPVK------AVAALSQSGGNALVVRKDSGIKSLADLKGKKVAVPGGSTSHYLLralLAK 144
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 145 H----PEITTVPYDSYQNAKLdLQNGRIDAVFGDTAVVTEWLKANDKLAAvgdkVTDKDYFG--TGLGIAVRQG----NT 214
Cdd:COG0715  145 AgldpKDVEIVNLPPPDAVAA-LLAGQVDAAVVWEPFESQAEKKGGGRVL----ADSADLVPgyPGDVLVASEDfleeNP 219
                        250
                 ....*....|..
gi 493171821 215 ELQQKFNAALEK 226
Cdd:COG0715  220 EAVKAFLRALLK 231
PBP2_iGluR_NMDA cd13687
The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate ...
72-240 3.89e-05

The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; The ligand-binding domain of the ionotropic NMDA subtype is structurally homologous to the periplasmic-binding fold type II superfamily, while the N-terminal domain belongs to the periplasmic-binding fold type I. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain.


Pssm-ID: 270405 [Multi-domain]  Cd Length: 239  Bit Score: 43.39  E-value: 3.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  72 LIPSLKFRRIDAVMAGMDITPEREKQVLFTTPYYD--------NSALFIG---QKGKYASVDLLKGKkvgVQNGTTHQKF 140
Cdd:cd13687   63 MIGELVSGRADMAVASLTINPERSEVIDFSKPFKYtgitilvkKRNELSGindPRLRNPSPPFRFGT---VPNSSTERYF 139
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 141 ---IMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVtEWLKAND---KLAAVGDKvtdkdYFGTGLGIAVRQgNT 214
Cdd:cd13687  140 rrqVELMHRYMEKYNYETVEEAIQALKNGKLDAFIWDSAVL-EYEASQDegcKLVTVGSL-----FARSGYGIGLQK-NS 212
                        170       180
                 ....*....|....*....|....*.
gi 493171821 215 ELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:cd13687  213 PWKRNVSLAILQFHESGFMEELDKKW 238
PBP2_iGluR_putative cd13717
The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 ...
32-125 6.30e-05

The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270435 [Multi-domain]  Cd Length: 360  Bit Score: 43.44  E-value: 6.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  32 PPFeSI---DANNKIVGFDVDLANALCKEIDATCTFS------------NQAFDSLIPSLKFRRIDAVMAGMDITPEREK 96
Cdd:cd13717   12 PPF-VYrdrDGSPIWEGYCIDLIEEISEILNFDYEIVepedgkfgtmdeNGEWNGLIGDLVRKEADIALAALSVMAEREE 90
                         90       100
                 ....*....|....*....|....*....
gi 493171821  97 QVLFTTPYYDNSALFIGQKGKYASVDLLK 125
Cdd:cd13717   91 VVDFTVPYYDLVGITILMKKPERPTSLFK 119
PRK10797 PRK10797
glutamate and aspartate transporter subunit; Provisional
1-242 1.16e-04

glutamate and aspartate transporter subunit; Provisional


Pssm-ID: 236763 [Multi-domain]  Cd Length: 302  Bit Score: 42.54  E-value: 1.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   1 MKKVLIAALLASVSLSATAAQTIRFATEA-----------------SYPPFESIDANNKIVGFDVDLANALCKEIDATCT 63
Cdd:PRK10797   3 LRKLATALLLLGLSAGLAQAEDAAPAAGStldkiakngvivvghreSSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLN 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  64 FSNQAFdSLIPSLKFRRIDAVMAG-MDI-------TPEREKQVLFT-TPYYDNSALFIGQKGKYASVDLLKGKKVGVQNG 134
Cdd:PRK10797  83 KPDLQV-KLIPITSQNRIPLLQNGtFDFecgsttnNLERQKQAAFSdTIFVVGTRLLTKKGGDIKDFADLKGKAVVVTSG 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 135 TTHQ----KFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVT-EWLKAN--DKLAAVGDKVTDKDYfgtglGI 207
Cdd:PRK10797 162 TTSEvllnKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAgERAKAKkpDNWEIVGKPQSQEAY-----GC 236
                        250       260       270
                 ....*....|....*....|....*....|....*
gi 493171821 208 AVRQGNTELQQKFNAALEKVKKDGTYETIYKKWFQ 242
Cdd:PRK10797 237 MLRKDDPQFKKLMDDTIAQAQTSGEAEKWFDKWFK 271
PBPe smart00079
Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic ...
122-243 7.47e-04

Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb


Pssm-ID: 197504 [Multi-domain]  Cd Length: 133  Bit Score: 38.42  E-value: 7.47e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   122 DLLKGKKV---GVQNGTTHQKFIMDKHPEI------TTVPYDSYQNAKLDLQNGR--IDAVFGDTAVVTEWLKANDKLAA 190
Cdd:smart00079   7 DLAKQTKIeygTQDGSSTLAFFKRSGNPEYsrmwpyMKSPEVFVKSYAEGVQRVRvsNYAFIMESPYLDYELSRNCDLMT 86
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 493171821   191 VGDKVTDKDYfgtglGIAVRQGNtELQQKFNAALEKVKKDGTYETIYKKWFQK 243
Cdd:smart00079  87 VGEEFGRKGY-----GIAFPKGS-PLRDDLSRAILKLSESGELEKLRNKWWKD 133
Lig_chan-Glu_bd pfam10613
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
32-106 1.10e-03

Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060.


Pssm-ID: 463166 [Multi-domain]  Cd Length: 111  Bit Score: 37.50  E-value: 1.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   32 PPF----ESIDANNKIVGFDVDLANALCKEIDATCTF-------------SNQAFDSLIPSLKFRRIDAVMAGMDITPER 94
Cdd:pfam10613  11 PPFvmlkENLEGNDRYEGFCIDLLKELAEILGFKYEIrlvpdgkygsldpTTGEWNGMIGELIDGKADLAVAPLTITSER 90
                          90
                  ....*....|..
gi 493171821   95 EKQVLFTTPYYD 106
Cdd:pfam10613  91 EKVVDFTKPFMT 102
PBP2_iGluR_delta_like cd13716
The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of ...
65-241 1.30e-03

The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This subfamily represents the ligand-binding domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of iGluRs belongs to the periplasmic-binding fold type I. Although the delta receptors are members of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRalpha2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans.


Pssm-ID: 270434 [Multi-domain]  Cd Length: 257  Bit Score: 39.05  E-value: 1.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  65 SNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTTPYYDNSALFIGQKGKyaSVDLLK--GKKVGVQNGTTHQKFIM 142
Cdd:cd13716   62 EDGTWNGLIGELVFKRADIGISALTITPERENVVDFTTRYMDYSVGVLLRKAE--SIQSLQdlSKQTDIPYGTVLDSAVY 139
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 143 DKHPEITTVPYD----------------SYQNAKLDLQNGRIDAVFGDTA-----VVTEWLKAND---KLAAVGDKVTDK 198
Cdd:cd13716  140 EYVRSKGTNPFErdsmysqmwrminrsnGSENNVSESSEGIRKVKYGNYAfvwdaAVLEYVAINDddcSFYTVGNTVADR 219
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 493171821 199 DYfgtglGIAVRQGnTELQQKFNAALEKVKKDGTYETIYKKWF 241
Cdd:cd13716  220 GY-----GIALQHG-SPYRDVFSQRILELQQNGDMDILKHKWW 256
PRK09959 PRK09959
acid-sensing system histidine kinase EvgS;
32-171 2.15e-03

acid-sensing system histidine kinase EvgS;


Pssm-ID: 182169 [Multi-domain]  Cd Length: 1197  Bit Score: 38.95  E-value: 2.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821   32 PPFESIDANNKIVGFDVDLANALCKEID-----ATCTFSNQAFDSLIPslkfrridavmAGMDITP------EREKQVLF 100
Cdd:PRK09959  313 PPYSMTDENGSVRGVMGDILNIITLQTGlnfspITVSHNIHAGTQLNP-----------GGWDIIPgaiyseDRENNVLF 381
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 493171821  101 TTPYYDNSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAV 171
Cdd:PRK09959  382 AEAFITTPYVFVMQKAPDSEQTLKKGMKVAIPYYYELHSQLKEMYPEVEWIKVDNASAAFHKVKEGELDAL 452
PBP2_PhnD_like cd01071
Substrate binding domain of phosphonate uptake system-like, a member of the type 2 ...
18-190 3.55e-03

Substrate binding domain of phosphonate uptake system-like, a member of the type 2 periplasmic-binding fold superfamily; This family includes alkylphosphonate binding domain PhnD. These domains are found in PhnD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake system (PhnCDE) that recognizes and binds phosphonate. PhnD belongs to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. The PBP2 have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270232 [Multi-domain]  Cd Length: 253  Bit Score: 37.63  E-value: 3.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  18 TAAQTIRFAteasYPPFESIDANNKIVGfdvDLANALCKEIDATCT-FSNQAFDSLIPSLKFRRIDAVMAGMDITPEREK 96
Cdd:cd01071    1 AAPKELRFG----LVPAEDADELKKEFE---PLADYLEEELGVPVElVVATSYAAVVEAMRNGKVDIAWLGPASYVLAHD 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821  97 Q---VLFTTPYYDNSA----LFIGQKG-KYASVDLLKGKKVGV--QNGTT---------HQKFIMDKHPEITTVPYDSYQ 157
Cdd:cd01071   74 RagaEALATEVRDGSPgyysVIIVRKDsPIKSLEDLKGKTVAFvdPSSTSgylfpramlKDAGIDPPDFFFEVVFAGSHD 153
                        170       180       190
                 ....*....|....*....|....*....|...
gi 493171821 158 NAKLDLQNGRIDAVFGDTAVVTEWLKANDKLAA 190
Cdd:cd01071  154 SALLAVANGDVDAAATYDSTLERAAAAGPIDPD 186
PBP2_NrtA_SsuA_CpmA_like cd01008
Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of ...
103-226 4.24e-03

Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily; This family represents the periplasmic binding proteins involved in nitrate, alkanesulfonate, and bicarbonate transport. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates. Other closest homologs involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB) are also included in this family. After binding their ligand with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. These binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270229 [Multi-domain]  Cd Length: 212  Bit Score: 37.27  E-value: 4.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493171821 103 PYYDNSALFIGQKGKYASVDLLKGKKVGVQNGTTHQKFIMD-------KHPEITTVPYDSyQNAKLDLQNGRIDAVFGDT 175
Cdd:cd01008   81 RSPNGNGIVVRKDSGITSLADLKGKKIAVTKGTTGHFLLLKalakaglSVDDVELVNLGP-ADAAAALASGDVDAWVTWE 159
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 493171821 176 AVVTEWLKANDKLAAVGDKVTDKDYFGtglGIAVRQG----NTELQQKFNAALEK 226
Cdd:cd01008  160 PFLSLAEKGGDARIIVDGGGLPYTDPS---VLVARRDfveeNPEAVKALLKALVE 211
PBP2_iGluR_putative cd13717
The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 ...
170-240 5.14e-03

The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270435 [Multi-domain]  Cd Length: 360  Bit Score: 37.66  E-value: 5.14e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 493171821 170 AVFGDTAVVTEWLKANDKLAAVGDKVTDKDYfgtglGIAVRQGnTELQQKFNAALEKVKKDGTYETIYKKW 240
Cdd:cd13717  294 AFIGDATDIKYEILTNCDLQEVGEEFSRKPY-----AIAVQQG-SPLKDELNYAILELQNDRFLEKLKAKW 358
PBP2_iGluR_delta_1 cd13730
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the ...
45-108 7.77e-03

The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the type 2 periplasmic-binding fold protein superfamily; This group contains the ligand-binding domain of the delta1 receptor of an orphan glutamate receptor family. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of delta receptors belongs to the periplasmic-binding fold type I. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRdelta2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans.


Pssm-ID: 270448 [Multi-domain]  Cd Length: 257  Bit Score: 36.86  E-value: 7.77e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 493171821  45 GFDVDLANALCKEI----------DAT--CTFSNQAFDSLIPSLKFRRIDAVMAGMDITPEREKQVLFTTPYYDNS 108
Cdd:cd13730   30 GFSIDVLDALAKALgfkyeiyqapDGKygHQLHNTSWNGMIGELISKRADLAISAITITPERESVVDFSKRYMDYS 105
 
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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