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Conserved domains on  [gi|556356369|ref|WP_023300074|]
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MULTISPECIES: ABC transporter substrate-binding protein [Enterobacter]

Protein Classification

ABC transporter substrate-binding protein( domain architecture ID 10194715)

ABC transporter substrate-binding protein such as the periplasmic-binding proteins, HisJ and LAO, that serve as initial receptors in the ABC transport of histidine and lysine-arginine-ornithine amino acids, belonging 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

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PBP2_HisJ_LAO cd13703
Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; ...
21-249 2.06e-117

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: 334.99  E-value: 2.06e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  21 ATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd13703    1 WKTLRIGTDATYPPFESKDADGELTGFDIDLGNALCAEMKVKCTWVEQDFDGLIPGLLARKFDAIISSMSITEERKKVVD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKHGVTVVSYKDQNMAWGDLLNGRIDASLVMS 180
Cdd:cd13703   81 FTDKYYHTPSRLVARKGSGIDPTPASLKGKRVGVQRGTTQEAYATDNWAPKGVDIKRYATQDEAYLDLVSGRVDAALQDA 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556356369 181 AAGQAGFLSKPQGKGFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13703  161 VAAEEGFLKKPAGKDFAFVGPSVTDKKYFGEGVGIALRKDDTELKAKLNKAIAAIRADGTYDKIQKKYF 229
 
Name Accession Description Interval E-value
PBP2_HisJ_LAO cd13703
Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; ...
21-249 2.06e-117

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: 334.99  E-value: 2.06e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  21 ATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd13703    1 WKTLRIGTDATYPPFESKDADGELTGFDIDLGNALCAEMKVKCTWVEQDFDGLIPGLLARKFDAIISSMSITEERKKVVD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKHGVTVVSYKDQNMAWGDLLNGRIDASLVMS 180
Cdd:cd13703   81 FTDKYYHTPSRLVARKGSGIDPTPASLKGKRVGVQRGTTQEAYATDNWAPKGVDIKRYATQDEAYLDLVSGRVDAALQDA 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556356369 181 AAGQAGFLSKPQGKGFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13703  161 VAAEEGFLKKPAGKDFAFVGPSVTDKKYFGEGVGIALRKDDTELKAKLNKAIAAIRADGTYDKIQKKYF 229
PRK15437 PRK15437
histidine ABC transporter substrate-binding protein HisJ; Provisional
3-249 2.19e-81

histidine ABC transporter substrate-binding protein HisJ; Provisional


Pssm-ID: 185334 [Multi-domain]  Cd Length: 259  Bit Score: 244.94  E-value: 2.19e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   3 LRALVVGIGLLCSFSS----FAA--TELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPG 76
Cdd:PRK15437   1 MKKLVLSLSLVLAFSSataaFAAipQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDALIPS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  77 LLAKKFDAINSAMNITEQRRKSIDFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKHGVTVV 156
Cdd:PRK15437  81 LKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIV 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 157 SYKDQNMAWGDLLNGRIDASLVMSAAGQAGFLSKPQGKGFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVR 236
Cdd:PRK15437 161 SYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMR 240
                        250
                 ....*....|...
gi 556356369 237 ADGTIAKLADKYF 249
Cdd:PRK15437 241 ADGTYEKLAKKYF 253
3A0103s03R TIGR01096
lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino ...
5-249 5.36e-79

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: 238.41  E-value: 5.36e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369    5 ALVVGIGLLCSFSSFAATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDA 84
Cdd:TIGR01096   7 ALVAGASSAATAAAAKEGSVRIGTETGYPPFESKDANGKLVGFDVDLAKALCKRMKAKCKFVEQNFDGLIPSLKAKKVDA 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   85 INSAMNITEQRRKSIDFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWeKHGVTVVSYKDQNMA 164
Cdd:TIGR01096  87 IMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDLAKTLEDLDGKTVGVQSGTTHEQYLKDYF-KPGVDIVEYDSYDNA 165
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  165 WGDLLNGRIDASLVMSAAGQAGFLSKPQGKGFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKL 244
Cdd:TIGR01096 166 NMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLRKGDTELKAAFNKALAAIRADGTYQKI 245

                  ....*
gi 556356369  245 ADKYF 249
Cdd:TIGR01096 246 SKKWF 250
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
24-250 5.08e-75

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: 227.56  E-value: 5.08e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQ 103
Cdd:COG0834    1 LRVGVDPDYPPFSFRDEDGKLVGFDVDLARAIAKRLGLKVEFVPVPWDRLIPALQSGKVDLIIAGMTITPEREKQVDFSD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 104 PIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKhgVTVVSYKDQNMAWGDLLNGRIDAsLVMSAAG 183
Cdd:COG0834   81 PYYTSGQVLLVRKDNSGIKSLADLKGKTVGVQAGTTYEEYLKKLGPN--AEIVEFDSYAEALQALASGRVDA-VVTDEPV 157
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556356369 184 QAGFLSKPQGKGFGFIGKPVSddtilGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYFP 250
Cdd:COG0834  158 AAYLLAKNPGDDLKIVGEPLS-----GEPYGIAVRKGDPELLEAVNKALAALKADGTLDKILEKWFG 219
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
24-249 3.35e-65

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: 202.14  E-value: 3.35e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQ 103
Cdd:pfam00497   1 LRVGTDGDYPPFEYVDENGKLVGFDVDLAKAIAKRLGVKVEFVPVSWDGLIPALQSGKVDLIIAGMTITPERAKQVDFSD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  104 PIYRIPSQLVGKAGSAVE--ATPEGLKGKTIGVLQGSIQETYAKEHwEKHGVTVVSYKDQNMAWGDLLNGRIDAsLVMSA 181
Cdd:pfam00497  81 PYYYSGQVILVRKKDSSKsiKSLADLKGKTVGVQKGSTAEELLKNL-KLPGAEIVEYDDDAEALQALANGRVDA-VVADS 158
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556356369  182 AGQAGFLSKPQGKGFGFIGKPVSddtilGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:pfam00497 159 PVAAYLIKKNPGLNLVVVGEPLS-----PEPYGIAVRKGDPELLAAVNKALAELKADGTLAKIYEKWF 221
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
23-249 3.80e-61

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 191.77  E-value: 3.80e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369    23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFT 102
Cdd:smart00062   1 TLRVGTNGDYPPFSFADEDGELTGFDVDLAKAIAKELGLKVEFVEVSFDSLLTALKSGKIDVVAAGMTITPERAKQVDFS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   103 QPIYRIPSQLVGKAGSAVEaTPEGLKGKTIGVLQGSIQETYAKEhwEKHGVTVVSYKDQNMAWGDLLNGRIDAsLVMSAA 182
Cdd:smart00062  81 DPYYRSGQVILVRKDSPIK-SLEDLKGKKVAVVAGTTAEELLKK--LYPEAKIVSYDSNAEALAALKAGRADA-AVADAP 156
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556356369   183 GQAGFLSKPQGKGFGFIGKPVSDDTilgsGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:smart00062 157 LLAALVKQHGLPELKIVPDPLDTPE----GYAIAVRKGDPELLDKINKALKELKADGTLKKISEKWF 219
 
Name Accession Description Interval E-value
PBP2_HisJ_LAO cd13703
Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; ...
21-249 2.06e-117

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: 334.99  E-value: 2.06e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  21 ATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd13703    1 WKTLRIGTDATYPPFESKDADGELTGFDIDLGNALCAEMKVKCTWVEQDFDGLIPGLLARKFDAIISSMSITEERKKVVD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKHGVTVVSYKDQNMAWGDLLNGRIDASLVMS 180
Cdd:cd13703   81 FTDKYYHTPSRLVARKGSGIDPTPASLKGKRVGVQRGTTQEAYATDNWAPKGVDIKRYATQDEAYLDLVSGRVDAALQDA 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556356369 181 AAGQAGFLSKPQGKGFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13703  161 VAAEEGFLKKPAGKDFAFVGPSVTDKKYFGEGVGIALRKDDTELKAKLNKAIAAIRADGTYDKIQKKYF 229
PBP2_HisJ_LAO_like cd01001
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and ...
21-249 7.83e-86

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: 254.91  E-value: 7.83e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  21 ATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd01001    1 ADTLRIGTEGDYPPFNFLDADGKLVGFDIDLANALCKRMKVKCEIVTQPWDGLIPALKAGKYDAIIASMSITDKRRQQID 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQPIYRIPSQLVGKAGSA-VEATPEGLKGKTIGVLQGSIQETYAKEHWekHGVTVVSYKDQNMAWGDLLNGRIDASLVM 179
Cdd:cd01001   81 FTDPYYRTPSRFVARKDSPiTDTTPAKLKGKRVGVQAGTTHEAYLRDRF--PEADLVEYDTPEEAYKDLAAGRLDAVFGD 158
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 180 SAAGQAGFLSKPQGKGFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd01001  159 KVALSEWLKKTKSGGCCKFVGPAVPDPKYFGDGVGIAVRKDDDALRAKLDKALAALKADGTYAEISKKYF 228
PRK15437 PRK15437
histidine ABC transporter substrate-binding protein HisJ; Provisional
3-249 2.19e-81

histidine ABC transporter substrate-binding protein HisJ; Provisional


Pssm-ID: 185334 [Multi-domain]  Cd Length: 259  Bit Score: 244.94  E-value: 2.19e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   3 LRALVVGIGLLCSFSS----FAA--TELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPG 76
Cdd:PRK15437   1 MKKLVLSLSLVLAFSSataaFAAipQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDALIPS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  77 LLAKKFDAINSAMNITEQRRKSIDFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKHGVTVV 156
Cdd:PRK15437  81 LKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIV 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 157 SYKDQNMAWGDLLNGRIDASLVMSAAGQAGFLSKPQGKGFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVR 236
Cdd:PRK15437 161 SYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMR 240
                        250
                 ....*....|...
gi 556356369 237 ADGTIAKLADKYF 249
Cdd:PRK15437 241 ADGTYEKLAKKYF 253
PRK15010 PRK15010
lysine/arginine/ornithine ABC transporter substrate-binding protein ArgT;
5-249 4.20e-81

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


Pssm-ID: 184972 [Multi-domain]  Cd Length: 260  Bit Score: 244.14  E-value: 4.20e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   5 ALVVGIGLLCSFSSFAA--TELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKF 82
Cdd:PRK15010   7 ALSLLVGLSAAASSYAAlpETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMCKRMQVKCTWVASDFDALIPSLKAKKI 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  83 DAINSAMNITEQRRKSIDFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKHGVTVVSYKDQN 162
Cdd:PRK15010  87 DAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLDSLKGKHVGVLQGSTQEAYANETWRSKGVDVVAYANQD 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 163 MAWGDLLNGRIDASLVMSAAGQAGFLSKPQGKGFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIA 242
Cdd:PRK15010 167 LVYSDLAAGRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELRQDGTYD 246

                 ....*..
gi 556356369 243 KLADKYF 249
Cdd:PRK15010 247 KMAKKYF 253
3A0103s03R TIGR01096
lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino ...
5-249 5.36e-79

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: 238.41  E-value: 5.36e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369    5 ALVVGIGLLCSFSSFAATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDA 84
Cdd:TIGR01096   7 ALVAGASSAATAAAAKEGSVRIGTETGYPPFESKDANGKLVGFDVDLAKALCKRMKAKCKFVEQNFDGLIPSLKAKKVDA 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   85 INSAMNITEQRRKSIDFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWeKHGVTVVSYKDQNMA 164
Cdd:TIGR01096  87 IMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDLAKTLEDLDGKTVGVQSGTTHEQYLKDYF-KPGVDIVEYDSYDNA 165
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  165 WGDLLNGRIDASLVMSAAGQAGFLSKPQGKGFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKL 244
Cdd:TIGR01096 166 NMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLRKGDTELKAAFNKALAAIRADGTYQKI 245

                  ....*
gi 556356369  245 ADKYF 249
Cdd:TIGR01096 246 SKKWF 250
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
24-250 5.08e-75

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: 227.56  E-value: 5.08e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQ 103
Cdd:COG0834    1 LRVGVDPDYPPFSFRDEDGKLVGFDVDLARAIAKRLGLKVEFVPVPWDRLIPALQSGKVDLIIAGMTITPEREKQVDFSD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 104 PIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKhgVTVVSYKDQNMAWGDLLNGRIDAsLVMSAAG 183
Cdd:COG0834   81 PYYTSGQVLLVRKDNSGIKSLADLKGKTVGVQAGTTYEEYLKKLGPN--AEIVEFDSYAEALQALASGRVDA-VVTDEPV 157
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556356369 184 QAGFLSKPQGKGFGFIGKPVSddtilGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYFP 250
Cdd:COG0834  158 AAYLLAKNPGDDLKIVGEPLS-----GEPYGIAVRKGDPELLEAVNKALAALKADGTLDKILEKWFG 219
PBP2_mlr5654_like cd13702
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
21-249 9.21e-74

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: 224.12  E-value: 9.21e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  21 ATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd13702    1 AKKIRIGTEGAYPPFNYVDADGKLGGFDVDIANALCAEMKAKCEIVAQDWDGIIPALQAKKFDAIIASMSITPERKKQVD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQPIYRIPSQLVGKAGSAVE-ATPEGLKGKTIGVLQGSIQETYAKEHWEKhgVTVVSYKDQNMAWGDLLNGRIDASLVM 179
Cdd:cd13702   81 FTDPYYTNPLVFVAPKDSTITdVTPDDLKGKVIGAQRSTTAAKYLEENYPD--AEVKLYDTQEEAYLDLASGRLDAVLSD 158
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 180 SAAgQAGFLSKPQGKGFGFIGKPVSDDTilgsGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13702  159 KFP-LLDWLKSPAGKCCELKGEPIADDD----GIGIAVRKGDTELREKFNKALAAIRADGTYKKINAKYF 223
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
23-248 4.07e-68

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: 209.41  E-value: 4.07e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFT 102
Cdd:cd13530    1 TLRVGTDADYPPFEYIDKNGKLVGFDVDLANAIAKRLGVKVEFVDTDFDGLIPALQSGKIDVAISGMTITPERAKVVDFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 103 QPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHweKHGVTVVSYKDQNMAWGDLLNGRIDAslVMSAA 182
Cdd:cd13530   81 DPYYYTGQVLVVKKDSKITKTVADLKGKKVGVQAGTTGEDYAKKN--LPNAEVVTYDNYPEALQALKAGRIDA--VITDA 156
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556356369 183 GQAGFLSKPQGKGFGFIGKPVSDDtilgsGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKY 248
Cdd:cd13530  157 PVAKYYVKKNGPDLKVVGEPLTPE-----PYGIAVRKGNPELLDAINKALAELKADGTLDKLLEKW 217
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
24-249 3.35e-65

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: 202.14  E-value: 3.35e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQ 103
Cdd:pfam00497   1 LRVGTDGDYPPFEYVDENGKLVGFDVDLAKAIAKRLGVKVEFVPVSWDGLIPALQSGKVDLIIAGMTITPERAKQVDFSD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  104 PIYRIPSQLVGKAGSAVE--ATPEGLKGKTIGVLQGSIQETYAKEHwEKHGVTVVSYKDQNMAWGDLLNGRIDAsLVMSA 181
Cdd:pfam00497  81 PYYYSGQVILVRKKDSSKsiKSLADLKGKTVGVQKGSTAEELLKNL-KLPGAEIVEYDDDAEALQALANGRVDA-VVADS 158
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556356369  182 AGQAGFLSKPQGKGFGFIGKPVSddtilGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:pfam00497 159 PVAAYLIKKNPGLNLVVVGEPLS-----PEPYGIAVRKGDPELLAAVNKALAELKADGTLAKIYEKWF 221
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
23-249 3.80e-61

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 191.77  E-value: 3.80e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369    23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFT 102
Cdd:smart00062   1 TLRVGTNGDYPPFSFADEDGELTGFDVDLAKAIAKELGLKVEFVEVSFDSLLTALKSGKIDVVAAGMTITPERAKQVDFS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   103 QPIYRIPSQLVGKAGSAVEaTPEGLKGKTIGVLQGSIQETYAKEhwEKHGVTVVSYKDQNMAWGDLLNGRIDAsLVMSAA 182
Cdd:smart00062  81 DPYYRSGQVILVRKDSPIK-SLEDLKGKKVAVVAGTTAEELLKK--LYPEAKIVSYDSNAEALAALKAGRADA-AVADAP 156
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556356369   183 GQAGFLSKPQGKGFGFIGKPVSDDTilgsGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:smart00062 157 LLAALVKQHGLPELKIVPDPLDTPE----GYAIAVRKGDPELLDKINKALKELKADGTLKKISEKWF 219
PBP2_Arg_Lys_His cd13624
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ...
23-249 1.96e-60

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: 190.01  E-value: 1.96e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFT 102
Cdd:cd13624    1 TLVVGTDATFPPFEFVDENGKIVGFDIDLIKAIAKEAGFEVEFKNMAFDGLIPALQSGKIDIIISGMTITEERKKSVDFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 103 QPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEkhGVTVVSYKDQNMAWGDLLNGRIDASLVMSAA 182
Cdd:cd13624   81 DPYYEAGQAIVVRKDSTIIKSLDDLKGKKVGVQIGTTGAEAAEKILK--GAKVKRFDTIPLAFLELKNGGVDAVVNDNPV 158
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556356369 183 GQAgFLSKPQGKGFGFIGKPVSDDtilgsGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13624  159 AAY-YVKQNPDKKLKIVGDPLTSE-----YYGIAVRKGNKELLDKINKALKKIKENGTYDKIYKKWF 219
PBP2_ml15202_like cd13701
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
21-249 3.10e-60

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: 189.98  E-value: 3.10e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  21 ATELRYGLEAE-YPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSI 99
Cdd:cd13701    1 ADPLKIGISAEpYPPFTSKDASGKWSGWEIDLIDALCARLDARCEITPVAWDGIIPALQSGKIDMIWNSMSITDERKKVI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 100 DFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWeKHGVTVVSYKDQNMAWGDLLNGRIDASLVM 179
Cdd:cd13701   81 DFSDPYYETPTAIVGAKSDDRRVTPEDLKGKVIGVQGSTNNATFARKHF-ADDAELKVYDTQDEALADLVAGRVDAVLAD 159
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 180 SAAGQAgFLSKPQGKGFGFIGKpVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13701  160 SLAFTE-FLKSDGGADFEVKGT-AADDPEFGLGIGAGLRQGDTALREKLNTAIASLRADGTYDEISARYF 227
PBP2_Arg_STM4351 cd13700
Substrate binding domain of arginine-specific ABC transporter; type 2 periplasmic-binding ...
21-249 1.00e-56

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: 180.72  E-value: 1.00e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  21 ATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd13700    1 AETIHFGTEATYPPFESIGAKGEIVGFDIDLANALCKQMQAECTFTNQAFDSLIPSLKFKKFDAVISGMDITPEREKQVS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQPIYRIPSQLVGKAGSAVeaTPEGLKGKTIGVLQGSIQETYAKEhwEKHGVTVVSYKDQNMAWGDLLNGRIDAslvms 180
Cdd:cd13700   81 FSTPYYENSAVVIAKKDTYK--TFADLKGKKIGVQNGTTHQKYLQD--KHKEITTVSYDSYQNAFLDLKNGRIDG----- 151
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 556356369 181 AAGQAGFLSK--PQGKGFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13700  152 VFGDTAVVAEwlKTNPDLAFVGEKVTDPNYFGTGLGIAVRKDNQALLEKLNAALAAIKANGEYQKIYDKWF 222
PBP2_Cystine_like cd13626
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ...
24-249 3.12e-56

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: 179.44  E-value: 3.12e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQ 103
Cdd:cd13626    2 LTVGTEGTYPPFTFKDEDGKLTGFDVEVGREIAKRLGLKVEFKATEWDGLLPGLNSGKFDVIANQVTITPEREEKYLFSD 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 104 PIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHweKHGVTVVSYKDQNMAWGDLLNGRIDASLVMSAAg 183
Cdd:cd13626   82 PYLVSGAQIIVKKDNTIIKSLEDLKGKVVGVSLGSNYEEVARDL--ANGAEVKAYGGANDALQDLANGRADATLNDRLA- 158
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556356369 184 qAGFLSKPQGKGFGFIGKPVSddtilGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13626  159 -ALYALKNSNLPLKIVGDIVS-----TAKVGFAFRKDNPELRKKVNKALAEMKADGTLKKLSEKWF 218
PBP2_OccT_like cd13699
Substrate binding domain of ABC-type octopine transporter-like; the type 2 periplasmic-binding ...
22-249 3.07e-55

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: 176.41  E-value: 3.07e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  22 TELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDF 101
Cdd:cd13699    2 KTLTIATEGAYAPWNLTDPDGKLGGFEIDLANVLCERMKVKCTFVVQDWDGMIPALNAGKFDVIMDAMSITAERKKVIDF 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 102 TQPiYripsqlvgkagsavEATPEGLKGKTIGVLQGSIQETYAKEHWeKHGVTVVSYKDQNMAWGDLLNGRIDASLVmSA 181
Cdd:cd13699   82 STP-Y--------------AATPNSFAVVTIGVQSGTTYAKFIEKYF-KGVADIREYKTTAERDLDLAAGRVDAVFA-DA 144
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556356369 182 AGQAGFLSKPQGKGFGFIGKPVSDDtILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13699  145 TYLAAFLAKPDNADLTLVGPKLSGD-IWGEGEGVGLRKGDTELKAKFDSAIKAAVADGTVKKLSEKWF 211
PBP2_MidA_like cd01004
Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 ...
23-248 2.11e-53

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: 172.43  E-value: 2.11e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFT 102
Cdd:cd01004    3 TLTVGTNPTYPPYEFVDEDGKLIGFDVDLAKAIAKRLGLKVEIVNVSFDGLIPALQSGRYDIIMSGITDTPERAKQVDFV 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 103 qPIYRIPSQLVGKAGSAVEAT-PEGLKGKTIGVLQGSIQETYAKEHWE------KHGVTVVSYKDQNMAWGDLLNGRIDA 175
Cdd:cd01004   83 -DYMKDGLGVLVAKGNPKKIKsPEDLCGKTVAVQTGTTQEQLLQAANKkckaagKPAIEIQTFPDQADALQALRSGRADA 161
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556356369 176 slVMSAAGQAGFLSKPQGKGFGFIGKPVSDDTilgsGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKY 248
Cdd:cd01004  162 --YLSDSPTAAYAVKQSPGKLELVGEVFGSPA----PIGIAVKKDDPALADAVQAALNALIADGTYKKILKKW 228
PRK15007 PRK15007
arginine ABC transporter substrate-binding protein;
5-249 7.58e-52

arginine ABC transporter substrate-binding protein;


Pssm-ID: 184969 [Multi-domain]  Cd Length: 243  Bit Score: 169.06  E-value: 7.58e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   5 ALVVGIgllcSFSSFAATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDA 84
Cdd:PRK15007   8 ALIAGF----SLSATAAETIRFATEASYPPFESIDANNQIVGFDVDLAQALCKEIDATCTFSNQAFDSLIPSLKFRRVEA 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  85 INSAMNITEQRRKSIDFTQPIYRIPSQLVGKAGSAveATPEGLKGKTIGVLQGSiqeTYAKEHWEKH-GVTVVSYKDQNM 163
Cdd:PRK15007  84 VMAGMDITPEREKQVLFTTPYYDNSALFVGQQGKY--TSVDQLKGKKVGVQNGT---THQKFIMDKHpEITTVPYDSYQN 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 164 AWGDLLNGRIDASLVMSAAGQAGFLSKPQgkgFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAK 243
Cdd:PRK15007 159 AKLDLQNGRIDAVFGDTAVVTEWLKDNPK---LAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYET 235

                 ....*.
gi 556356369 244 LADKYF 249
Cdd:PRK15007 236 IYNKWF 241
PBP2_Cystine_like_1 cd13713
Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ...
23-249 6.40e-50

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: 163.22  E-value: 6.40e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFT 102
Cdd:cd13713    1 ELRFAMSGQYPPFNFLDEDNQLVGFDVDVAKAIAKRLGVKVEPVTTAWDGIIAGLWAGRYDIIIGSMTITEERLKVVDFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 103 QPIYRIPSQLVGKAGSAVeATPEGLKGKTIGVLQGSIQETYAKEHWEkhGVTVVSYKDQNMAWGDLLNGRIDASL----- 177
Cdd:cd13713   81 NPYYYSGAQIFVRKDSTI-TSLADLKGKKVGVVTGTTYEAYARKYLP--GAEIKTYDSDVLALQDLALGRLDAVItdrvt 157
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556356369 178 VMSAAGQAGFLSKPqgkgfgfIGKPVSDDtilgsGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13713  158 GLNAIKEGGLPIKI-------VGKPLYYE-----PMAIAIRKGDPELRAAVNKALAEMKADGTLEKISKKWF 217
PBP2_ArtJ cd00999
The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold ...
19-248 5.04e-49

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: 160.95  E-value: 5.04e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  19 FAATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKS 98
Cdd:cd00999    1 MDKDVIIVGTESTYPPFEFRDEKGELVGFDIDLAEAISEKLGKKLEWRDMAFDALIPNLLTGKIDAIAAGMSATPERAKR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  99 IDFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKehwEKHGVTVVSYKDQNMAWGDLLNGRIDASLV 178
Cdd:cd00999   81 VAFSPPYGESVSAFVTVSDNPIKPSLEDLKGKSVAVQTGTIQEVFLR---SLPGVEVKSFQKTDDCLREVVLGRSDAAVM 157
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 179 MSAAGQAgFLSKPQgkgFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKY 248
Cdd:cd00999  158 DPTVAKV-YLKSKD---FPGKLATAFTLPEWGLGKALAVAKDDPALKEAVNKALDELKKEGELAALRKKW 223
PBP2_FliY cd13712
Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ...
24-249 8.96e-49

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: 160.24  E-value: 8.96e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQ 103
Cdd:cd13712    2 LRIGLEGTYPPFNFKDETGQLTGFEVDVAKALAAKLGVKPEFVTTEWSGILAGLQAGKYDVIINQVGITPERQKKFDFSQ 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 104 P-IYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEkhGVTVVSYKDQNMAWGDLLNGRIDASLVMSAA 182
Cdd:cd13712   82 PyTYSGIQLIVRKNDTRTFKSLADLKGKKVGVGLGTNYEQWLKSNVP--GIDVRTYPGDPEKLQDLAAGRIDAALNDRLA 159
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556356369 183 gqAGFLSKPQGKgfgfigKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13712  160 --ANYLVKTSLE------LPPTGGAFARQKSGIPFRKGNPKLKAAINKAIEDLRADGTLAKLSEKWF 218
PBP2_Dsm1740 cd13629
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ...
23-249 2.95e-48

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: 158.89  E-value: 2.95e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFT 102
Cdd:cd13629    1 VLRVGMEAGYPPFEMTDKKGELIGFDVDLAKALAKDLGVKVEFVNTAWDGLIPALQTGKFDLIISGMTITPERNLKVNFS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 103 QPiYRIPSQ--LVGKAGSAVEATPEGL--KGKTIGVLQGSIQETYAKEHWEKhgVTVVSYKDQNMAWGDLLNGRIDAslV 178
Cdd:cd13629   81 NP-YLVSGQtlLVNKKSAAGIKSLEDLnkPGVTIAVKLGTTGDQAARKLFPK--ATILVFDDEAAAVLEVVNGKADA--F 155
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 556356369 179 MSAAGQAGFLSKPQGKGFGFIGKPVSDdtilgSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13629  156 IYDQPTPARFAKKNDPTLVALLEPFTY-----EPLGFAIRKGDPDLLNWLNNFLKQIKGDGTLDELYDKWF 221
PBP2_GlnH cd00994
Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; ...
23-249 3.03e-43

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: 145.88  E-value: 3.03e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNaSGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFT 102
Cdd:cd00994    1 TLTVATDTTFVPFEFKQ-DGKYVGFDIDLWEAIAKEAGFKYELQPMDFKGIIPALQTGRIDIAIAGITITEERKKVVDFS 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 103 QPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKHGVTVVSYKDQnmAWGDLLNGRIDAslVMSAA 182
Cdd:cd00994   80 DPYYDSGLAVMVKADNNSIKSIDDLAGKTVAVKTGTTSVDYLKENFPDAQLVEFPNIDN--AYMELETGRADA--VVHDT 155
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556356369 183 GQAGFLSKPQGKGfgfiGKPVSDDTILGSGIGFGLRKGDEATKKqLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd00994  156 PNVLYYAKTAGKG----KVKVVGEPLTGEQYGIAFPKGSELREK-VNAALKTLKADGTYDEIYKKWF 217
PRK11260 PRK11260
cystine ABC transporter substrate-binding protein;
4-255 5.52e-43

cystine ABC transporter substrate-binding protein;


Pssm-ID: 183061 [Multi-domain]  Cd Length: 266  Bit Score: 146.79  E-value: 5.52e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   4 RALVVGIGLL----CSFSSFAATE----------LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETS 69
Cdd:PRK11260   9 QALMGVMAVAlvagMSVKSFADEGllnkvkergtLLVGLEGTYPPFSFQGEDGKLTGFEVEFAEALAKHLGVKASLKPTK 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  70 FDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQPiYRIP--SQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEH 147
Cdd:PRK11260  89 WDGMLASLDSKRIDVVINQVTISDERKKKYDFSTP-YTVSgiQALVKKGNEGTIKTAADLKGKKVGVGLGTNYEQWLRQN 167
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 148 WEkhGVTVVSYKDQNMAWGDLLNGRIDASLVMSAAgqAGFLSKPQGKGFGFIGKPVSDdtiLGSGIgfGLRKGDEATKKQ 227
Cdd:PRK11260 168 VQ--GVDVRTYDDDPTKYQDLRVGRIDAILVDRLA--ALDLVKKTNDTLAVAGEAFSR---QESGV--ALRKGNPDLLKA 238
                        250       260
                 ....*....|....*....|....*...
gi 556356369 228 LDAAIDKVRADGTIAKLADKYFpGIDVS 255
Cdd:PRK11260 239 VNQAIAEMQKDGTLKALSEKWF-GADVT 265
PBP2_Cys_DEBP_like cd01000
Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ...
24-249 1.40e-40

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: 139.37  E-value: 1.40e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAA---ALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd01000   10 LIVGVKPDLPPFGARDANGKIQGFDVDVAKALAKDLlgdPVKVKFVPVTSANRIPALQSGKVDLIIATMTITPERAKEVD 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQPIYRIPSQLVGKAGSAVEaTPEGLKGKTIGVLQGSIQETYAKEHWEKhgVTVVSYKDQNMAWGDLLNGRIDAsLVMS 180
Cdd:cd01000   90 FSVPYYADGQGLLVRKDSKIK-SLEDLKGKTILVLQGSTAEAALRKAAPE--AQLLEFDDYAEAFQALESGRVDA-MATD 165
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556356369 181 AAGQAGFLSKPQGKgFGFIGKPVSDDTilgsgIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd01000  166 NSLLAGWAAENPDD-YVILPKPFSQEP-----YGIAVRKGDTELLKAVNATIAKLKADGELAEIYKKWL 228
PBP2_Ala cd13628
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ...
24-248 1.99e-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: 138.76  E-value: 1.99e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNAS-GELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFT 102
Cdd:cd13628    2 LNMGTSPDYPPFEFKIGDrGKIVGFDIELAKTIAKKLGLKLQIQEYDFNGLIPALASGQADLALAGITPTPERKKVVDFS 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 103 QPIYRIPSQLVGKAGSAVEAtPEGLKGKTIGVLQGSIQETYAKEHWEKH-GVTVVSYKDQNMAWGDLLNGRIDASLVMSA 181
Cdd:cd13628   82 EPYYEASDTIVS*KDRKIKQ-LQDLNGKSLGVQLGTIQEQLIKELSQPYpGLKTKLYNRVNELVQALKSGRVDAAIVEDI 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556356369 182 AGQAGFLSKPQGKGFGFIGKPVSddtilGSGIGFglRKGDEATKKqLDAAIDKVRADGTIAKLADKY 248
Cdd:cd13628  161 VAETFAQKKN*LLESRYIPKEAD-----GSAIAF--PKGSPLRDD-FNRWLKEMGDSGELELMVRRW 219
PBP2_AA_binding_like_1 cd13625
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
20-248 1.17e-39

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: 137.12  E-value: 1.17e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  20 AATELRYGLEAEYPPFESRNAsGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSI 99
Cdd:cd13625    3 KRGTITVATEADYAPFEFVEN-GKIVGFDRDLLDEMAKKLGVKVEQQDLPWSGILPGLLAGKFDMVATSVTITKERAKRF 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 100 DFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWE----KHG---VTVVSYKDQNMAWGDLLNGR 172
Cdd:cd13625   82 AFTLPIAEATAALLKRAGDDSIKTIEDLAGKVVGVQAGSAQLAQLKEFNEtlkkKGGngfGEIKEYVSYPQAYADLANGR 161
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556356369 173 IDAslVMSAAGQAGFLSKPQGKGFGfIGKPVSDDTIlgsgIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKY 248
Cdd:cd13625  162 VDA--VANSLTNLAYLIKQRPGVFA-LVGPVGGPTY----FAWVIRKGDAELRKAINDALLALKKSGKLAALQQKW 230
PBP2_AatB_like cd00996
Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong ...
27-249 4.72e-39

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: 135.40  E-value: 4.72e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  27 GLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQPiY 106
Cdd:cd00996    9 GLDDTFAPMGFRDENGEIVGFDIDLAKEVAKRLGVEVEFQPIDWDMKETELNSGNIDLIWNGLTITDERKKKVAFSKP-Y 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 107 RIPSQ-LVGKAGSAVeATPEGLKGKTIGVLQGSIQETyAKEHWEKHGVT---VVSYKDQNMAWGDLLNGRIDASLVMSAA 182
Cdd:cd00996   88 LENRQiIVVKKDSPI-NSKADLKGKTVGVQSGSSGED-ALNADPNLLKKnkeVKLYDDNNDAFMDLEAGRIDAVVVDEVY 165
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556356369 183 GQAgFLSKpqgkgfgfigKPVSDDTILGSGI-----GFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd00996  166 ARY-YIKK----------KPLDDYKILDESFgseeyGVGFRKEDTELKEKINKALDEMKADGTAAKISQKWF 226
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
21-249 3.08e-37

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: 130.40  E-value: 3.08e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  21 ATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAInSAMNITEQRRKSID 100
Cdd:cd13704    1 ARTVIVGGDKNYPPYEFLDENGNPTGFNVDLLRAIAEEMGLKVEIRLGPWSEVLQALENGEIDVL-IGMAYSEERAKLFD 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHweKHGVTVVSYKDQNMAWGDLLNGRIDASLVMS 180
Cdd:cd13704   80 FSDPYLEVSVSIFVRKGSSIINSLEDLKGKKVAVQRGDIMHEYLKER--GLGINLVLVDSPEEALRLLASGKVDAAVVDR 157
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556356369 181 AAGQAgFLSKPQGKGFGFIGKPvsddtILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13704  158 LVGLY-LIKELGLTNVKIVGPP-----LLPLKYCFAVRKGNPELLAKLNEGLAILKASGEYDEIYEKWF 220
PBP2_HisGluGlnArgOpine cd13698
Substrate binding domain of ABC-type histidine/glutamate/glutamine/arginine/opine transporter; ...
21-249 1.58e-36

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: 128.57  E-value: 1.58e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  21 ATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd13698    1 GKTIRMGTEGAYPPYNFINDAGEVDGFERELGDELCKRAELTCEWVTNEWDSIIPNLVSGNYDTIIAGMSITDERDEVID 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQPIYRipsqlvgKAGSAVEATPEGLK--GKTIGVLQGSIQETYAKEhwekHGVTVVSYKDQNMAWGDLLNGRIDASLV 178
Cdd:cd13698   81 FTQNYIP-------PTASAYVALSDDADdiGGVVAAQTSTIQAGHVAE----SGATLLEFATPDETVAAVRNGEADAVFA 149
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 556356369 179 MSAAGQAgfLSKPQGKGFGFIGkpvsDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13698  150 DKDYLVP--IVEESGGELMFVG----DDVPLGGGIGMGLRESDGELREKFDAAITSMKEDGSLNTLLKKWF 214
PBP2_BsGlnH cd13689
Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ...
23-249 1.20e-35

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: 126.58  E-value: 1.20e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNA-SGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDF 101
Cdd:cd13689    9 VLRCGVFDDVPPFGFIDPkTREIVGFDVDLCKAIAKKLGVKLELKPVNPAARIPELQNGRVDLVAANLTYTPERAEQIDF 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 102 TQPIYRIPSQLVGKAGSAVeATPEGLKGKTIGVLQGSIQETYAKEHWEKhgVTVVSYKDQNMAWGDLLNGRIDAsLVMSA 181
Cdd:cd13689   89 SDPYFVTGQKLLVKKGSGI-KSLKDLAGKRVGAVKGSTSEAAIREKLPK--ASVVTFDDTAQAFLALQQGKVDA-ITTDE 164
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556356369 182 AGQAGFLSK-PQGKGFGFIGKPVSDDTilgsgIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13689  165 TILAGLLAKaPDPGNYEILGEALSYEP-----YGIGVPKGESALRDFVNETLADLEKDGEADKIYDKWF 228
PBP2_GlnP cd13619
Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold ...
27-248 1.25e-35

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: 126.28  E-value: 1.25e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  27 GLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQPIY 106
Cdd:cd13619    5 ATDSTFAPFEFQNDDGKYVGIDVDLLNAIAKDQGFKVELKPMGFDAAIQAVQSGQADGVIAGMSITDERKKTFDFSDPYY 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 107 RIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKHGVTVVSYKDQNMAWGDLLNGRIDASL----VMSAA 182
Cdd:cd13619   85 DSGLVIAVKKDNTSIKSYEDLKGKTVAVKNGTAGATFAESNKEKYGYTIKYFDDSDSMYQAVENGNADAAMddypVIAYA 164
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556356369 183 GQagflskpQGKGFGFIGKPvsddtILGSGIGFGLRKGDEAT-KKQLDAAIDKVRADGTIAKLADKY 248
Cdd:cd13619  165 IK-------QGQKLKIVGDK-----ETGGSYGFAVKKGQNPElLEKFNKGLKNLKANGEYDKILNKY 219
PBP2_Ngo0372_TcyA cd13711
Substrate binding domain of ABC transporters involved in cystine import; the type 2 ...
23-254 1.62e-35

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: 126.26  E-value: 1.62e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFT 102
Cdd:cd13711    2 VLTIGTEGTYAPFTYHDKSGKLTGFDVEVARAVAKKLGVKVEFVETQWDSMIAGLDAGRFDVVANQVGITDERKKKYDFS 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 103 QPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSiqeTYAKEHwEKHGVTVVSYKDQNMAWGDLLNGRIDASLVMSAA 182
Cdd:cd13711   82 TPYIYSRAVLIVRKDNSDIKSFADLKGKKSAQSLTS---NWGKIA-KKYGAQVVGVDGFAQAVELITQGRADATINDSLA 157
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556356369 183 GQAGFLSKPqgkgfgfiGKPV--SDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYFpGIDV 254
Cdd:cd13711  158 FLDYKKQHP--------DAPVkiAAETDDASESAFLVRKGNDELVAAINKALKELKADGTLKKISEKYF-GKDV 222
PBP2_YxeM cd13709
Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein ...
22-255 1.41e-34

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: 124.00  E-value: 1.41e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  22 TELRYGLEAEYPPFeSRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDF 101
Cdd:cd13709    1 KVIKVGSSGSSYPF-TFKENGKLKGFEVDVWNAIGKRTGYKVEFVTADFSGLFGMLDSGKVDTIANQITITPERQEKYDF 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 102 TQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKHGVTVVSYKDQNMAWGDLLNGRIDAsLVMSA 181
Cdd:cd13709   80 SEPYVYDGAQIVVKKDNNSIKSLEDLKGKTVAVNLGSNYEKILKAVDKDNKITIKTYDDDEGALQDVALGRVDA-YVNDR 158
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556356369 182 AgQAGFLSKPQGKGFGFIGKPVSDDTilgsgIGFGLRKGDEATK--KQLDAAIDKVRADGTIAKLADKYFpGIDVS 255
Cdd:cd13709  159 V-SLLAKIKKRGLPLKLAGEPLVEEE-----IAFPFVKNEKGKKllEKVNKALEEMRKDGTLKKISEKWF-GIDIT 227
PBP2_Arg_3 cd13622
Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding ...
24-249 2.67e-34

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: 123.18  E-value: 2.67e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQ 103
Cdd:cd13622    4 LIVGVGKFNPPFEMQGTNNELFGFDIDLMNEICKRIQRTCQYKPMRFDDLLAALNNGKVDVAISSISITPERSKNFIFSL 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 104 PIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKHgVTVVSYKDQNMAWGDLLNGRIDASLVMSAAg 183
Cdd:cd13622   84 PYLLSYSQFLTNKDNNISSFLEDLKGKRIGILKGTIYKDYLLQMFVIN-PKIIEYDRLVDLLEALNNNEIDAILLDNPI- 161
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556356369 184 qAGFLSKPQGKGFGFIGKPVSDdtilGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13622  162 -AKYWASNSSDKFKLIGKPIPI----GNGLGIAVNKDNAALLTKINKALLEIENDGTYLKIYNKYF 222
PBP2_SMa0082_like cd01072
The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic ...
24-249 5.53e-30

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: 112.36  E-value: 5.53e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQ 103
Cdd:cd01072   15 LKVGVLVDAPPFGFVDASMQPQGYDVDVAKLLAKDLGVKLELVPVTGANRIPYLQTGKVDMLIASLGITPERAKVVDFSQ 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 104 PIYRIPSQLVGKAGSAVEaTPEGLKGKTIGVLQGSIQETyAKEHWEKHGVTVVSYKDQNMAWGDLLNGRIDASLVMSAag 183
Cdd:cd01072   95 PYAAFYLGVYGPKDAKVK-SPADLKGKTVGVTRGSTQDI-ALTKAAPKGATIKRFDDDASTIQALLSGQVDAIATGNA-- 170
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556356369 184 QAGFLSKPQGKgfgfiGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd01072  171 IAAQIAKANPD-----KKYELKFVLRTSPNGIGVRKGEPELLKWVNTFIAKNKANGELNALSQKWF 231
PBP2_Ehub_like cd01002
Substrate binding domain of ectoine/hydroxyectoine specific ABC transport system; the type 2 ...
30-248 6.72e-29

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: 109.29  E-value: 6.72e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  30 AEYPPFESRNASGELEGFDVELGNAICKAAALK-CSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQPIYRI 108
Cdd:cd01002   17 ANEPPYAYIDADGEVTGESPEVARAVLKRLGVDdVEGVLTEFGSLIPGLQAGRFDVIAAGMFITPERCEQVAFSEPTYQV 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 109 PSQLVGKAGSaveatPEGLK---------GKTIGVLQGSIQETYAKEhwekHGVT---VVSYKDQNMAWGDLLNGRIDAs 176
Cdd:cd01002   97 GEAFLVPKGN-----PKGLHsyadvaknpDARLAVMAGAVEVDYAKA----SGVPaeqIVIVPDQQSGLAAVRAGRADA- 166
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556356369 177 LVMSAAGQAGFLSKPQGKGFGFI--GKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKY 248
Cdd:cd01002  167 FALTALSLRDLAAKAGSPDVEVAepFQPVIDGKPQIGYGAFAFRKDDTDLRDAFNAELAKFKGSGEHLEILEPF 240
PBP2_Atu4678_like cd13696
The substrate binding domain of putative amino acid transporter; the type 2 periplasmic ...
24-249 4.01e-26

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: 101.69  E-value: 4.01e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQ 103
Cdd:cd13696   10 LRCGVCLDFPPFGFRDAAGNPVGYDVDYAKDLAKALGVKPEIVETPSPNRIPALVSGRVDVVVANTTRTLERAKTVAFSI 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 104 PIYRIPSQLVGKAGSAVeATPEGLKGKTIGVLQGSIQETYAKEHWEKhgVTVVSYKDQNMAWGDLLNGRIDASLVMS--A 181
Cdd:cd13696   90 PYVVAGMVVLTRKDSGI-KSFDDLKGKTVGVVKGSTNEAAVRALLPD--AKIQEYDTSADAILALKQGQADAMVEDNtvA 166
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556356369 182 AGQAgflSKPQGKGFGFIGK-PVSDDTilgsgIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13696  167 NYKA---SSGQFPSLEIAGEaPYPLDY-----VAIGVRKGDYDWLRYLNLFVFQQNASGRYAELYQKWF 227
PBP2_GltS cd13620
Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 ...
24-247 2.01e-25

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: 99.72  E-value: 2.01e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFE---SRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd13620    6 LVVGTSADYAPFEfqkMKDGKNQVVGADIDIAKAIAKELGVKLEIKSMDFDNLLASLQSGKVDMAISGMTPTPERKKSVD 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQPIYR-IPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEhwEKHGVTVVSYKDQNMAWGDLLNGRIDAsLVM 179
Cdd:cd13620   86 FSDVYYEaKQSLLVKKADLDKYKSLDDLKGKKIGAQKGSTQETIAKD--QLKNAKLKSLTKVGDLILELKSGKVDG-VIM 162
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556356369 180 SAAGQAGFLSKPqgKGFGFIGKPVSDDTILGSGIgfGLRKGDEATKKQLDAAIDKVRADGTIAKLADK 247
Cdd:cd13620  163 EEPVAKGYANNN--SDLAIADVNLENKPDDGSAV--AIKKGSKDLLDAVNKTIKKLKDSGQIDKFVED 226
PBP2_GltI_DEBP cd13688
Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic ...
33-249 7.16e-25

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: 98.86  E-value: 7.16e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  33 PPFESRNASGELEGFDVELGNAIckAAALKCS---------WVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQ 103
Cdd:cd13688   19 VPFSYLDDNGKPVGYSVDLCNAI--ADALKKKlalpdlkvrYVPVTPQDRIPALTSGTIDLECGATTNTLERRKLVDFSI 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 104 PIYRIPSQLVGKAGSAVEaTPEGLKGKTIGVLQGSIQETYAKEHWEKHGV--TVVSYKDQNMAWGDLLNGRIDAsLVMSA 181
Cdd:cd13688   97 PIFVAGTRLLVRKDSGLN-SLEDLAGKTVGVTAGTTTEDALRTVNPLAGLqaSVVPVKDHAEGFAALETGKADA-FAGDD 174
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556356369 182 AGQAGFLSK-PQGKGFGFIGKPVSddtilGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13688  175 ILLAGLAARsKNPDDLALIPRPLS-----YEPYGLMLRKDDPDFRLLVDRALAQLYQSGEIEKLYDKWF 238
PBP2_YfhD_N cd01009
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ...
41-249 1.99e-23

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: 94.59  E-value: 1.99e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  41 SGELEGFDVELGNAICKAAALKCSWVET-SFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQPIYRIPSQLVGKAGSA 119
Cdd:cd01009   18 RGGPRGFEYELAKAFADYLGVELEIVPAdNLEELLEALEEGKGDLAAAGLTITPERKKKVDFSFPYYYVVQVLVYRKGSP 97
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 120 VEATPEGLKGKTIGVLQGSIQETYAKEHWEKHGVTVVSYKDQNMAwGDLL----NGRIDASLVMS--AAGQAGFLskPQg 193
Cdd:cd01009   98 RPRSLEDLSGKTIAVRKGSSYAETLQKLNKGGPPLTWEEVDEALT-EELLemvaAGEIDYTVADSniAALWRRYY--PE- 173
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 556356369 194 kgfgfigkpVSDDTILG--SGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd01009  174 ---------LRVAFDLSepQPLAWAVRKNSPSLLAALNRFLAQIKKDGTLARLYERYY 222
PBP2_GluB cd13690
Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein ...
23-250 9.03e-23

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: 93.10  E-value: 9.03e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRN-ASGELEGFDVELGNAICKA---AALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKS 98
Cdd:cd13690    9 RLRVGVKFDQPGFSLRNpTTGEFEGFDVDIARAVARAiggDEPKVEFREVTSAEREALLQNGTVDLVVATYSITPERRKQ 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  99 IDFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHweKHGVTVVSYKDQNMAWGDLLNGRIDAsLV 178
Cdd:cd13690   89 VDFAGPYYTAGQRLLVRAGSKIITSPEDLNGKTVCTAAGSTSADNLKKN--APGATIVTRDNYSDCLVALQQGRVDA-VS 165
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556356369 179 MSAAGQAGFLSKPQGkGFGFIGKPVSDDtilgsGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYFP 250
Cdd:cd13690  166 TDDAILAGFAAQDPP-GLKLVGEPFTDE-----PYGIGLPKGDDELVAFVNGALEDMRADGTWQALFDRWLG 231
glnH PRK09495
glutamine ABC transporter periplasmic protein; Reviewed
1-249 1.06e-22

glutamine ABC transporter periplasmic protein; Reviewed


Pssm-ID: 236540 [Multi-domain]  Cd Length: 247  Bit Score: 93.27  E-value: 1.06e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   1 MKLRALVVGIGLLCSF---SSFAATELRYGLEAEYPPFESRNASgELEGFDVELGNAICKAAALKCSWVETSFDALIPGL 77
Cdd:PRK09495   1 MKSVLKVSLAALTLAFavsSHAADKKLVVATDTAFVPFEFKQGD-KYVGFDIDLWAAIAKELKLDYTLKPMDFSGIIPAL 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  78 LAKKFDAINSAMNITEQRRKSIDFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEkhGVTVVS 157
Cdd:PRK09495  80 QTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDIKSVKDLDGKVVAVKSGTGSVDYAKANIK--TKDLRQ 157
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 158 YKDQNMAWGDLLNGRIDAslVMSAAGQAGFLSKPQGKG-FGFIGKPVSDDTIlgsGIGFglRKGDEATKKqLDAAIDKVR 236
Cdd:PRK09495 158 FPNIDNAYLELGTGRADA--VLHDTPNILYFIKTAGNGqFKAVGDSLEAQQY---GIAF--PKGSELREK-VNGALKTLK 229
                        250
                 ....*....|...
gi 556356369 237 ADGTIAKLADKYF 249
Cdd:PRK09495 230 ENGTYAEIYKKWF 242
PBP2_BvgS_HisK_like cd01007
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
23-249 1.89e-22

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: 91.83  E-value: 1.89e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVET-SFDALIPGLLAKKFDAInSAMNITEQRRKSIDF 101
Cdd:cd01007    3 VIRVGVDPDWPPFEFIDEGGEPQGIAADYLKLIAKKLGLKFEYVPGdSWSELLEALKAGEIDLL-SSVSKTPEREKYLLF 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 102 TQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEkhGVTVVSYKDQNMAWGDLLNGRIDAsLVMSA 181
Cdd:cd01007   82 TKPYLSSPLVIVTRKDAPFINSLSDLAGKRVAVVKGYALEELLRERYP--NINLVEVDSTEEALEAVASGEADA-YIGNL 158
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556356369 182 AgQAGFLSkpqgKGFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADgTIAKLADKYF 249
Cdd:cd01007  159 A-VASYLI----QKYGLSNLKIAGLTDYPQDLSFAVRKDWPELLSILNKALASISPE-ERQAIRNKWL 220
PBP2_AA_binding_like_2 cd13627
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
24-248 6.89e-22

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: 90.92  E-value: 6.89e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFE------SRNA-------SGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMN 90
Cdd:cd13627    2 LRVGMEAAYAPFNwtqetaSEYAipiingqGGYADGYDVQIAKKLAEKLDMKLVIKKIEWNGLIPALNSGDIDLIIAGMS 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  91 ITEQRRKSIDFTQPIYRIPSQLVGKAGSAVE--ATPEGLKGKTIGVLQGSIQETYAKEhwEKHGVTVVSYKDQNMAWGDL 168
Cdd:cd13627   82 KTPEREKTIDFSDPYYISNIVMVVKKDSAYAnaTNLSDFKGATITGQLGTMYDDVIDQ--IPDVVHTTPYDTFPTMVAAL 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 169 LNGRIDASLVMSAAGQAGFLSKPQ------GKGFGFIGKPVSDDtilgsgIGFGLRKGDEATKKQLDAAIDKVRADgTIA 242
Cdd:cd13627  160 QAGTIDGFTVELPSAISALETNPDlviikfEQGKGFMQDKEDTN------VAIGCRKGNDKLKDKINEALKGISSE-ERD 232

                 ....*.
gi 556356369 243 KLADKY 248
Cdd:cd13627  233 EMMDKA 238
ectoine_ehuB TIGR02995
ectoine/hydroxyectoine ABC transporter solute-binding protein; Members of this family are the ...
30-248 1.04e-21

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: 91.13  E-value: 1.04e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   30 AEYPPFESRNASGELEGFDVELGNAICKAAALK-CSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQPIYRI 108
Cdd:TIGR02995  40 ANEPPFTYVGADGKVSGAAPDVARAIFKRLGIAdVNASITEYGALIPGLQAGRFDAIAAGLFIKPERCKQVAFTQPILCD 119
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  109 PSQLVGKAGSaveatPEGLKG---------KTIGVLQGSIQETYAKEHWEKHGvTVVSYKDQNMAWGDLLNGRIDASL-- 177
Cdd:TIGR02995 120 AEALLVKKGN-----PKGLKSykdiaknpdAKIAAPGGGTEEKLAREAGVKRE-QIIVVPDGQSGLKMVQDGRADAYSlt 193
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 556356369  178 VMSAAGqagfLSKPQGKGFGFIGKPVSDDTILGSGiGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKY 248
Cdd:TIGR02995 194 VLTIND----LASKAGDPNVEVLAPFKDAPVRYYG-GAAFRPEDKELRDAFNVELAKLKESGEFAKIIAPY 259
PBP2_TcyK cd13710
Substrate binding domain of an ABC transporter TcyJKLMN; the type 2 periplasmic binding ...
22-255 1.47e-21

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: 89.66  E-value: 1.47e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  22 TELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAA-LKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd13710    1 KTVKVATGADTPPFSYEDKKGELTGYDIEVLKAIDKKLPqYKFKFKVTEFSSILTGLDSGKYDMAANNFSKTKERAKKFL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FT-QPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQ----ETYAKEHWEKHGVTVVSYKDQNMAWGDLLNGRIDA 175
Cdd:cd13710   81 FSkVPYGYSPLVLVVKKDSNDINSLDDLAGKTTIVVAGTNYakvlEAWNKKNPDNPIKIKYSGEGINDRLKQVESGRYDA 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 176 sLVMSAAGQAgFLSKPQGKGFGFIGKPVSDDTilgsGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYFpGIDVS 255
Cdd:cd13710  161 -LILDKFSVD-TIIKTQGDNLKVVDLPPVKKP----YVYFLFNKDQQKLQKDIDKALKELKKDGTLKKLSKKYF-GGDYF 233
PBP2_polar_AA cd13693
Substrate binding domain of polar amino-acid uptake ABC transporter; the type 2 periplasmic ...
23-248 2.18e-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: 89.30  E-value: 2.18e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAIckAAALKCSWVETSFDAL--IPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd13693    9 KLIVGVKNDYPPFGFLDPSGEIVGFEVDLAKDI--AKRLGVKLELVPVTPSnrIQFLQQGKVDLLIATMGDTPERRKVVD 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQP-IYRIPSQLVGKAGSAVEaTPEGLKGKTIGVLQGSiqeTYAKEHWEKHGVTVVSYKDQNMAWGDLLNGRIDASLVM 179
Cdd:cd13693   87 FVEPyYYRSGGALLAAKDSGIN-DWEDLKGKPVCGSQGS---YYNKPLIEKYGAQLVAFKGTPEALLALRDGRCVAFVYD 162
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556356369 180 SAAGQAGFLSKPQGKGFGfigkpVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKY 248
Cdd:cd13693  163 DSTLQLLLQEDGEWKDYE-----IPLPTIEPSPWVIAVRKGETAFQNALDEIIKDWHRTGKLIELEKKW 226
PBP2_Cysteine cd13694
Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein ...
24-249 2.54e-21

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: 88.95  E-value: 2.54e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAA---ALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSID 100
Cdd:cd13694   10 IRIGVFGDKPPFGYVDENGKFQGFDIDLAKQIAKDLfgsGVKVEFVLVEAANRVPYLTSGKVDLILANFTVTPERAEVVD 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 101 FTQPIYRIPSQLVGKAGSAVEaTPEGLKGKTIGVLQGSIQETYAKEhwEKHGVTVVSYKDQNMAWGDLLNGRIDA----- 175
Cdd:cd13694   90 FANPYMKVALGVVSPKDSNIT-SVAQLDGKTLLVNKGTTAEKYFTK--NHPEIKLLKYDQNAEAFQALKDGRADAyahdn 166
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556356369 176 SLVMSAAgqagflskPQGKGFGFIGKPVSDDtilgSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13694  167 ILVLAWA--------KSNPGFKVGIKNLGDT----DFIAPGVQKGNKELLEFINAEIKKLGKENFFKKAYEKTL 228
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
42-249 5.12e-19

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


Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 85.50  E-value: 5.12e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  42 GELEGFDVELGNAICKAAALKCSW-VETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQPIYRIPSQLVGKAGSAV 120
Cdd:COG4623   40 GGPMGFEYELAKAFADYLGVKLEIiVPDNLDELLPALNAGEGDIAAAGLTITPERKKQVRFSPPYYSVSQVLVYRKGSPR 119
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 121 EATPEGLKGKTIGVLQGSIQETYAKEhWEKHGVTVVSYKDQNMAWGDLL----NGRIDASLVMSAAGQAGFLSKPQGKgf 196
Cdd:COG4623  120 PKSLEDLAGKTVHVRAGSSYAERLKQ-LNQEGPPLKWEEDEDLETEDLLemvaAGEIDYTVADSNIAALNQRYYPNLR-- 196
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 556356369 197 gfIGKPVSDDtilgSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:COG4623  197 --VAFDLSEP----QPIAWAVRKNDPSLLAALNEFFAKIKKGGTLARLYERYF 243
PBP2_GluR0 cd00997
Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ...
33-249 1.95e-18

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: 81.23  E-value: 1.95e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  33 PPFeSRNASGELEGFDVELGNAICKAAALKCSWVET-SFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQPIYRIPSQ 111
Cdd:cd00997   13 PPF-VFYNDGELTGFSIDLWRAIAERLGWETEYVRVdSVSALLAAVAEGEADIAIAAISITAEREAEFDFSQPIFESGLQ 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 112 LVGKAGSAVEAtPEGLKGKTIGVLQGSIQETYAKEhwekHGVTVVSYKDQNMAWGDLLNGRIDAslVMSAAGQAGFLSKP 191
Cdd:cd00997   92 ILVPNTPLINS-VNDLYGKRVATVAGSTAADYLRR----HDIDVVEVPNLEAAYTALQDKDADA--VVFDAPVLRYYAAH 164
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 556356369 192 QGKGFGFIGKPVSDDtilgSGIGFGLRKGDeATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd00997  165 DGNGKAEVTGSVFLE----ENYGIVFPTGS-PLRKPINQALLNLREDGTYDELYEKWF 217
PBP2_PheC cd01069
Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein ...
23-249 2.61e-18

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: 80.85  E-value: 2.61e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFT 102
Cdd:cd01069   11 VLRVGTTGDYKPFTYRDNQGQYEGYDIDMAEALAKSLGVKVEFVPTSWPTLMDDLAADKFDIAMGGISITLERQRQAFFS 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 103 QPIYRipsqlVGKAG----------SAVEATPEglKGKTIGVLQGSIQETYAKEHWEKhgVTVVSYKDQNMAWGDLLNGR 172
Cdd:cd01069   91 APYLR-----FGKTPlvrcadvdrfQTLEAINR--PGVRVIVNPGGTNEKFVRANLKQ--ATITVHPDNLTIFQAIADGK 161
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556356369 173 IDAslVMSAAGQAGFLSKPQGKgfgfIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd01069  162 ADV--MITDAVEARYYQKLDPR----LCAVHPDKPFTFSEKAYMIPRDDQALKRYVDQWLHIMEGSGLLDQLSNKWL 232
PBP2_Peb1a_like cd13691
Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 ...
24-248 7.70e-16

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: 74.03  E-value: 7.70e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRN-ASGELEGFDVELGNAICKAA-ALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDF 101
Cdd:cd13691   10 LRVGVKNDVPGFGYQDpETGKYEGMEVDLARKLAKKGdGVKVEFTPVTAKTRGPLLDNGDVDAVIATFTITPERKKSYDF 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 102 TQPIYR-IPSQLVGKAGSAVEAtpEGLKGKTIGVLQGSIQ----ETYAKEHWEkhGVTVVSYKDQNMAWGDLLNGRIDAs 176
Cdd:cd13691   90 STPYYTdAIGVLVEKSSGIKSL--ADLKGKTVGVASGATTkkalEAAAKKIGI--GVSFVEYADYPEIKTALDSGRVDA- 164
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556356369 177 LVMSAAGQAGFLSKpqgkgfgfiGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKY 248
Cdd:cd13691  165 FSVDKSILAGYVDD---------SREFLDDEFAPQEYGVATKKGSTDLSKYVDDAVKKWLADGTLEALIKKW 227
PBP2_AA_binding_like_3 cd13621
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
20-249 1.06e-15

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: 74.01  E-value: 1.06e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  20 AATELRYGLEAEYPPFESRN-ASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAInSAMNITEQRRKS 98
Cdd:cd13621    6 KRGVLRIGVALGEDPYFKKDpSTGEWTGFGIDMAEDIAKDLGVKVEPVETTWGNAVLDLQAGKIDVA-FALDATPERALA 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  99 IDFTQPIYRIPSQLVGKAGSAVEATPEGLKGK-TIGVLQGSIQETYAKEHWEKhgVTVVSYKDQNMAWGDLLNGRIDASL 177
Cdd:cd13621   85 IDFSTPLLYYSFGVLAKDGLAAKSWEDLNKPEvRIGVDLGSATDRIATRRLPN--AKIERFKNRDEAVAAFMTGRADANV 162
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556356369 178 VMSAAGQAgFLSKPQGKGFGFIGKPVsddtiLGSGIGFGLRK-GDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13621  163 LTHPLLVP-ILSKIPTLGEVQVPQPV-----LALPTSIGVRReEDKVFKSFLSAWIQKLRRSGQTQKIILKYL 229
PBP2_YckB cd01003
Substrate binding domain of an ABC cystine transporter; the type 2 periplasmic binding protein ...
32-255 1.47e-14

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: 70.76  E-value: 1.47e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  32 YPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQPI-YRIPS 110
Cdd:cd01003   12 YPTSYHDTDSDKLTGYEVEVVREAGKRLGLKIEFKEMGIDGMLTAVNSGQVDAAANDIEVTKDREKKFAFSTPYkYSYGT 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 111 QLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKehweKHGVTVVSY----KDQNMAwgDLLNGRIDASLvmsaagQAG 186
Cdd:cd01003   92 AVVRKDDLSGISSLKDLKGKKAAGAATTVYMEIAR----KYGAEEVIYdnatNEVYLK--DVANGRTDVIL------NDY 159
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556356369 187 FLSKpqgkgFGFIGKPVSDDTI------LGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYFPGIDVS 255
Cdd:cd01003  160 YLQT-----MAVAAFPDLNITIhpdikyYPNKQALVMKKSNAALQEKVNKALKEMSKDGTLTKISEQFFNGADVS 229
PBP2_Mlr3796_like cd13695
The substrate-binding domain of putative amino aicd transporter; the type 2 periplasmic ...
33-178 1.91e-14

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: 70.28  E-value: 1.91e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  33 PPFESRNASGELEGFDVELGNAICKAA---ALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQPIYRIP 109
Cdd:cd13695   19 APWHFKSADGELQGFDIDMGRIIAKALfgdPQKVEFVNQSSDARIPNLTTDKVDITCQFMTVTAERAQQVAFTIPYYREG 98
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 556356369 110 SQLVGKAGSAVeATPEGLKGKTIGVLQGSIQETYAKE--HWEKHGVTVVSYKDQNMAWGDLLNGRIDASLV 178
Cdd:cd13695   99 VALLTKADSKY-KDYDALKAAGASVTIAVLQNVYAEDlvHAALPNAKVAQYDTVDLMYQALESGRADAAAV 168
PBP2_BvgS_D2 cd13707
The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
23-178 3.44e-13

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: 66.86  E-value: 3.44e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVET-SFDALIPGLLAKKFDAInSAMNITEQRRKSIDF 101
Cdd:cd13707    3 VVRVVVNPDLAPLSFFDSNGQFRGISADLLELISLRTGLRFEVVRAsSPAEMIEALRSGEADMI-AALTPSPEREDFLLF 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 102 TQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGS-----IQETYAKEHWekhgVTVVSYKDQnMAWgdLLNGRIDAS 176
Cdd:cd13707   82 TRPYLTSPFVLVTRKDAAAPSSLEDLAGKRVAIPAGSaledlLRRRYPQIEL----VEVDNTAEA-LAL--VASGKADAT 154

                 ..
gi 556356369 177 LV 178
Cdd:cd13707  155 VA 156
PBP2_ArtJ_like cd13697
Putative substrate-binding domain of ABC arginine transporter; the type 2 periplasmic-binding ...
20-249 6.64e-13

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: 66.01  E-value: 6.64e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  20 AATELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKSI 99
Cdd:cd13697    6 ASKKLVVGVNPNLPPLGAYDDKNVIEGFDVDVAKKLADRLGVKLELVPVSSADRVPFLMAGKIDAVLGGLTRTPDRAKVI 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 100 DFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGV-LQGSIQETYAKEHWEKHGVTVV-SYKDQNMAwgdLLNGRIDASL 177
Cdd:cd13697   86 DFSDPVNTEVLGILTTAVKPYKDLDDLADPRVRLVqVRGTTPVKFIQDHLPKAQLLLLdNYPDAVRA---IAQGRGDALV 162
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556356369 178 -VMSAAGQagFLSKPQGKGFGFIGKPVS--DDTIlgsgigfGLRKGDEATKKQLDAAIDKVRADGTIAKLADKYF 249
Cdd:cd13697  163 dVLDYMGR--YTKNYPAKWRVVDDPAIEvdYDCI-------GVAQGNTALLEVVNGELADLHKDGFIQASYKRWF 228
PBP2_HisK_like_1 cd13706
Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein; This ...
32-235 9.60e-13

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: 65.27  E-value: 9.60e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  32 YPPFESRNASGELEGFDVELgnaickaaalkcsW--------VETSFDAL-----IPGLLAKKFDAINsAMNITEQRRKS 98
Cdd:cd13706   12 YPPFSFLDEDGEPQGILVDL-------------WrlwsektgIPVEFVLLdwnesLEAVRQGEADVHD-GLFKSPEREKY 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  99 IDFTQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHWEKhgVTVVSYKdqNMAwgDLL----NGRID 174
Cdd:cd13706   78 LDFSQPIATIDTYLYFHKDLSGITNLSDLKGFRVGVVKGDAEEEFLRAHGPI--LSLVYYD--NYE--AMIeaakAGEID 151
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 556356369 175 AsLVMSAAGQAGFLSKpqgkgFGFIGKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKV 235
Cdd:cd13706  152 V-FVADEPVANYYLYK-----YGLPDEFRPAFRLYSGQLHPAVAKGNSALLDLINRGFALI 206
PRK10797 PRK10797
glutamate and aspartate transporter subunit; Provisional
74-249 1.63e-10

glutamate and aspartate transporter subunit; Provisional


Pssm-ID: 236763 [Multi-domain]  Cd Length: 302  Bit Score: 60.26  E-value: 1.63e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  74 IPGLLAKKFD-AINSAMNITEqRRKSIDFTQPIYRIPSQLVGKAGSAVEATPEgLKGKTIGVLQGSIQETYAKEHWE--K 150
Cdd:PRK10797  99 IPLLQNGTFDfECGSTTNNLE-RQKQAAFSDTIFVVGTRLLTKKGGDIKDFAD-LKGKAVVVTSGTTSEVLLNKLNEeqK 176
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 151 HGVTVVSYKDQNMAWGDLLNGRIDASLVMSA--AGQAGFLSKPQGkgFGFIGKPVSDDtilgsGIGFGLRKGDEATKKQL 228
Cdd:PRK10797 177 MNMRIISAKDHGDSFRTLESGRAVAFMMDDAllAGERAKAKKPDN--WEIVGKPQSQE-----AYGCMLRKDDPQFKKLM 249
                        170       180
                 ....*....|....*....|.
gi 556356369 229 DAAIDKVRADGTIAKLADKYF 249
Cdd:PRK10797 250 DDTIAQAQTSGEAEKWFDKWF 270
PRK10859 PRK10859
membrane-bound lytic murein transglycosylase MltF;
46-249 1.30e-09

membrane-bound lytic murein transglycosylase MltF;


Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 57.96  E-value: 1.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  46 GFDVELGNAIckAAALKcswVE------TSFDALIPGLLAKKFDAINSAMNITEQRRKSIDFTQPIYRIPSQLVGKAGSA 119
Cdd:PRK10859  65 GFEYELAKRF--ADYLG---VKleikvrDNISQLFDALDKGKADLAAAGLTYTPERLKQFRFGPPYYSVSQQLVYRKGQP 139
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 120 VEATPEGLKGKTIGVLQGS--------IQETYAKEHWEKHgvtvvsyKDQNMAwgDLL----NGRIDASLVMSAAGQAGF 187
Cdd:PRK10859 140 RPRSLGDLKGGTLTVAAGSshvetlqeLKKKYPELSWEES-------DDKDSE--ELLeqvaEGKIDYTIADSVEISLNQ 210
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556356369 188 LSKPQGKgfgfIGKPVSDDtilgSGIGFGLRKGDEAtkkQLDAAI----DKVRADGTIAKLADKYF 249
Cdd:PRK10859 211 RYHPELA----VAFDLTDE----QPVAWALPPSGDD---SLYAALldffNQIKEDGTLARLEEKYF 265
PBP2_BztA cd13692
Substrate bindng domain of ABC glutamate/glutamine/aspartate/asparagine transporter; the type ...
24-175 1.51e-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: 56.49  E-value: 1.51e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNASGELEGFDVELGNAIckAAAL-----KCSWVE----TSFDALIPG---LLAKkfdaiNSAMNI 91
Cdd:cd13692   10 LRCGVSEGLPGFSAVDDDGVWRGFDVDLCRAV--AAAVlgdatAVEFVPlsasDRFTALASGevdVLSR-----NTTWTL 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  92 TEQRRKSIDFTqPIYRIPSQ--LVGKAGSAveATPEGLKGKTIGVLQGSIQETYAKEHWEKHG--VTVVSYKDQNMAWGD 167
Cdd:cd13692   83 SRDTELGVDFA-PVYLYDGQgfLVRKDSGI--TSAKDLDGATICVQAGTTTETNLADYFKARGlkFTPVPFDSQDEARAA 159

                 ....*...
gi 556356369 168 LLNGRIDA 175
Cdd:cd13692  160 YFSGECDA 167
PBP2_AA_hypothetical cd13623
Substrate-binding domain of putative amino-acid transport system; the type 2 periplasmic ...
24-248 6.24e-09

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: 54.60  E-value: 6.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  24 LRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVEtsFDALipgllAKKFDAINSA------MNITEQRRK 97
Cdd:cd13623    6 LRVAINLGNPVLAVEDATGGPRGVSVDLAKELAKRLGVPVELVV--FPAA-----GAVVDAASDGewdvafLAIDPARAE 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  98 SIDFTQPIYRIPSQLVGKAGSAVeATPEGL--KGKTIGVLQGSIQETYAKEHWeKHGvTVVSYKDQNMAWGDLLNGRIDA 175
Cdd:cd13623   79 TIDFTPPYVEIEGTYLVRADSPI-RSVEDVdrPGVKIAVGKGSAYDLFLTREL-QHA-ELVRAPTSDEAIALFKAGEIDV 155
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556356369 176 slvmsAAGQAGFLSKPQGKGFGFigkPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKVRADGTIAKLADKY 248
Cdd:cd13623  156 -----AAGVRQQLEAMAKQHPGS---RVLDGRFTAIHQAIAIPKGRPAALEYLNEFVEEAKASGLLERALQRA 220
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
57-205 2.13e-07

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


Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 50.77  E-value: 2.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  57 KAAALKCSWVE-TSFDALIPGLLAKKFDA----INSAMNITEQRRKSIDFTQPIYRIPSQLVGKAGSAVEaTPEGLKGKT 131
Cdd:COG0715   47 KKEGLDVELVEfAGGAAALEALAAGQADFgvagAPPALAARAKGAPVKAVAALSQSGGNALVVRKDSGIK-SLADLKGKK 125
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556356369 132 IGVLQGSIQETYAKEHWEKHGVTVVSYKDQNMAWGD----LLNGRIDAslvmsAAGQAGFLSKPQGKGFGFIGKPVSD 205
Cdd:COG0715  126 VAVPGGSTSHYLLRALLAKAGLDPKDVEIVNLPPPDavaaLLAGQVDA-----AVVWEPFESQAEKKGGGRVLADSAD 198
Imp COG2358
TRAP-type uncharacterized transport system, periplasmic component [General function prediction ...
104-208 8.17e-07

TRAP-type uncharacterized transport system, periplasmic component [General function prediction only];


Pssm-ID: 441925 [Multi-domain]  Cd Length: 303  Bit Score: 49.07  E-value: 8.17e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 104 PIYRIPSQLVGKAGSAVEaTPEGLKGKTIGV-LQGSIQETYAKEHWEKHGVTVVSYKDQNMAWGD----LLNGRIDASLV 178
Cdd:COG2358   98 SLYPEPVHLVVRADSGIK-SLADLKGKRVSVgPPGSGTEVTAERLLEAAGLTYDDVKVEYLGYGEaadaLKDGQIDAAFF 176
                         90       100       110
                 ....*....|....*....|....*....|
gi 556356369 179 MSAAGQAGFLSKPQGKGFGFIgkPVSDDTI 208
Cdd:COG2358  177 VAGLPTGAVTELAATTDIRLL--PVDDEAI 204
PBP2_BvgS_like_1 cd13708
Putative sensor domain similar to BvgS; the type 2 periplasmic binding protein domain; BvgS is ...
23-182 1.05e-06

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: 48.28  E-value: 1.05e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRNASGELEGFDVELGNAICKAAALKCSWVET-SFDALIPGLLAKKFDAINSAMNiTEQRRKSIDF 101
Cdd:cd13708    3 EITMCVDPDWMPYEGIDEGGKHVGIAADYLKLIAERLGIPIELVPTkSWSESLEAAKEGKCDILSLLNQ-TPEREEYLNF 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 102 TQPIYRIPSQLVGKAGSAVEATPEGLKGKTIGVLQGSIQETYAKEHW----------EKHG---------------VTVV 156
Cdd:cd13708   82 TKPYLSDPNVLVTREDHPFIADLSDLGDKTIGVVKGYAIEEILRQKYpnlnivevdsEEEGlkkvsngelfgfidsLPVA 161
                        170       180
                 ....*....|....*....|....*..
gi 556356369 157 SYKDQNMAWGDL-LNGRIDASLVMSAA 182
Cdd:cd13708  162 AYTIQKEGLFNLkISGKLDEDNELRIG 188
PBP2_TAXI_TRAP cd13520
Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic ...
104-208 1.01e-05

Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold; This group includes Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family and closely related proteins. TRAP transporters are ubiquitous in prokaryotes, but absent from eukaryotes. They are comprised of an SBP (substrate-binding protein) of the DctP or TAXI families and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. The substrate-binding domain of TAXI proteins 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 tworeceptor cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270238 [Multi-domain]  Cd Length: 285  Bit Score: 45.69  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 104 PIYRIPSQLVGKAGSAVEaTPEGLKGKTIGV-LQGSIQETYAKEHWEKHGVTVVSYKDQNMAWGD----LLNGRIDASLV 178
Cdd:cd13520   86 SLYPEYLHLVVRKDSGIK-SIADLKGKRVAVgPPGSGTELTARRLLEAYGLTDDDVKAEYLGLSDaadaLKDGQIDAFFW 164
                         90       100       110
                 ....*....|....*....|....*....|
gi 556356369 179 MSAAGQAGFLSKPQGKGFGFIgkPVSDDTI 208
Cdd:cd13520  165 VGGLPASAITELAATRDIRLL--PIDDEEI 192
PBP2_iGluR_ligand_binding cd00998
The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic ...
33-249 1.48e-05

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: 45.06  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  33 PPF-------ESRNASGELEGFDVELGNAICKAAALK-----------CSWVETSFDALIPGLLAKKFDAINSAMNITEQ 94
Cdd:cd00998   11 PPFvmfvtgsNAVTGNGRFEGYCIDLLKELSQSLGFTyeyylvpdgkfGAPVNGSWNGMVGEVVRGEADLAVGPITITSE 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  95 RRKSIDFTQPIYRIPSQLVGKAGSAveatpEGLKGKT---IGVLQGSIQETY--------AKEHWEKHGVTVVSYKDQNM 163
Cdd:cd00998   91 RSVVIDFTQPFMTSGIGIMIPIRSI-----DDLKRQTdieFGTVENSFTETFlrssgiypFYKTWMYSEARVVFVNNIAE 165
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 164 AWGDLLNGRIDAsLVMSAAGQAGFLSKPQgkgfgfIGKPVSDDTILGSGIGFGLRKGDEATkKQLDAAIDKVRADGTIAK 243
Cdd:cd00998  166 GIERVRKGKVYA-FIWDRPYLEYYARQDP------CKLIKTGGGFGSIGYGFALPKNSPLT-NDLSTAILKLVESGVLQK 237

                 ....*.
gi 556356369 244 LADKYF 249
Cdd:cd00998  238 LKNKWL 243
PBP2_BvgS_D1 cd13705
The first of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
23-235 1.73e-04

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: 41.42  E-value: 1.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYG-LEAEYPPFESRNASGELEGFDVELGNAICKAAALKcswVET----SFDALIPGLLAKKFDAINSAmNITEQRRK 97
Cdd:cd13705    3 TLRVGvSAPDYPPFDITSSGGRYEGITADYLGLIADALGVR---VEVrrypDREAALEALRNGEIDLLGTA-NGSEAGDG 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  98 SIDFTQPIYRIPSQLVGKAGsAVEATPEGLKGKTIGVLQGSIQETYAKEHWekHGVTVVSYKDQNMAWGDLLNGRIDASL 177
Cdd:cd13705   79 GLLLSQPYLPDQPVLVTRIG-DSRQPPPDLAGKRVAVVPGYLPAEEIKQAY--PDARIVLYPSPLQALAAVAFGQADYFL 155
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 556356369 178 VMSAAgqAGFL-SKPQGKGFgfigKPVSDDTILGSGIGFGLRKGDEATKKQLDAAIDKV 235
Cdd:cd13705  156 GDAIS--ANYLiSRNYLNNL----RIVRFAPLPSRGFGFAVRPDNTRLLRLLNRALAAI 208
orph_peri_GRRM TIGR04262
extracellular substrate-binding orphan protein, GRRM family; This subfamily belongs to ...
22-185 2.17e-04

extracellular substrate-binding orphan protein, GRRM family; This subfamily belongs to bacterial extracellular solute-binding protein family 3 (pfam00497). In that family, most members are ABC transporter periplasmic substrate-binding proteins. However, members of the present subfamily are orphans in the sense of being adjacent to neither ABC transporter ATP-binding proteins or permease subunits. Instead, most members are encoded next to the two signature proteins of the proposed Glycine-Rich Repeat Modification (GRRM) system, a radical SAM/SPASM protein GrrM (TIGR04261) and the Gly-rich repeat protein itself GrrA (TIGR04260).


Pssm-ID: 275088 [Multi-domain]  Cd Length: 257  Bit Score: 41.58  E-value: 2.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   22 TELRYGLEAEYPPFeSRNASGELEGFDVELGNAI---CKAAALKCSWVE----TSFDALIPGLLAKKFDaINSAMNITEQ 94
Cdd:TIGR04262   1 GVLRAVVRGDVLPL-YQKDDAGYDGLSFDVLELIrdqLQAELGKPITIQfvvvNSVQEGLPKLRSGKAD-IACGVAFTWE 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369   95 RRKSIDFTQPIYRIPSQLVGKAGSavEATPEGLKGKTIGVLQGSIQETYAKEHWEKhgVTVVSYKDQNMAWGDLLNGRID 174
Cdd:TIGR04262  79 RQMFVDYSLPFAVSGIRLLAPKGN--DGTPESLEGKTVGVVKDSVAAAVLANVVPK--ATLQPFATPAEALAALKAGKVD 154
                         170
                  ....*....|....*
gi 556356369  175 A----SLVMSAAGQA 185
Cdd:TIGR04262 155 AlagdSLWLAANRQR 169
PRK11917 PRK11917
bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
23-155 3.92e-04

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


Pssm-ID: 183381 [Multi-domain]  Cd Length: 259  Bit Score: 40.68  E-value: 3.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  23 ELRYGLEAEYPPFESRN-ASGELEGFDVELGNAICK---AAALKCSWVETSFDALIPGLLAKKFDAINSAMNITEQRRKS 98
Cdd:PRK11917  39 QLIVGVKNDVPHYALLDqATGEIKGFEIDVAKLLAKsilGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRI 118
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 556356369  99 IDFTQPIYRIPSQLVGKAGSAVEATPEgLKGKTIGVLQGSIQETYAKEHWEKHGVTV 155
Cdd:PRK11917 119 YNFSEPYYQDAIGLLVLKEKNYKSLAD-MKGANIGVAQAATTKKAIGEAAKKIGIDV 174
PBP2_TtGluBP cd13567
Substrate binding domain of Thermus thermophilus GluBP (TtGluBP) of TAXI family of the ...
111-186 1.31e-03

Substrate binding domain of Thermus thermophilus GluBP (TtGluBP) of TAXI family of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold; This subgroup includes TtGluBP of TAXI-TRAP family and closely related proteins. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function.


Pssm-ID: 270285 [Multi-domain]  Cd Length: 284  Bit Score: 39.12  E-value: 1.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 111 QLVGKAGSAVEaTPEGLKGKTIGV-LQGSIQETYAKEHWEKHGVTV----VSYKDQNMAWGDLLNGRIDASLVMSAAGQA 185
Cdd:cd13567   93 QIVVRADSGIK-TVADLKGKRVSVgAPGSGTEVNARQILEAAGLTYddikVVYLSFAEAAEALKDGQIDAAFVTSGLPTA 171

                 .
gi 556356369 186 G 186
Cdd:cd13567  172 A 172
Periplasmic_Binding_Protein_Type_2 cd00648
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
43-192 2.81e-03

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: 37.94  E-value: 2.81e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369  43 ELEGFDVELGNAICKAAALKCSWVE-TSFDALIPGLLAKKFDAINSAMNITEQ------RRKSIDFTQPIYRIPSQLVGK 115
Cdd:cd00648   11 PYAGFAEDAAKQLAKETGIKVELVPgSSIGTLIEALAAGDADVAVGPIAPALEaaadklAPGGLYIVPELYVGGYVLVVR 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 116 AGSAVEATPEG--LKGKTIGVLQGS------IQETYAKEHWEKHGVTVVSYKDQNMAWGDLLNGRIDASLVMSAAGQAGF 187
Cdd:cd00648   91 KGSSIKGLLAVadLDGKRVGVGDPGstavrqARLALGAYGLKKKDPEVVPVPGTSGALAAVANGAVDAAIVWVPAAERAQ 170

                 ....*
gi 556356369 188 LSKPQ 192
Cdd:cd00648  171 LGNVQ 175
NMT1 pfam09084
NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed ...
109-175 5.91e-03

NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine.3]. They are regulated by thiamine. The protein adopts a fold related to the periplasmic binding protein (PBP) family. Both pyridoxal-5'-phosphate (PLP) and an iron atom are bound to the protein suggesting numerous residues of the active site necessary for HMP-P biosynthesis. The yeast protein is a dimer and, although exceptionally using PLP as a substrate, has notable similarities with enzymes dependent on this molecule as a cofactor.


Pssm-ID: 430398 [Multi-domain]  Cd Length: 216  Bit Score: 36.81  E-value: 5.91e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556356369  109 PSQLVGKAGSAVEaTPEGLKGKTIGVLQGSIQETYAKEHWEKHG-----VTVVSYKDQNMAwGDLLNGRIDA 175
Cdd:pfam09084  74 LSGVISLKDSGIK-SPKDLKGKRIGYSGSPFEEALLKALLKKDGgdpddVTIVNVGGMNLF-PALLTGKVDA 143
PBP2_ThiY_THI5_like_1 cd13652
Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 ...
109-205 6.47e-03

Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 periplasmic binding protein fold; This subfamily is phylogenetically similar to ThiY, which is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are THI5, which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes, and periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport. After binding the ligand, 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. The ThiY/THI5 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: 270370 [Multi-domain]  Cd Length: 217  Bit Score: 36.98  E-value: 6.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556356369 109 PSQLVGKAGSAVEaTPEGLKGKTIGV-LQGSIQETYAKEHWEKHGVTVVSYKDQNMAWGD----LLNGRIDASLVMSAag 183
Cdd:cd13652   89 PFAIVVRADSGIT-SPADLVGKKIAVsTLTNILEYTTNAYLKKNGLDPDKVEFVEVAFPQmvpaLENGNVDAAVLAEP-- 165
                         90       100
                 ....*....|....*....|..
gi 556356369 184 qagFLSKPQGKGFGFIGKPVSD 205
Cdd:cd13652  166 ---FLSRARSSGAKVVASDYAD 184
 
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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