NCBI Conserved Domain Search

oligopeptide ABC transporter substrate-binding protein OppA; Provisional

Pssm-ID: 185059 [Multi-domain] Cd Length: 543 Bit Score: 264.72 E-value: 8.24e-88

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681   1 MTIITKKRLIAAGVLSALIAGNMAMAADVPAGVQLAEKQTLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPkD 80
Cdd:PRK15104    1 MTNITKKSLIAAGVLAALMAGNVALAADVPAGVQLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLISDP-D 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2127477681  81 GHPIPGVAESWDNKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQRLV 128
Cdd:PRK15104   80 GHPAPGVAESWDNKDFKVWTFHLRKDAKWSNGTPVTAQDFVYSWQRLA 127

ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism];

Pssm-ID: 443327 [Multi-domain] Cd Length: 543 Bit Score: 166.54 E-value: 5.03e-50

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681   6 KKRLIAAGVLSALIAGNMAMAADVPAGVQLAEKQTLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPkDGHPIP 85
Cdd:COG4166     4 RKALLLLALALALALAACGSGGKYPAGDKVNDAKVLRLNNGTEPDSLDPALATGTAAAGVLGLLFEGLVSLDE-DGKPYP 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2127477681  86 GVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQRLV 128
Cdd:COG4166    83 GLAESWEvSEDGLTYTFHLRPDAKWSDGTPVTAEDFVYSWKRLL 126

The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173869 [Multi-domain] Cd Length: 498 Bit Score: 155.79 E-value: 3.06e-46

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  39 QTLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPkDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTA 117
Cdd:cd08504     1 QVLNLGIGSEPPTLDPAKATDSASSNVLNNLFEGLYRLDK-DGKIVPGLAESWEvSDDGLTYTFHLRKDAKWSNGDPVTA 79

                          90
                  ....*....|.
gi 2127477681 118 QDFVYSWQRLV 128
Cdd:cd08504    80 QDFVYSWRRAL 90

The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Similar to the ABC-type dipeptide and oligopeptide import systems, nickel transporter is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, which is the initial nickel receptor that controls the chemotactic response away from nickel. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand binding domains of ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173853 [Multi-domain] Cd Length: 466 Bit Score: 108.55 E-value: 7.13e-29

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPkDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQ 118
Cdd:cd00995     1 TLTVALGSDPTSLDPAFATDASSGRVLRLIYDGLVRYDP-DGELVPDLAESWEvSDDGKTYTFKLRDGVKFHDGTPLTAE 79

                          90
                  ....*....|
gi 2127477681 119 DFVYSWQRLV 128
Cdd:cd00995    80 DVVFSFERLA 89

ABC-type transport system, periplasmic component [Amino acid transport and metabolism];

Pssm-ID: 440510 [Multi-domain] Cd Length: 464 Bit Score: 94.61 E-value: 8.38e-24

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2127477681  52 LDPNKIEGVPEANISRDLFEGLLNTSPkDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQRLV 128
Cdd:COG0747     1 MDPALSTDAASANVASLVYEGLVRYDP-DGELVPDLAESWEvSDDGKTYTFTLRDGVKFHDGTPLTAEDVVFSLERLL 77

ABC transporter substrate-binding protein;

Pssm-ID: 182060 Cd Length: 535 Bit Score: 90.59 E-value: 2.67e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  15 LSALIAGNMAMAADVPAGVQLAEKQTLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSpKDGHPIPGVAESWDNK 94
Cdd:PRK09755    9 LVSLVSAAPLYAADVPANTPLAPQQVFRYNNHSDPGTLDPQKVEENTAAQIVLDLFEGLVWMD-GEGQVQPAQAERWEIL 87

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2127477681  95 D-FKVWTFHLRKDAKWSNGEPVTAQDFVYSWQRLV 128
Cdd:PRK09755   88 DgGKRYIFHLRSGLQWSDGQPLTAEDFVLGWQRAV 122

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173877 Cd Length: 476 Bit Score: 89.19 E-value: 7.93e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  38 KQTLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPKD-GHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPV 115
Cdd:cd08512     2 KDTLVVATSADINTLDPAVAYEVASGEVVQNVYDRLVTYDGEDtGKLVPELAESWEvSDDGKTYTFHLRDGVKFHDGNPV 81

                          90
                  ....*....|...
gi 2127477681 116 TAQDFVYSWQRLV 128
Cdd:cd08512    82 TAEDVKYSFERAL 94

The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; This family represents the substrate-binding domain of an ATP-binding cassette (ABC)-type dipeptide import system. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173858 [Multi-domain] Cd Length: 482 Bit Score: 88.39 E-value: 1.33e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPKDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQ 118
Cdd:cd08493     1 TLVYCSEGSPESLDPQLATDGESDAVTRQIYEGLVEFKPGTTELEPGLAESWEvSDDGLTYTFHLRKGVKFHDGRPFNAD 80


                  ....*....
gi 2127477681 119 DFVYSWQRL 127
Cdd:cd08493    81 DVVFSFNRW 89

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173863 [Multi-domain] Cd Length: 481 Bit Score: 87.62 E-value: 2.53e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSpKDGHPIPGVAESWDNKDFKVWTFHLRKDAKWSNGEPVTAQD 119
Cdd:cd08498     1 TLRIALAADPTSLDPHFHNEGPTLAVLHNIYDTLVRRD-ADLKLEPGLATSWEAVDDTTWRFKLREGVKFHDGSPFTAED 79


                  ....*...
gi 2127477681 120 FVYSWQRL 127
Cdd:cd08498    80 VVFSLERA 87

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173865 [Multi-domain] Cd Length: 499 Bit Score: 85.37 E-value: 1.88e-20

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2127477681  64 NISRDLFEGLLNTSPKDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQRLV 128
Cdd:cd08500    32 DIIGLGYAGLVRYDPDTGELVPNLAESWEvSEDGREFTFKLREGLKWSDGQPFTADDVVFTYEDIY 97

Bacterial extracellular solute-binding proteins, family 5 Middle; The borders of this family are based on the PDBSum definitions of the domain edges for Swiss:P06202.

Pssm-ID: 425718 Cd Length: 368 Bit Score: 84.38 E-value: 2.19e-20

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2127477681  83 PIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQRLV 128
Cdd:pfam00496   2 VVPALAESWEvSDDGKTYTFKLRKGVKFSDGTPLTADDVVFSFERIL 48

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173868 [Multi-domain] Cd Length: 460 Bit Score: 84.16 E-value: 5.10e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  45 SGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPkDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFVYS 123
Cdd:cd08503    13 GGSTADTLDPHTADSSADYVRGFALYEYLVEIDP-DGTLVPDLAESWEpNDDATTWTFKLRKGVTFHDGKPLTADDVVAS 91


                  ....
gi 2127477681 124 WQRL 127
Cdd:cd08503    92 LNRH 95

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173857 [Multi-domain] Cd Length: 484 Bit Score: 83.05 E-value: 1.18e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPkDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQ 118
Cdd:cd08492     3 TLTYALGQDPTCLDPHTLDFYPNGSVLRQVVDSLVYQDP-TGEIVPWLAESWEvSDDGTTYTFHLRDGVTFSDGTPLDAE 81

                          90
                  ....*....|
gi 2127477681 119 DFVYSWQRLV 128
Cdd:cd08492    82 AVKANFDRIL 91

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173882 [Multi-domain] Cd Length: 480 Bit Score: 82.99 E-value: 1.24e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPKDGhPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQ 118
Cdd:cd08517     3 TLNVVVQPEPPSLNPALKSDGPTQLISGKIFEGLLRYDFDLN-PQPDLATSWEvSEDGLTYTFKLRPGVKWHDGKPFTSA 81


                  ....*....
gi 2127477681 119 DFVYSWQRL 127
Cdd:cd08517    82 DVKFSIDTL 90

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173881 [Multi-domain] Cd Length: 457 Bit Score: 82.68 E-value: 1.36e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  47 AEPQSLDPNKIEGVPEANISRDLFEGLLNTSPkDGHPIPGVAESWDN-KDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQ 125
Cdd:cd08516     8 TDPDSLDPHKATAAASEEVLENIYEGLLGPDE-NGKLVPALAESWEVsDDGLTYTFKLRDGVKFHNGDPVTAADVKYSFN 86


                  ..
gi 2127477681 126 RL 127
Cdd:cd08516    87 RI 88

The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold; This family includes the substrate-binding domain of an ABC-type oligopeptide-binding protein Hb8 from Thermus thermophilius and its closest homologs from other bacteria. The structural topology of this substrate-binding domain is similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium, and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. Ligands are then transported across the cytoplasmic membrane energized by ATP hydrolysis or electrochemical ion gradient. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173878 [Multi-domain] Cd Length: 482 Bit Score: 80.40 E-value: 1.03e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPkDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQ 118
Cdd:cd08513     1 TLVIGLSQEPTTLNPLLASGATDAEAAQLLFEPLARIDP-DGSLVPVLAEEIPtSENGLSVTFTLRPGVKWSDGTPVTAD 79


                  ....*..
gi 2127477681 119 DFVYSWQ 125
Cdd:cd08513    80 DVVFTWE 86

The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold; This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two oligopeptide-binding proteins (OppA and AppA) with overlapping specificity. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173879 [Multi-domain] Cd Length: 483 Bit Score: 77.27 E-value: 1.47e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPkDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQ 118
Cdd:cd08514     1 TLVLATGGDPSNLNPILSTDSASSEVAGLIYEGLLKYDK-DLNFEPDLAESWEvSDDGKTYTFKLRKDVKWHDGEPLTAD 79


                  ....*..
gi 2127477681 119 DFVYSWQ 125
Cdd:cd08514    80 DVKFTYK 86

Methanobactin MbnE, a periplasmic binding protein of the TonB-dependent transport system, and similar proteins; Methanobactin MbnE is a periplasmic binding protein that is involved in the TonB-dependent transport system in bacteria. The function of MbnE is to bind to methanobactin and transport it across the periplasmic space to the TonB receptor on the outer membrane of the cell. The binding of MbnE to methanobactin allows the bacteria to scavenge iron from the environment, which is essential for many biological processes. The evolutionary relationship between MbnE and the ABC transport system is not clear, as they are distinct systems that have evolved separately. However, it is possible that there have been some functional convergences between these systems in terms of nutrient uptake and transport.

Pssm-ID: 173862 [Multi-domain] Cd Length: 491 Bit Score: 76.02 E-value: 3.66e-17

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2127477681  51 SLDPNKIEGVPEANISRDLFEGLLNTSP-KDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQ 125
Cdd:cd08497    28 SLNPFILKGTAAAGLFLLVYETLMTRSPdEPFSLYGLLAESVEyPPDRSWVTFHLRPEARFSDGTPVTAEDVVFSFE 104

The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis pathway of the beta-lactamase inhibitor clavulanic acid contains the type 2 periplasmic binding fold; Clavulanic acid (CA), a clinically important beta-lactamase inhibitor, is one of a family of clavams produced as secondary metabolites by fermentation of Streptomyces clavuligeru. The biosynthesis of CA proceeds via multiple steps from the precursors, glyceraldehyde-3-phosphate and arginine. CA possesses a characteristic (3R,5R) stereochemistry essential for reaction with penicillin-binding proteins and beta-lactamases. Two genes (oppA1 and oppA2) in the clavulanic acid gene cluster encode oligopeptide-binding proteins that are required for CA biosynthesis. OppA1/2 is involved in the binding and transport of peptides across the cell membrane of Streptomyces clavuligerus. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173871 [Multi-domain] Cd Length: 466 Bit Score: 75.76 E-value: 4.44e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPKDGH----PIPGVAESWD--NKDFKVWTFHLRKDAKWSNGE 113
Cdd:cd08506     1 TLRLLSSADFDHLDPARTYYADGWQVLRLIYRQLTTYKPAPGAegteVVPDLATDTGtvSDDGKTWTYTLRDGLKFEDGT 80

                          90
                  ....*....|....
gi 2127477681 114 PVTAQDFVYSWQRL 127
Cdd:cd08506    81 PITAKDVKYGIERS 94

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173880 [Multi-domain] Cd Length: 460 Bit Score: 71.09 E-value: 1.79e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  38 KQTLVRNSGAEPQSLDPNKI---EGVPeanISRDLFEGLLNTSPKDGHPIPGVAESWDNKDFKVWTFHLRKDAKWSNGEP 114
Cdd:cd08515     1 RDTLVIAVQKEPPTLDPYYNtsrEGVI---ISRNIFDTLIYRDPDTGELVPGLATSWKWIDDTTLEFTLREGVKFHDGSP 77

                          90
                  ....*....|....
gi 2127477681 115 VTAQDFVYSWQRLV 128
Cdd:cd08515    78 MTAEDVVFTFNRVR 91

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173855 [Multi-domain] Cd Length: 470 Bit Score: 69.56 E-value: 5.61e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  39 QTLVRNSGAEPQSLDPNKIEGVpeaNISR-DLFEGLLNTSpKDGHPIPGVAESWDNKDFKVWTFHLRKDAKWSNGEPVTA 117
Cdd:cd08490     1 KTLTVGLPFESTSLDPASDDGW---LLSRyGVAETLVKLD-DDGKLEPWLAESWEQVDDTTWEFTLRDGVKFHDGTPLTA 76

                          90
                  ....*....|
gi 2127477681 118 QDFVYSWQRL 127
Cdd:cd08490    77 EAVKASLERA 86

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173867 [Multi-domain] Cd Length: 472 Bit Score: 68.75 E-value: 1.35e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  47 AEPQSLDPnkieGVPEANISRD----LFEGLLNTSpKDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFV 121
Cdd:cd08502     8 ADLRTLDP----IVTTAYITRNhgymIYDTLFGMD-ANGEPQPQMAESWEvSDDGKTYTFTLRDGLKFHDGSPVTAADVV 82


                  ....*
gi 2127477681 122 YSWQR 126
Cdd:cd08502    83 ASLKR 87

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173883 [Multi-domain] Cd Length: 464 Bit Score: 66.84 E-value: 5.28e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEP-QSLDPnkIEGVPEANISRdLFEGLLnTSPKDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTA 117
Cdd:cd08518     2 ELVLAVGSEPeTGFNP--LLGWGEHGEPL-IFSGLL-KRDENLNLVPDLATSYKvSDDGLTWTFTLRDDVKFSDGEPLTA 77


                  ....*.
gi 2127477681 118 QDFVYS 123
Cdd:cd08518    78 EDVAFT 83

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173884 [Multi-domain] Cd Length: 469 Bit Score: 66.49 E-value: 6.79e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  49 PQSLDPNKIEGVPEANISRDLFEGLLNTSPKDGHPIPGVAESW--DNKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQR 126
Cdd:cd08519    10 VRTLDPAGAYDLGSWQLLSNLGDTLYTYEPGTTELVPDLATSLpfVSDDGLTYTIPLRQGVKFHDGTPFTAKAVKFSLDR 89

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173873 Cd Length: 470 Bit Score: 66.64 E-value: 7.09e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPKDGHPI---PGVAESWDNKDFK-VWTFHLRKDAKWS-NGEP 114
Cdd:cd08508     2 LRIGSAADDIRTLDPHFATGTTDKGVISWVFNGLVRFPPGSADPYeiePDLAESWESSDDPlTWTFKLRKGVMFHgGYGE 81

                          90
                  ....*....|..
gi 2127477681 115 VTAQDFVYSWQR 126
Cdd:cd08508    82 VTAEDVVFSLER 93

The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold; This family represents the substrate-binding domain of a cellulose-binding protein from the hyperthermophilic bacterium Thermotoga maritima (TmCBP) and its closest related proteins. TmCBP binds a variety of lengths of beta-1,4-linked glucose oligomers, ranging from two sugar rings (cellobiose) to five (cellopentose). TmCBP is structurally homologous to domains I and III of the ATP-binding cassette (ABC)-type oligopeptide-binding proteins and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. Ligands are then transported across the cytoplasmic membrane energized by ATP hydrolysis or electrochemical ion gradient. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173874 [Multi-domain] Cd Length: 509 Bit Score: 66.19 E-value: 8.69e-14

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2127477681  69 LFEGLLNTSPKDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQ 125
Cdd:cd08509    33 IYEPLAIYNPLTGEFIPWLAESWTwSDDFTTLTVTLRKGVKWSDGEPFTADDVVFTFE 90

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173856 Cd Length: 473 Bit Score: 65.09 E-value: 2.15e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  46 GAEPQSLDP-NKIEGVPEANISRDLFEGLLNTSPKDGHPIPGVAESWDNKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSW 124
Cdd:cd08491     7 PEEPDSLEPcDSSRTAVGRVIRSNVTEPLTEIDPESGTVGPRLATEWEQVDDNTWRFKLRPGVKFHDGTPFDAEAVAFSI 86


                  ....
gi 2127477681 125 QRLV 128
Cdd:cd08491    87 ERSM 90

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173859 [Multi-domain] Cd Length: 448 Bit Score: 64.57 E-value: 3.79e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEPQSLDP--NKIEGVPEANISrDLFEGLLNTSPkDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVT 116
Cdd:cd08494     1 TLTIGLTLEPTSLDIttTAGAAIDQVLLG-NVYETLVRRDE-DGKVQPGLAESWTiSDDGLTYTFTLRSGVTFHDGTPFD 78

                          90
                  ....*....|..
gi 2127477681 117 AQDFVYSWQRLV 128
Cdd:cd08494    79 AADVKFSLQRAR 90

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173885 [Multi-domain] Cd Length: 468 Bit Score: 63.49 E-value: 9.67e-13

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2127477681  69 LFEGLLntSPKDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFVYS 123
Cdd:cd08520    32 IFDSLV--WKDEKGFIPWLAESWEvSEDGLTYTFHLREGAKWHDGEPLTAEDVAFT 85

The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold; A novel family of SgrR transcriptional regulator contains a two-domain structure with an N terminal DNA-binding domain of the winged helix family and a C-terminal solute-binding domain. The C-terminal domain shows strong homology with the ABC-type oligopeptide-binding protein family, a member of the type 2 periplasmic-binding fold protein (PBP2) superfamily that also includes the C-terminal substrate-binding domain of LysR-type transcriptional regulators. SgrR (SugaR transport-related Regulator) is negatively autoregulated and activates transcription of divergent operon SgrS, which encodes a small RNA required for recovery from glucose-phosphate stress. Hence, the small RNA SgrS and SgrR, the transcription factor that controls sgrS expression, are both required for recovery from glucose-phosphate stress. Most of periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.

Pssm-ID: 173872 [Multi-domain] Cd Length: 448 Bit Score: 61.90 E-value: 3.36e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2127477681  51 SLDPNKIEGVPEANISRDLFEGLLNTSPKDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQRL 127
Cdd:cd08507    17 TLDPGTPLRRSESHLVRQIFDGLVRYDEENGEIEPDLAHHWEsNDDLTHWTFYLRKGVRFHNGRELTAEDVVFTLLRL 94

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173860 [Multi-domain] Cd Length: 482 Bit Score: 60.04 E-value: 1.46e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  48 EPQSLDPNK-IEGVPEANISrdLFEGL----LNTSPKDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFV 121
Cdd:cd08495     9 PLTTLDPDQgAEGLRFLGLP--VYDPLvrwdLSTADRPGEIVPGLAESWEvSPDGRRWTFTLRPGVKFHDGTPFDADAVV 86


                  ....*.
gi 2127477681 122 YSWQRL 127
Cdd:cd08495    87 WNLDRM 92

The substrate binding component of an ABC-type lactococcal OppA-like transport system contains; This family represents the substrate binding domain of an ATP-binding cassette (ABC)-type oligopeptide import system from Lactococcus lactis and other gram-positive bacteria, as well as its closet homologs from gram-negative bacteria. Oligopeptide-binding protein (OppA) from Lactococcus lactis can bind peptides of length from 4 to at least 35 residues without sequence preference. The oligopeptide import system OppABCDEF is consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173875 [Multi-domain] Cd Length: 516 Bit Score: 58.43 E-value: 5.73e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2127477681  58 EGVPEANISRDLFEGLLNTSpKDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSW 124
Cdd:cd08510    24 EDNTDAEIMGFGNEGLFDTD-KNYKITDSGAAKFKlDDKAKTVTITIKDGVKWSDGKPVTAKDLEYSY 90

The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173854 [Multi-domain] Cd Length: 488 Bit Score: 57.24 E-value: 1.32e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2127477681  69 LFEGLLNTSpKDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQR 126
Cdd:cd08489    28 VYEPLVKYG-EDGKIEPWLAESWEiSEDGKTYTFHLRKGVKFSDGTPFNAEAVKKNFDA 85

The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173864 [Multi-domain] Cd Length: 474 Bit Score: 54.53 E-value: 1.27e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  40 TLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLnTSPKDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQ 118
Cdd:cd08499     1 DLVIAVLSDATSLDPHDTNDTPSASVQSNIYEGLV-GFDKDMKIVPVLAESWEqSDDGTTWTFKLREGVKFHDGTPFNAE 79

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This family represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173876 [Multi-domain] Cd Length: 467 Bit Score: 47.66 E-value: 2.57e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  39 QTLVRNSGAEPQSLDPNKIEGVPEANISRDLFEGLLNTSPkDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTA 117
Cdd:cd08511     1 GTLRIGLEADPDRLDPALSRTFVGRQVFAALCDKLVDIDA-DLKIVPQLATSWEiSPDGKTLTLKLRKGVKFHDGTPFDA 79

                          90
                  ....*....|
gi 2127477681 118 QDFVYSWQRL 127
Cdd:cd08511    80 AAVKANLERL 89

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173870 [Multi-domain] Cd Length: 528 Bit Score: 46.50 E-value: 7.76e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127477681  47 AEPQSLDPNKIEGVPEANISRDLFEGLLNTspkdgHP-------IPGVAE-----SWDNKDFKVWTFHLRKDAKWSN--- 111
Cdd:cd08505     8 ARPKGLDPAQSYDSYSAEIIEQIYEPLLQY-----HYlkrpyelVPNTAAampevSYLDVDGSVYTIRIKPGIYFQPdpa 82

                          90       100
                  ....*....|....*....|..
gi 2127477681 112 -----GEPVTAQDFVYSWQRLV 128
Cdd:cd08505    83 fpkgkTRELTAEDYVYSIKRLA 104

The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic binding fold; LpqW is one of key players in synthesis and transport of the unique components of the mycobacterial cell wall which is a complex structure rich in two related lipoglycans, the phosphatidylinositol mannosides (PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly conserved lipoprotein that transport intermediates from a pathway for mature PIMs production into a pathway for LAMs biosynthesis, thus controlling the relative abundance of these two essential components of cell wall. LpqW is thought to have been adapted by the cell-wall biosynthesis machinery of mycobacteria and other closely related pathogens, evolving to play an important role in PIMs/LAMs biosynthesis. Most of periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the LpqW protein. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173866 [Multi-domain] Cd Length: 486 Bit Score: 44.64 E-value: 3.16e-06

                          10        20        30
                  ....*....|....*....|....*....|....
gi 2127477681  92 DNKDFKVWTFHLRKDAKWSNGEPVTAQDFVYSWQ 125
Cdd:cd08501    58 TSDDPQTVTYTINPEAQWSDGTPITAADFEYLWK 91

The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA can bind peptides of a wide range of lengths (2-35 amino-acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

Pssm-ID: 173861 [Multi-domain] Cd Length: 454 Bit Score: 44.64 E-value: 3.20e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2127477681  47 AEPQSLDPNKIEGVPEANISRDLFEGLLNTSPkDGHPIPGVAESWD-NKDFKVWTFHLRKDAKWSNGEPVTAQ 118
Cdd:cd08496     8 ADPTSWDPAQGGSGADHDYLWLLYDTLIKLDP-DGKLEPGLAESWEyNADGTTLTLHLREGLTFSDGTPLDAA 79