ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  61 FTYTPVEDPALYKDAFADFQTHLSKVTGKRVIYYTVHSNSAQVEAMRSGRLHVAGFSTGPTGYAVNLAGYVPIAVKGDEK 140
Cdd:pfam12974   1 FGVLPDESPDELKARYQPLADYLSEELGVPVELVVATDYAAVVEALRAGQVDIAYFGPLAYVQAVDRAGAEPLATPVEPD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 141 GFHGYNLITIVRKDSGINSMADLKGKKVAHTSASSNSGNLAPRA-LFPAQGLVPDVDYKVFYSGKHDQSILGVFNGDYDA 219
Cdd:pfam12974  81 GSAGYRSVIIVRKDSPIQSLEDLKGKTVAFGDPSSTSGYLVPLAlLFAEAGLDPEDDFKPVFSGSHDAVALAVLNGDADA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1108362880 220 APVASDVYDRMVDAGRVDGSVLKIIYRSPRFPTSAFGYAHNLKPELAKKIQEAFYSYRFTDEMSASFK--GADRFAPIT 296
Cdd:pfam12974 161 GAVNSEVLERLVAEGPIDRDQLRVIAESPPIPNDPLVARPDLPPELKEKIRDALLALDETPEGRKVLEalGIDGFVPAD 239

phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein; Phosphonates are a varied class of phosphorus-containing organic compound in which a direct C-P bond is found, rather than a C-O-P linkage of the phosphorus through an oxygen atom. They may be toxic but also may be used as sources of phosphorus and energy by various bacteria. Phosphonate utilization systems typically are encoded in 14 or more genes, including a three gene ABC transporter. This family includes the periplasmic binding protein component of ABC transporters for phosphonates as well as other, related binding components for closely related substances such as phosphate and phosphite. A number of members of this family are found in genomic contexts with components of selenium metabolic processes suggestive of a role in selenate or other selenium-compound transport. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system (GenProp0232) has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates. [Transport and binding proteins, Anions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  48 KDPSDWSD-PSTLVFTYTPVEDPALYKDAFADFQTHLSKVTGKRVIYYTVHSNSAQVEAMRSGRLHVAGFstGPTGY--A 124
Cdd:TIGR01098  22 KKAAEAAAvPKELNFGILPGENASNLTRRWEPLADYLEKKLGIKVQLFVATDYSAVIEAMRFGRVDIAWF--GPSSYvlA 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 125 VNLAGYVPIAVK-GDEKGFHGYNLITIVRKDSGINSMADLKGKKVAHTSASSNSGNLAPRALFPAQG--LVPDVDYKVFY 201
Cdd:TIGR01098 100 HYRANAEVFALTaVSTDGSPGYYSVIIVKADSPIKSLKDLKGKTFAFGDPASTSGYLVPRYQLKKEGglDADGFFSEVVF 179

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1108362880 202 SGKHDQSILGVFNGDYDAAPVASDVYDRMVDAGRVDGSVLKIIYRSPRFPTSAFGYAHNLKPELAKKIQEAFYSY 276
Cdd:TIGR01098 180 SGSHDASALAVANGKVDAATNNSSAIGRLKKRGPSDMKKVRVIWKSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254

alkanesulfonate transporter substrate-binding subunit; Provisional

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1108362880 150 IVRKDSGINSMADLKGKKVAHTSASSnSGNLAPRAL 185
Cdd:PRK11553  114 LVAENSPIKTVADLKGHKVAFQKGSS-SHNLLLRAL 148

ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  61 FTYTPVEDPALYKDAFADFQTHLSKVTGKRVIYYTVHSNSAQVEAMRSGRLHVAGFSTGPTGYAVNLAGYVPIAVKGDEK 140
Cdd:pfam12974   1 FGVLPDESPDELKARYQPLADYLSEELGVPVELVVATDYAAVVEALRAGQVDIAYFGPLAYVQAVDRAGAEPLATPVEPD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 141 GFHGYNLITIVRKDSGINSMADLKGKKVAHTSASSNSGNLAPRA-LFPAQGLVPDVDYKVFYSGKHDQSILGVFNGDYDA 219
Cdd:pfam12974  81 GSAGYRSVIIVRKDSPIQSLEDLKGKTVAFGDPSSTSGYLVPLAlLFAEAGLDPEDDFKPVFSGSHDAVALAVLNGDADA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1108362880 220 APVASDVYDRMVDAGRVDGSVLKIIYRSPRFPTSAFGYAHNLKPELAKKIQEAFYSYRFTDEMSASFK--GADRFAPIT 296
Cdd:pfam12974 161 GAVNSEVLERLVAEGPIDRDQLRVIAESPPIPNDPLVARPDLPPELKEKIRDALLALDETPEGRKVLEalGIDGFVPAD 239

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  54 SDPSTLVFTYTPVEDPALYKDAFADFQTHLSKVTGKRVIYYTVHSNSAQVEAMRSGRLHVAGFSTGPTGYAVNLAGYVPI 133
Cdd:cd01071     1 AAPKELRFGLVPAEDADELKKEFEPLADYLEEELGVPVELVVATSYAAVVEAMRNGKVDIAWLGPASYVLAHDRAGAEAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 134 AVKGDEKGFhGYNLITIVRKDSGINSMADLKGKKVAHTSASSNSGNLAPRALFPAQGLVP-DVDYKVFYSGKHDQSILGV 212
Cdd:cd01071    81 ATEVRDGSP-GYYSVIIVRKDSPIKSLEDLKGKTVAFVDPSSTSGYLFPRAMLKDAGIDPpDFFFEVVFAGSHDSALLAV 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 213 FNGDYDAAPVASDVYDRMVDAGRVDGSVLKIIYRSPRFPTSAFGYAHNLKPELAKKIQEAFYSYRFTDEMSASFK--GAD 290
Cdd:cd01071   160 ANGDVDAAATYDSTLERAAAAGPIDPDDLRVIWRSPPIPNDPLVVRKDLPPALKAKIRDALLDLDETDEGQKLLAglGLT 239

                         250
                  ....*....|....
gi 1108362880 291 RFAPITYKEEWGVI 304
Cdd:cd01071   240 GFVPATDDDYDPIR 253

phosphonate ABC transporter, periplasmic phosphonate binding protein; This model is a subset of the broader subfamily of phosphate/phosphonate binding protein ABC transporter components, TIGR01098. In this model all members of the seed have support from genomic context for association with pathways for the metabolims of phosphonates, particularly the C-P lyase system, GenProp0232. This model includes the characterized phnD gene from E. coli. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  43 VADTPKDPSDWsdPSTLVFTYTPVEDPALYKDAFADFQTHLSKVTGKRVIYYTVHSNSAQVEAMRSGRLHVAGFstGPTG 122
Cdd:TIGR03431  15 LISSNAQAEDW--PKELNFGIIPTENASDLKQRWEPLADYLSKKLGVKVKLFFATDYAGVIEGMRFGKVDIAWY--GPSS 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 123 Y--AVNLAGYVPIAVKGDEKGFHGYNLITIVRKDSGINSMADLKGKKVAHTSASSNSGNLAPRALFPAQGLVPDVDY--K 198
Cdd:TIGR03431  91 YaeAYQKANAEAFAIEVNADGSTGYYSVLIVKKDSPIKSLEDLKGKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYfkK 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 199 VFYSGKHDQSILGVFNGDYDAAPVASDVYDRMVDAGRVDGSV-LKIIYRSPRFPTSAFGYAHNLKPELAKKIQEAFYSYR 277
Cdd:TIGR03431 171 VTFSGSHEAAILAVANGTVDAATTNDENLDRMIRKGQPDAMEdLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYH 250

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1108362880 278 FTDEMSASFKGADRFAPITYKE--EWGVIRDIAHATGT 313
Cdd:TIGR03431 251 KTDKACFEKIAGGDLKGFVAASdkDYDPIRDLKKAKIK 288

Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding components of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  56 PSTLVFTYTPVEDPALYKDAFADFQTHLSKVTGKRVIYYTVHSNSAQVEAMRSGRLHVAGFSTGPTGYAVNLAGYVPIAV 135
Cdd:cd13571     3 SPPLRIGLASVLSPRETLALYDPLAEYLERKLGRPVEFVQRRTYAEINELLKNGKVDLAFVCSGAYVQARDKAGLELLAV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 136 KG--DEKGFHGYnliTIVRKDSGINSMADLKGKKVAHTSASSNSGNLAPRALFPAQGLVPDVDY-KVFYSGKHDQSILGV 212
Cdd:cd13571    83 PEinGQPTYRSY---IIVPADSPAKSLEDLKGKRFAFTDPLSNSGFLVPMYLLAELGLDPERFFsRVFFTGSHDKSIQAV 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 213 FNGDYDAAPVASDVYDRMVDAG-RVDGSVlKIIYRSPRFPTSAFGYAHNLKPELAKKIQEAFYSYRFTDEMSASFKGA-- 289
Cdd:cd13571   160 ANGLVDGAAVDSLVYEYAVEKGpELAANV-RIIWRSEPIGNPPVVARPGLDPELKAALQEAFLSMHEDPEGRAALEGLgi 238

                  ....*
gi 1108362880 290 DRFAP 294
Cdd:cd13571   239 DRFVP 243

Substrate binding domain of ABC-type phosphonate uptake system; contains the type 2 periplasmic binding fold; This subfamily includes the Escherichia coli PhnD (EcPhnD) which exhibits high affinity for the environmentally abundant 2-aminoethylphosphonate (2-AEP), a precursor in the biosynthesis of phosphonolipids, phosphonoproteins, and phosphonoglycans. The Escherichia coli phn operon encodes 14 genes involved in binding, uptake and metabolism of phosphonate, and is activated under phophophate-limiting conditions. PhnD belongs to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. The PBP2 have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake system (PhnCDE) that recognizes and binds phosphonate.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  55 DPSTLVFTYTPVEDPALYKDAFADFQTHLSKVTGKRVIYYTVHSNSAQVEAMRSGRLHVAGFSTGPTGYAVNLAGYVPIA 134
Cdd:cd13575     2 DEKALNFGIISTESQQNLRAQWEPFLAAMEKKLGVKVNAFFAPDYAGIIEGMRFNKVQIAWYGNKSAMEAVDRANGEVFA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 135 VKGDEKGFHGYNLITIVRKDSGINSMADL--KGKKVAHTSA--SSNSGNLAPR-ALFPAQGLVPDVDYKVFYSGKHDQSI 209
Cdd:cd13575    82 QTVAADGSPGYYSHLIVNKDSPINSLNDVlaKAKDLTFGNGdpNSTSGFLVPGyYVFAKNGIDPKKFFKRTVNANHETNA 161

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1108362880 210 LGVFNGDYDAAPVASDVYDRMVDAGRVDGSVLKIIYRSPRFPTSAFGYAHNLKPELAKKIQEAFYSYRFTDE 281
Cdd:cd13575   162 LAVANKQVDVATNNTENLDRLKERAPEKLKQLRIIWTSPLIPGDPLVWRKDLPEAVKKKIADFFFGYGQTAE 233

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  98 SNSAQVEAMRSGRLHVAgfSTGPTGYAVNLAGYVPIAVKGDEKGFHGYNLItiVRKDSGINSMADLKGKKVAHTSASSNS 177
Cdd:COG0715    60 GGAAALEALAAGQADFG--VAGAPPALAARAKGAPVKAVAALSQSGGNALV--VRKDSGIKSLADLKGKKVAVPGGSTSH 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 178 GNLapRALFPAQGLVPDvDYKVFYSGkHDQSILGVFNGDYDAAPVASDVYDRMVDAGrvdgsVLKIIYRS----PRFPTS 253
Cdd:COG0715   136 YLL--RALLAKAGLDPK-DVEIVNLP-PPDAVAALLAGQVDAAVVWEPFESQAEKKG-----GGRVLADSadlvPGYPGD 206

                         170       180
                  ....*....|....*....|....*
gi 1108362880 254 AFG----YAHNlKPELAKKIQEAFY 274
Cdd:COG0715   207 VLVasedFLEE-NPEAVKAFLRALL 230

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  98 SNSAQVEAMRSGRLHVAGFSTGPTGYAvnLAGYVPIAVKGDEKGFHGYNLItIVRKDSGINSMADLKGKKVAHTSASsnS 177
Cdd:cd01008    40 SGPPALEALAAGSLDFGTGGDTPALLA--AAGGVPVVLIAALSRSPNGNGI-VVRKDSGITSLADLKGKKIAVTKGT--T 114

                          90
                  ....*....|....*..
gi 1108362880 178 GNLAPRALFPAQGLVPD 194
Cdd:cd01008   115 GHFLLLKALAKAGLSVD 131

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 103 VEAMRSGRLHVaGFSTGPTGYAvnlagyvPIAVKGDEKGFHGYNLITI-----------VRKDSGINSMADLKGKKVAHT 171
Cdd:cd13520    45 LRLLESGEADF-GLAQSDVAYD-------AYNGTGPFEGKPIDNLRAVaslypeylhlvVRKDSGIKSIADLKGKRVAVG 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 172 SASSNSGNLApRALFPAQGLVPDvDYKVFYSGkhdqsilgvfngdydaapvASDVYDRMVDaGRVDGSVLKIIyrsprFP 251
Cdd:cd13520   117 PPGSGTELTA-RRLLEAYGLTDD-DVKAEYLG-------------------LSDAADALKD-GQIDAFFWVGG-----LP 169

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1108362880 252 TSAF---GYAHNLK-----PELAKKIQEAFYSYR 277
Cdd:cd13520   170 ASAItelAATRDIRllpidDEEIAKLLAEYPYYV 203

ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins. [Transport and binding proteins, Other]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  79 FQTHLSKVtgkRVIYYTVHSNSAQVEAMRSGRLHVAGFSTGPT-GYAVNLAGYVPIAVKGDEKGFhgynlITIVRKDSGI 157
Cdd:TIGR01728  22 LEKELGKT---KVEWVEFPAGPPALEALGAGSLDFGYIGPGPAlFAYAAGADIKAVGLVSDNKAT-----AIVVIKGSPI 93

                          90       100
                  ....*....|....*....|....*...
gi 1108362880 158 NSMADLKGKKVAHTSASSNSgNLAPRAL 185
Cdd:TIGR01728  94 RTVADLKGKRIAVPKGGSGH-DLLLRAL 120

Taurine-binding periplasmic protein; the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA 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. The SsuA 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  83 LSKVTGKRVIYYTVHSNSAQVEAMRSGRLHVAGFSTGPTgyAVNLAGYVPIavkgdeKGFHGYNLIT-----IVRKDSGI 157
Cdd:cd13560    22 LEKALGVKVNWRKFDSGADVNAAMASGSIDIGLLGSPPA--AVAIAAGLPI------EVIWIADVIGdaealVVRKGSGI 93

                          90
                  ....*....|....*..
gi 1108362880 158 NSMADLKGKKVAHTSAS 174
Cdd:cd13560    94 KSLKDLAGKKVAVPFGS 110

ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  54 SDPSTLVFTYTPVEDPALYKDAFADFQthlsKVTGKRVIYYTVHSNSAQVEAMRSGRLHVAGFstGPTGYAVNLAGYVPI 133
Cdd:COG4521    25 AAAKEVTIGYQTIPNPELVAKADGALE----KALGAKVNWRKFDSGADVITALASGDVDIGSI--GSSPFAAALSRGLPI 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1108362880 134 ------AVKGDEKGFhgynlitIVRKDSGINSMADLKGKKVA 169
Cdd:COG4521    99 eviwiaDVIGDAEAL-------VVRNGSGITSPKDLKGKKIA 133

Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA 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. The SsuA 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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1108362880 102 QVEAMRSGRLHVagFSTGPTGYAVNLAGYVP-IAVKGDEkgFHGYNLItiVRKDSGINSMADLKGKKVAHTSASS 175
Cdd:cd13561    43 LVAALGSGSLDV--GYTGPVAFNLPASGQAKvVLINNLE--NATASLI--VRADSGIASIADLKGKKIGTPSGTT 111

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1108362880 150 IVRKD-SGINSMADLKGKKVAHtSASSNSGNLAPRA---LFPAQGLVPDVD 196
Cdd:cd13711    92 IVRKDnSDIKSFADLKGKKSAQ-SLTSNWGKIAKKYgaqVVGVDGFAQAVE 141

Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA 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. The SsuA 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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1108362880 127 LAGYVPIAVKGDEKGFHGYNLITIVRKDSGINSMADLKGKKVAHTSASSNSGNLApRALfPAQGLVPDVDYKV 199
Cdd:cd13559    83 SAGYRSVFIAFLGGSPDGSGNAIVVPKDSPVNSLDDLKGKTVSVPFGSSAHGMLL-RAL-DRAGLNPDTDVTI 153

Substrate binding domain of putative sulfonate binding protein, a member of the type 2 periplasmic binding fold superfamily; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA 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. The SsuA 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 150 IVRKDSGINSMADLKGKKVAHTSASSNSGNLApRALFPAqGLVPDvdykvfysgkhDQSILGVFNGDYDAAPVASDV--- 226
Cdd:cd13556    88 VVRKDSPIRSVADLKGKKVAVTKGTDPYIFLL-RALNTA-GLSKN-----------DIEIVNLQHADGRTALEKGDVdaw 154

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1108362880 227 --YDRMVDAGRVD-GSvlKIIYRSPRFPTSAF 255
Cdd:cd13556   155 agLDPFMAQTELEnGS--RLFYRNPDFNTYGV 184

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880  58 TLVFTYTPVEDpalYKDAFADFQTHLSKVTGKRVIYYTVHSNSAQVEAMRSGRLHVAGFSTGPTgyavnLAGYVPIAVKG 137
Cdd:cd00648     1 TLTVASIGPPP---YAGFAEDAAKQLAKETGIKVELVPGSSIGTLIEALAAGDADVAVGPIAPA-----LEAAADKLAPG 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1108362880 138 DEKGF---HGYNLITIVRKDSGI---NSMADLKGKKVAHTSASSNSGNLAPRALFPAQGLVPDVDYKVFYSGkhDQSILG 211
Cdd:cd00648    73 GLYIVpelYVGGYVLVVRKGSSIkglLAVADLDGKRVGVGDPGSTAVRQARLALGAYGLKKKDPEVVPVPGT--SGALAA 150

                         170
                  ....*....|....
gi 1108362880 212 VFNGDYDAAPVASD 225
Cdd:cd00648   151 VANGAVDAAIVWVP 164

Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold; This subgroup includes uncharacterized periplasmic binding proteins that are related to Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family. 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.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1108362880 143 HGYNLITIVRKDSGINSMADLKGKKVahtsassNSGN 179
Cdd:cd13568    91 HPEAFTVVARADSGIKSFDDLKGKRV-------NIGN 120