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Conserved domains on  [gi|1359100139|gb|AVJ46688|]
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sugar ABC transporter substrate-binding protein [Enterococcus faecium]

Protein Classification

type 2 periplasmic-binding domain-containing protein( domain architecture ID 229383)

type 2 periplasmic-binding protein (PBP2) is typically comprised of two globular subdomains connected by a flexible hinge; it binds its ligand in the cleft between these domains in a manner resembling a Venus flytrap; similar to the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 33-415 7.01e-80

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.


The actual alignment was detected with superfamily member cd14749:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 388  Bit Score: 251.53  E-value: 7.01e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  33 KVEIEFFNQKKEMTQTIQEIAKDFEAKNPDIHVKVVDVP--NAGEVIKTRMLAGDVPDVINLYPqSIELKEWAKAGYLED 110
Cdd:cd14749     1 TITYWQYFTGDTKKKYMDELIADFEKENPNIKVKVVVFPydNYKTKLKTAVAAGEGPDVFNLWP-GGWLAEFVKAGLLLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 111 LT----EEPYLENIKNGYAQRFAIEDRVYSIPLTANVYGFYYNKTAFEEMGI-QAPETWAEFEKIVAEIKDQNKVPFAIA 185
Cdd:cd14749    80 LTdyldPNGVDKRFLPGLADAVTFNGKVYGIPFAARALALFYNKDLFEEAGGvKPPKTWDELIEAAKKDKFKAKGQTGFG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 186 GAEGW-TLNGYHQLAIATAAGGEEEAN--NVWRFSEVNGINAESKEMqkdfnrlDLLREpKALQNNWQGAGYNDTVVTFT 262
Cdd:cd14749   160 LLLGAqGGHWYFQYLVRQAGGGPLSDDgsGKATFNDPAFVQALQKLQ-------DLVKA-GAFQEGFEGIDYDDAGQAFA 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 263 KGDALIMPNGSWAMPMIHSQNPDFEVGTFPFPADEAG-QSLTIGAGDLALSVSATSQHKEEAKRFVEYMTTPEAMQKYYD 341
Cdd:cd14749   232 QGKAAMNIGGSWDLGAIKAGEPGGKIGVFPFPTVGKGaQTSTIGGSDWAIAISANGKKKEAAVKFLKYLTSPEVMKQYLE 311

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1359100139 342 VDGAPCAVEGVIE---NTQDSPLSGLTELAFTDRHLVWLAKDWNSENDFYTLTTNYLHNGNQKAMINALNAFFNPMK 415
Cdd:cd14749   312 DVGLLPAKEVVAKdedPDPVAILGPFADVLNAAGSTPFLDEYWPAAAQVHKDAVQKLLTGKIDPEQVVKQAQSAAAK 388
 
Name Accession Description Interval E-value
PBP2_XBP1_like cd14749
The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; ...
 33-415 7.01e-80

The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; possesses type 2 periplasmic binding fold; This group represents the periplasmic component of an ABC transport system XBP1 that shows preference for xylo-oligosaccharides in the order of xylotriose > xylobiose > xylotetraose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270452 [Multi-domain]  Cd Length: 388  Bit Score: 251.53  E-value: 7.01e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  33 KVEIEFFNQKKEMTQTIQEIAKDFEAKNPDIHVKVVDVP--NAGEVIKTRMLAGDVPDVINLYPqSIELKEWAKAGYLED 110
Cdd:cd14749     1 TITYWQYFTGDTKKKYMDELIADFEKENPNIKVKVVVFPydNYKTKLKTAVAAGEGPDVFNLWP-GGWLAEFVKAGLLLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 111 LT----EEPYLENIKNGYAQRFAIEDRVYSIPLTANVYGFYYNKTAFEEMGI-QAPETWAEFEKIVAEIKDQNKVPFAIA 185
Cdd:cd14749    80 LTdyldPNGVDKRFLPGLADAVTFNGKVYGIPFAARALALFYNKDLFEEAGGvKPPKTWDELIEAAKKDKFKAKGQTGFG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 186 GAEGW-TLNGYHQLAIATAAGGEEEAN--NVWRFSEVNGINAESKEMqkdfnrlDLLREpKALQNNWQGAGYNDTVVTFT 262
Cdd:cd14749   160 LLLGAqGGHWYFQYLVRQAGGGPLSDDgsGKATFNDPAFVQALQKLQ-------DLVKA-GAFQEGFEGIDYDDAGQAFA 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 263 KGDALIMPNGSWAMPMIHSQNPDFEVGTFPFPADEAG-QSLTIGAGDLALSVSATSQHKEEAKRFVEYMTTPEAMQKYYD 341
Cdd:cd14749   232 QGKAAMNIGGSWDLGAIKAGEPGGKIGVFPFPTVGKGaQTSTIGGSDWAIAISANGKKKEAAVKFLKYLTSPEVMKQYLE 311

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1359100139 342 VDGAPCAVEGVIE---NTQDSPLSGLTELAFTDRHLVWLAKDWNSENDFYTLTTNYLHNGNQKAMINALNAFFNPMK 415
Cdd:cd14749   312 DVGLLPAKEVVAKdedPDPVAILGPFADVLNAAGSTPFLDEYWPAAAQVHKDAVQKLLTGKIDPEQVVKQAQSAAAK 388
UgpB COG1653
ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport ...
 6-339 1.99e-71

ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport and metabolism];


Pssm-ID: 441259 [Multi-domain]  Cd Length: 363  Bit Score: 228.78  E-value: 1.99e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139   6 KIILACIALGATISLTACG---KNQEDASGKVEIEFFNQKKEMTQTIQEIAKDFEAKNPDIHVKVVDVPNAG--EVIKTR 80
Cdd:COG1653     2 RRLALALAAALALALAACGgggSGAAAAAGKVTLTVWHTGGGEAAALEALIKEFEAEHPGIKVEVESVPYDDyrTKLLTA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  81 MLAGDVPDVINLYpqSIELKEWAKAGYLEDLTE-----EPYLENIKNGYAQRFAIEDRVYSIPLTANVYGFYYNKTAFEE 155
Cdd:COG1653    82 LAAGNAPDVVQVD--SGWLAEFAAAGALVPLDDlldddGLDKDDFLPGALDAGTYDGKLYGVPFNTDTLGLYYNKDLFEK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 156 MGIQAPETWAEFEKIVAEIKDQN-KVPFAIAGAEGWTLngyhqLAIATAAGGEEeannvwrFSEVNGINAESKEMQKDFN 234
Cdd:COG1653   160 AGLDPPKTWDELLAAAKKLKAKDgVYGFALGGKDGAAW-----LDLLLSAGGDL-------YDEDGKPAFDSPEAVEALE 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 235 RLDLLREPKALQNNWQGAGYNDTVVTFTKGDALIMPNGSWAMPMIHSQNPDFEVGTFPFPADEAGQSLTIGAGDLALSVS 314
Cdd:COG1653   228 FLKDLVKDGYVPPGALGTDWDDARAAFASGKAAMMINGSWALGALKDAAPDFDVGVAPLPGGPGGKKPASVLGGSGLAIP 307

                         330       340
                  ....*....|....*....|....*
gi 1359100139 315 ATSQHKEEAKRFVEYMTTPEAMQKY 339
Cdd:COG1653   308 KGSKNPEAAWKFLKFLTSPEAQAKW 332
SBP_bac_1 pfam01547
Bacterial extracellular solute-binding protein; This family also includes the bacterial ...
 47-337 5.45e-36

Bacterial extracellular solute-binding protein; This family also includes the bacterial extracellular solute-binding protein family POTD/POTF.


Pssm-ID: 460248 [Multi-domain]  Cd Length: 294  Bit Score: 133.70  E-value: 5.45e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  47 QTIQEIAKDFEAKNPDIHVKVVDVPNAG--EVIKTRMLAGDVP-DVINLYPQSIelKEWAKAGYLEDLTEEPYLENIKng 123
Cdd:pfam01547   8 AALQALVKEFEKEHPGIKVEVESVGSGSlaQKLTTAIAAGDGPaDVFASDNDWI--AELAKAGLLLPLDDYVANYLVL-- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 124 yaqrfaIEDRVYSIPLTANVYGFYYNKTAFEEMGIQAPETWAEFEKIVAEIKDQNKVPFAIAGAEGWTLNGYHQLAIATA 203
Cdd:pfam01547  84 ------GVPKLYGVPLAAETLGLIYNKDLFKKAGLDPPKTWDELLEAAKKLKEKGKSPGGAGGGDASGTLGYFTLALLAS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 204 AGGEEEANNVWRFSevNGINAESKEMQKDFNRLDLLREpKALQNNWQGAGYNDTVVTFTKGDALIMPNGSWAM------- 276
Cdd:pfam01547 158 LGGPLFDKDGGGLD--NPEAVDAITYYVDLYAKVLLLK-KLKNPGVAGADGREALALFEQGKAAMGIVGPWAAlaankvk 234

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1359100139 277 ----PMIHSQNPDFEVGTFPFPADEAGqsltiGAGDLALSVSATSQHKEEAKRFVEYMTTPEAMQ 337
Cdd:pfam01547 235 lkvaFAAPAPDPKGDVGYAPLPAGKGG-----KGGGYGLAIPKGSKNKEAAKKFLDFLTSPEAQA 294
bind_CPR_0540 TIGR03850
carbohydrate ABC transporter substrate-binding protein, CPR_0540 family; Members of this ...
 5-354 7.91e-25

carbohydrate ABC transporter substrate-binding protein, CPR_0540 family; Members of this protein are the substrate-binding protein of a predicted carbohydrate transporter operon, together with permease subunits of ABC transporter homology families. This substrate-binding protein frequently co-occurs in genomes with a family of disaccharide phosphorylases, TIGR02336, suggesting that the molecule transported will include beta-D-galactopyranosyl-(1->3)-N-acetyl-D-glucosamine and related carbohydrates. Members of this family are sporadically strain by strain, often in species with a human host association, including Propionibacterium acnes and Clostridium perfringens, and Bacillus cereus. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids]


Pssm-ID: 274815 [Multi-domain]  Cd Length: 437  Bit Score: 105.54  E-value: 7.91e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139   5 KKIILACIALGATISLTACGKNQEDASGKVEIEFFN----QKKEMTQTIQEIAKDFEAKNPDIHVKVVDVPNAGEVIKTR 80
Cdd:TIGR03850   2 KLLALALALAMAASSLAGCGSGTADGASTGEEVTLKvaafEGGYGTKMWEEVVEAFEKSHEGVKVELTVSKNLEDVITPQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  81 MLAGDVPDVInlypqsiELKEWAKAGYLEDLTEEPYLENI-----KNGYAQRFAIED------------------RVYSI 137
Cdd:TIGR03850  82 IQAGDYPDVV-------YLATGRESGLTETLIKDKALADLtdvldMKVPGEDVTVKDkilpgfvgssatnpygdgKTYLA 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 138 PLTANVYGFYYNKTAFEEMGIQAPETWAEFEKIVAEIKDQNKVPFAIAGAegwtlnGYHQ---LAIATAAGGEEEANNVW 214
Cdd:TIGR03850 155 PMFYSPTGLFYNKTLFEEKGWEVPTTWDEMFALGDKAKAEGISLFTYPTT------GYFDaffYALLAEAGGDDFFNKAM 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 215 RFSEVNGINAESKEMQKDFNRLDLLREPKALQN-NWQGAGYNDTVVTFTKgdALIMPNGSWAM-PMIHSQNPD-FEVGTF 291
Cdd:TIGR03850 229 NYEEGIWDTEEAKKAFDTVGKLATYTEPTTVANaNNQDFTKNQQLVLDNK--ALFMPNGTWVVgEMKDAPRADgFEWGMT 306

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1359100139 292 PFPADEAGQSLTIGAGDLALSVSATSQHKEEAKRFVEYMTTPEAMqKYYDVDGAPCAVEGVIE 354
Cdd:TIGR03850 307 ALPAVKEGGDRYSYTFFEQMWIPAAAKNKDLAKEFIAFLYSDEAA-KIFAKSGAVQPVKGIAD 368
PRK10974 PRK10974
sn-glycerol-3-phosphate ABC transporter substrate-binding protein UgpB;
8-344 1.35e-09

sn-glycerol-3-phosphate ABC transporter substrate-binding protein UgpB;


Pssm-ID: 182876 [Multi-domain]  Cd Length: 438  Bit Score: 59.81  E-value: 1.35e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139   8 ILACIALGATISLTACGKNqedasgkvEIEFFNQ-KKEMTQTIQEIAKDFEAKNPDIHVKVVDVPNAGEVIKTRMLA--- 83
Cdd:PRK10974    8 TALGLALGLALSGNAQAVT--------EIPFWHSmEGELGKEVDSLAQRFNASQPDYKIVPVYKGNYEQSLAAGIAAfrs 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  84 GDVPDVINLY--------------PQSIELKEwakAGylEDLTEEPYLENIKNGYAQrfAIEDRVYSIPLTANVYGFYYN 149
Cdd:PRK10974   80 GNAPAILQVYevgtatmmaskaikPVYDVFKD---AG--IPFDESQFVPTVAGYYSD--AKTGHLLSQPFNSSTPVLYYN 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 150 KTAFEEMGI---QAPETWAEFEKIVAEIKDQNKVPFAIAGAEGW----TLNGYHQLAIATAAGGEEEANNVWRFS---EV 219
Cdd:PRK10974  153 KDAFKKAGLdpeQPPKTWQDLAAYAAKLRAAGMKCGYASGWQGWiqleNFSAWHGLPFASKNNGFDGTDAVLEFNkpeQV 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 220 NGInAESKEMQKD-----FNRLDllrEPKAlqnnwqgagyndtvvTFTKGDALIMPNGSWAMPMI-HSQNPDFEVGTFPF 293
Cdd:PRK10974  233 KHI-ALLEEMNKKgdftyVGRKD---ESTE---------------KFYNGDCAITTASSGSLANIrKYAKFNYGVGMMPY 293

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1359100139 294 PADEAG--QSLTIGAGDL-ALSVSATSQHKEEAKrFVEYMTTPEAMQKYYDVDG 344
Cdd:PRK10974  294 DADVKGapQNAIIGGASLwVMQGKDKETYKGVAK-FLDFLAKPENAAEWHQKTG 346
 
Name Accession Description Interval E-value
PBP2_XBP1_like cd14749
The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; ...
 33-415 7.01e-80

The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; possesses type 2 periplasmic binding fold; This group represents the periplasmic component of an ABC transport system XBP1 that shows preference for xylo-oligosaccharides in the order of xylotriose > xylobiose > xylotetraose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270452 [Multi-domain]  Cd Length: 388  Bit Score: 251.53  E-value: 7.01e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  33 KVEIEFFNQKKEMTQTIQEIAKDFEAKNPDIHVKVVDVP--NAGEVIKTRMLAGDVPDVINLYPqSIELKEWAKAGYLED 110
Cdd:cd14749     1 TITYWQYFTGDTKKKYMDELIADFEKENPNIKVKVVVFPydNYKTKLKTAVAAGEGPDVFNLWP-GGWLAEFVKAGLLLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 111 LT----EEPYLENIKNGYAQRFAIEDRVYSIPLTANVYGFYYNKTAFEEMGI-QAPETWAEFEKIVAEIKDQNKVPFAIA 185
Cdd:cd14749    80 LTdyldPNGVDKRFLPGLADAVTFNGKVYGIPFAARALALFYNKDLFEEAGGvKPPKTWDELIEAAKKDKFKAKGQTGFG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 186 GAEGW-TLNGYHQLAIATAAGGEEEAN--NVWRFSEVNGINAESKEMqkdfnrlDLLREpKALQNNWQGAGYNDTVVTFT 262
Cdd:cd14749   160 LLLGAqGGHWYFQYLVRQAGGGPLSDDgsGKATFNDPAFVQALQKLQ-------DLVKA-GAFQEGFEGIDYDDAGQAFA 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 263 KGDALIMPNGSWAMPMIHSQNPDFEVGTFPFPADEAG-QSLTIGAGDLALSVSATSQHKEEAKRFVEYMTTPEAMQKYYD 341
Cdd:cd14749   232 QGKAAMNIGGSWDLGAIKAGEPGGKIGVFPFPTVGKGaQTSTIGGSDWAIAISANGKKKEAAVKFLKYLTSPEVMKQYLE 311

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1359100139 342 VDGAPCAVEGVIE---NTQDSPLSGLTELAFTDRHLVWLAKDWNSENDFYTLTTNYLHNGNQKAMINALNAFFNPMK 415
Cdd:cd14749   312 DVGLLPAKEVVAKdedPDPVAILGPFADVLNAAGSTPFLDEYWPAAAQVHKDAVQKLLTGKIDPEQVVKQAQSAAAK 388
UgpB COG1653
ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport ...
 6-339 1.99e-71

ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport and metabolism];


Pssm-ID: 441259 [Multi-domain]  Cd Length: 363  Bit Score: 228.78  E-value: 1.99e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139   6 KIILACIALGATISLTACG---KNQEDASGKVEIEFFNQKKEMTQTIQEIAKDFEAKNPDIHVKVVDVPNAG--EVIKTR 80
Cdd:COG1653     2 RRLALALAAALALALAACGgggSGAAAAAGKVTLTVWHTGGGEAAALEALIKEFEAEHPGIKVEVESVPYDDyrTKLLTA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  81 MLAGDVPDVINLYpqSIELKEWAKAGYLEDLTE-----EPYLENIKNGYAQRFAIEDRVYSIPLTANVYGFYYNKTAFEE 155
Cdd:COG1653    82 LAAGNAPDVVQVD--SGWLAEFAAAGALVPLDDlldddGLDKDDFLPGALDAGTYDGKLYGVPFNTDTLGLYYNKDLFEK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 156 MGIQAPETWAEFEKIVAEIKDQN-KVPFAIAGAEGWTLngyhqLAIATAAGGEEeannvwrFSEVNGINAESKEMQKDFN 234
Cdd:COG1653   160 AGLDPPKTWDELLAAAKKLKAKDgVYGFALGGKDGAAW-----LDLLLSAGGDL-------YDEDGKPAFDSPEAVEALE 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 235 RLDLLREPKALQNNWQGAGYNDTVVTFTKGDALIMPNGSWAMPMIHSQNPDFEVGTFPFPADEAGQSLTIGAGDLALSVS 314
Cdd:COG1653   228 FLKDLVKDGYVPPGALGTDWDDARAAFASGKAAMMINGSWALGALKDAAPDFDVGVAPLPGGPGGKKPASVLGGSGLAIP 307

                         330       340
                  ....*....|....*....|....*
gi 1359100139 315 ATSQHKEEAKRFVEYMTTPEAMQKY 339
Cdd:COG1653   308 KGSKNPEAAWKFLKFLTSPEAQAKW 332
PBP2_TMBP_like cd13585
The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and ...
 44-346 6.35e-49

The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and similar oligosaccharides; possess type 2 periplasmic binding fold; This family includes the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270303 [Multi-domain]  Cd Length: 383  Bit Score: 170.66  E-value: 6.35e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  44 EMTQTIQEIAKDFEAKNPDIHVKVVDVPNAG--EVIKTRMLAGDVPDVINLYPQsiELKEWAKAGYLEDLT----EEPYL 117
Cdd:cd13585    11 AETAALKKLIDAFEKENPGVKVEVVPVPYDDywTKLTTAAAAGTAPDVFYVDGP--WVPEFASNGALLDLDdyieKDGLD 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 118 ENIKNGYAQRFAIEDRVYSIPLTANVYGFYYNKTAFEEMG--IQAPETWAEFEKIVAEIKDQNKVPFAIAgAEGWTLNGY 195
Cdd:cd13585    89 DDFPPGLLDAGTYDGKLYGLPFDADTLVLFYNKDLFDKAGpgPKPPWTWDELLEAAKKLTDKKGGQYGFA-LRGGSGGQT 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 196 HQLAIATAAGGEEeannvwrFSEVNG-INAESKEMQKDFNRL-DLLRE---PKALQNNWQGAgyndtVVTFTKGDALIMP 270
Cdd:cd13585   168 QWYPFLWSNGGDL-------LDEDDGkATLNSPEAVEALQFYvDLYKDgvaPSSATTGGDEA-----VDLFASGKVAMMI 235

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1359100139 271 NGSWAMPMIHSQNPDFEVGTFPFPADEAGQSLTIGAGDlALSVSATSQHKEEAKRFVEYMTTPEAMQKYYDVDGAP 346
Cdd:cd13585   236 DGPWALGTLKDSKVKFKWGVAPLPAGPGGKRASVLGGW-GLAISKNSKHPEAAWKFIKFLTSKENQLKLGGAAGPA 310
MalE COG2182
Maltose-binding periplasmic protein MalE [Carbohydrate transport and metabolism];
1-346 1.86e-43

Maltose-binding periplasmic protein MalE [Carbohydrate transport and metabolism];


Pssm-ID: 441785 [Multi-domain]  Cd Length: 410  Bit Score: 156.65  E-value: 1.86e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139   1 MKWSKKIILAcIALGATISLTACGKNQED------ASGKVEIEFFNQKKEmTQTIQEIAKDFEAKnPDIHVKVVDVPNAG 74
Cdd:COG2182     1 MKRRLLAALA-LALALALALAACGSGSSSsgsssaAGAGGTLTVWVDDDE-AEALEEAAAAFEEE-PGIKVKVVEVPWDD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  75 --EVIKTRMLAGDVPDVINL-YPQsieLKEWAKAGYLEDLTE-EPYLENIKNGYAQRFAIEDRVYSIPLTANVYGFYYNK 150
Cdd:COG2182    78 lrEKLTTAAPAGKGPDVFVGaHDW---LGELAEAGLLAPLDDdLADKDDFLPAALDAVTYDGKLYGVPYAVETLALYYNK 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 151 TAFEEmgiQAPETWAEFEKIVAEIKDQNKVPFAIAGAegwtlNGYHQLAIATAAGGE---EEANNVwrfsevNGINAESK 227
Cdd:COG2182   155 DLVKA---EPPKTWDELIAAAKKLTAAGKYGLAYDAG-----DAYYFYPFLAAFGGYlfgKDGDDP------KDVGLNSP 220

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 228 EMQKDFNRLDLLREPKALQNNwqgAGYNDTVVTFTKGDALIMPNGSWAMPMIhSQNPDFEVGTFPFPADEAGQSLTIGAG 307
Cdd:COG2182   221 GAVAALEYLKDLIKDGVLPAD---ADYDAADALFAEGKAAMIINGPWAAADL-KKALGIDYGVAPLPTLAGGKPAKPFVG 296

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 1359100139 308 DLALSVSATSQHKEEAKRFVEYMTTPEAMQKYYDVDGAP 346
Cdd:COG2182   297 VKGFGVSAYSKNKEAAQEFAEYLTSPEAQKALFEATGRI 335
PBP2_UgpB cd14748
The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; ...
 35-339 2.84e-43

The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; possesses type 2 periplasmic binding fold; This group includes the periplasmic component of an ABC transport system specific for sn-glycerol-3-phosphate (G3P) and closely related proteins from archaea and bacteria. Under phophate starvation conditions, Escherichia coli can utilize G3P as phosphate source when exclusively imported by an ATP-binding cassette (ABC) transporter composed of the periplasmic binding protein, UgpB, the transmembrane subunits, UgpA and UgpE, and a homodimer of the nucleotide binding subunit, UgpC. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270451 [Multi-domain]  Cd Length: 385  Bit Score: 155.53  E-value: 2.84e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  35 EIEF-FNQKKEMTQTIQEIAKDFEAKNPDIHVKVVDVPNAGEV---IKTRMLAGDVPDVINLYpqSIELKEWAKAGYLED 110
Cdd:cd14748     1 EITFwHGMSGPDGKALEELVDEFNKSHPDIKVKAVYQGSYDDTltkLLAALAAGTAPDVAQVD--ASWVAQLADSGALEP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 111 LTE-----EPYLENIKNGYAQRFAIEDRVYSIPLTANVYGFYYNKTAFEEMGI---QAPETWAEFEKIVAEIKDQNK--- 179
Cdd:cd14748    79 LDDyidkdGVDDDDFYPAALDAGTYDGKLYGLPFDTSTPVLYYNKDLFEEAGLdpeKPPKTWDELEEAAKKLKDKGGktg 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 180 -VPFAIA-GAEGWTLngyhqLAIATAAGGE---EEANNVWrFSEVNGINAesKEMQKDfnrldLLREPKALQNNWQGAGY 254
Cdd:cd14748   159 rYGFALPpGDGGWTF-----QALLWQNGGDlldEDGGKVT-FNSPEGVEA--LEFLVD-----LVGKDGVSPLNDWGDAQ 225

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 255 NDtvvtFTKGDALIMPNGSWAMPMIHSQNPDFEVGTFPFPADEAGQSLTIGAGDlALSVSA-TSQHKEEAKRFVEYMTTP 333
Cdd:cd14748   226 DA----FISGKVAMTINGTWSLAGIRDKGAGFEYGVAPLPAGKGKKGATPAGGA-SLVIPKgSSKKKEAAWEFIKFLTSP 300


                  ....*.
gi 1359100139 334 EAMQKY 339
Cdd:cd14748   301 ENQAKW 306
SBP_bac_1 pfam01547
Bacterial extracellular solute-binding protein; This family also includes the bacterial ...
 47-337 5.45e-36

Bacterial extracellular solute-binding protein; This family also includes the bacterial extracellular solute-binding protein family POTD/POTF.


Pssm-ID: 460248 [Multi-domain]  Cd Length: 294  Bit Score: 133.70  E-value: 5.45e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  47 QTIQEIAKDFEAKNPDIHVKVVDVPNAG--EVIKTRMLAGDVP-DVINLYPQSIelKEWAKAGYLEDLTEEPYLENIKng 123
Cdd:pfam01547   8 AALQALVKEFEKEHPGIKVEVESVGSGSlaQKLTTAIAAGDGPaDVFASDNDWI--AELAKAGLLLPLDDYVANYLVL-- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 124 yaqrfaIEDRVYSIPLTANVYGFYYNKTAFEEMGIQAPETWAEFEKIVAEIKDQNKVPFAIAGAEGWTLNGYHQLAIATA 203
Cdd:pfam01547  84 ------GVPKLYGVPLAAETLGLIYNKDLFKKAGLDPPKTWDELLEAAKKLKEKGKSPGGAGGGDASGTLGYFTLALLAS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 204 AGGEEEANNVWRFSevNGINAESKEMQKDFNRLDLLREpKALQNNWQGAGYNDTVVTFTKGDALIMPNGSWAM------- 276
Cdd:pfam01547 158 LGGPLFDKDGGGLD--NPEAVDAITYYVDLYAKVLLLK-KLKNPGVAGADGREALALFEQGKAAMGIVGPWAAlaankvk 234

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1359100139 277 ----PMIHSQNPDFEVGTFPFPADEAGqsltiGAGDLALSVSATSQHKEEAKRFVEYMTTPEAMQ 337
Cdd:pfam01547 235 lkvaFAAPAPDPKGDVGYAPLPAGKGG-----KGGGYGLAIPKGSKNKEAAKKFLDFLTSPEAQA 294
PBP2_GacH cd14751
The periplasmic-binding component of the putative oligosacchride ABC transporter GacHFG; ...
 44-338 4.03e-35

The periplasmic-binding component of the putative oligosacchride ABC transporter GacHFG; possesses type 2 periplasmic binding fold; This group represents the periplasmic component GacH of an ABC import system. GacH is identified as a maltose/maltodextrin-binding protein with a low affinity for acarbose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270454 [Multi-domain]  Cd Length: 376  Bit Score: 133.27  E-value: 4.03e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  44 EMTQTIQEIAKDFEAKNPDIHVKVVDVPNAG--EVIKTRMLAGDVPDVINLypQSIELKEWAKAGYLEDLTEEPYLENIK 121
Cdd:cd14751    11 EEKVLYEKLIPAFEKEYPKIKVKAVRVPFDGlhNQIKTAAAGGQAPDVMRA--DIAWVPEFAKLGYLQPLDGTPAFDDIV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 122 NGYAQRFA---IEDRVYSIPLTANVYGFYYNKTAFEEMGIQAPETWAEFEKIVAEIKD-QNKVPFAIAGAEGWTLNGYhq 197
Cdd:cd14751    89 DYLPGPMEtnrYNGHYYGVPQVTNTLALFYNKRLLEEAGTEVPKTMDELVAAAKAIKKkKGRYGLYISGDGPYWLLPF-- 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 198 laiATAAGGE---EEANNVWRFSEvnginAESKEMQKdfnRLDLLREPKALQnnWQGAGYNDTVVTFTKGDALIMPNGSW 274
Cdd:cd14751   167 ---LWSFGGDltdEKKATGYLNSP-----ESVRALET---IVDLYDEGAITP--CASGGYPNMQDGFKSGRYAMIVNGPW 233

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1359100139 275 AMPMIHSQN---PDFEVGTFPFPADEAGQSLTIGAGDLalSVSATSQHKEEAKRFVEYMTTPEAMQK 338
Cdd:cd14751   234 AYADILGGKefkDPDNLGIAPVPAGPGGSGSPVGGEDL--VIFKGSKNKDAAWKFVKFMSSAEAQAL 298
PBP2_MalE cd14747
Maltose-binding protein MalE; possesses type 2 periplasmic binding fold; This group includes ...
 47-344 4.26e-35

Maltose-binding protein MalE; possesses type 2 periplasmic binding fold; This group includes the periplasmic maltose-binding component of an ABC transport system from the phytopathogen Xanthomonas citri and its related bacterial proteins. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270450 [Multi-domain]  Cd Length: 386  Bit Score: 133.59  E-value: 4.26e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  47 QTIQEIAKDFEAKNPDIHVKVVDVP--NAGEVIKTRMLAGDVPDVINLypQSIELKEWAKAGYLEDLTeePYLENIKN-- 122
Cdd:cd14747    14 ELLKELADEFEKENPGIEVKVQVLPwgDAHTKITTAAASGDGPDVVQL--GNTWVAEFAAMGALEDLT--PYLEDLGGdk 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 123 ----GYAQRFAIEDRVYSIPLTANVYGFYYNKTAFEEMG-IQAPETWAEFEKIVA--EIKDQNKVPFAIAGAEgwtlNGY 195
Cdd:cd14747    90 dlfpGLVDTGTVDGKYYGVPWYADTRALFYRTDLLKKAGgDEAPKTWDELEAAAKkiKADGPDVSGFAIPGKN----DVW 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 196 HQLAIATAAGGEEEANNVWRFSEVNGinAESKEMQKDFNRL-DLLREPKALQNNWQgagynDTVVTFTKGDALIMPNGSW 274
Cdd:cd14747   166 HNALPFVWGAGGDLATKDKWKATLDS--PEAVAGLEFYTSLyQKGLSPKSTLENSA-----DVEQAFANGKVAMIISGPW 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1359100139 275 AMPMIHSQNP--DFEVGTFPFPADEAGQSLT-IGAGDLAlsVSATSQHKEEAKRFVEYMTTPEAMQKYYDVDG 344
Cdd:cd14747   239 EIGAIREAGPdlAGKWGVAPLPGGPGGGSPSfAGGSNLA--VFKGSKNKDLAWKFIEFLSSPENQAAYAKATG 309
PBP2_TMBP cd14750
The periplasmic-binding component of ABC transport systems specific for trehalose/maltose; ...
 49-339 2.18e-32

The periplasmic-binding component of ABC transport systems specific for trehalose/maltose; possesses type 2 periplasmic binding fold; This group represents the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270453 [Multi-domain]  Cd Length: 385  Bit Score: 126.26  E-value: 2.18e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  49 IQEIAKDFEAKNPDIHVKVVDVPN-AGEV---IKTRMLAGD-VPDVINLypQSIELKEWAKAGYLEDLTEE--------P 115
Cdd:cd14750    16 LKKAIAAFEKKHPDIKVEIEELPAsSDDQrqqLVTALAAGSsAPDVLGL--DVIWIPEFAEAGWLLPLTEYlkeeedddF 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 116 YLENIKNGYAQrfaieDRVYSIPLTANVYGFYYNKTAFEEMGIQAPETWAEFEKIVAEIKDQNKV--PFAIAGA--EGWT 191
Cdd:cd14750    94 LPATVEANTYD-----GKLYALPWFTDAGLLYYRKDLLEKYGPEPPKTWDELLEAAKKRKAGEPGiwGYVFQGKqyEGLV 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 192 LNGYHQLAiatAAGGE--EEANNVWRFSEVNGINAeskemqkdfnrLDLLR---EPKALQNNWQGAGYNDTVVTFTKGDA 266
Cdd:cd14750   169 CNFLELLW---SNGGDifDDDSGKVTVDSPEALEA-----------LQFLRdliGEGISPKGVLTYGEEEARAAFQAGKA 234

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1359100139 267 LIMPNGSWAMPMIHSQNPDFE--VGTFPFPADEAGQSLTIgAGDLALSVSATSQHKEEAKRFVEYMTTPEaMQKY 339
Cdd:cd14750   235 AFMRNWPYAYALLQGPESAVAgkVGVAPLPAGPGGGSAST-LGGWNLAISANSKHKEAAWEFVKFLTSPE-VQKR 307
SBP_bac_8 pfam13416
Bacterial extracellular solute-binding protein; This family includes bacterial extracellular ...
 51-344 5.83e-28

Bacterial extracellular solute-binding protein; This family includes bacterial extracellular solute-binding proteins.


Pssm-ID: 433189 [Multi-domain]  Cd Length: 281  Bit Score: 111.73  E-value: 5.83e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  51 EIAKDFEAKNpDIHVKVV--DVPNAGEVIKTRMLAGDVPDVINLYPQSIELKEWAKAGYLEDLTEEPYLENIKNGYAQrF 128
Cdd:pfam13416   1 ALAKAFEKKT-GVTVEVEpqASNDLQAKLLAAAAAGNAPDLDVVWIAADQLATLAEAGLLADLSDVDNLDDLPDALDA-A 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 129 AIEDRVYSIPLTANV-YGFYYNKTAFEEMGiQAPETWAEFEKIVAEIKdqnkvpfaiaGAEGWTLNGYHQLAIATAAGGe 207
Cdd:pfam13416  79 GYDGKLYGVPYAASTpTVLYYNKDLLKKAG-EDPKTWDELLAAAAKLK----------GKTGLTDPATGWLLWALLADG- 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 208 eeannvWRFSEVNGINAESKEMQKDFnrldllrepKALQNNWQGAGYN-DTVVTFTKGDALIMPNGSWAMPMIHSQNPDF 286
Cdd:pfam13416 147 ------VDLTDDGKGVEALDEALAYL---------KKLKDNGKVYNTGaDAVQLFANGEVAMTVNGTWAAAAAKKAGKKL 211

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1359100139 287 EVgTFPfpadeaGQSLTIGAGDLALSVSATSQhKEEAKRFVEYMTTPEAMQKYYDVDG 344
Cdd:pfam13416 212 GA-VVP------KDGSFLGGKGLVVPAGAKDP-RLAALDFIKFLTSPENQAALAEDTG 261
PBP2_Maltose_binding_like cd13586
The periplasmic-binding component of ABC transport systems specific for maltose and related ...
 47-346 2.86e-26

The periplasmic-binding component of ABC transport systems specific for maltose and related polysaccharides; possess type 2 periplasmic binding fold; This subfamily represents the periplasmic binding component of ABC transport systems involved in uptake of polysaccharides including maltose, maltodextrin, and cyclodextrin. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270304 [Multi-domain]  Cd Length: 367  Bit Score: 108.54  E-value: 2.86e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  47 QTIQEIAKDFEAKNpDIHVKVVDVPNAG--EVIKTRMLAGDVPDVInlYPQSIELKEWAKAGYLEDLTE--EPYLENIKN 122
Cdd:cd13586    13 EYLKELAEEFEKKY-GIKVEVVYVDSGDtrEKFITAGPAGKGPDVF--FGPHDWLGELAAAGLLAPIPEylAVKIKNLPV 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 123 GYAQrFAIEDRVYSIPLTANVYGFYYNKtafeEMGIQAPETWAEFEKIVAEI--KDQNKVPFAIagaeGWTlNGYHQLAI 200
Cdd:cd13586    90 ALAA-VTYNGKLYGVPVSVETIALFYNK----DLVPEPPKTWEELIALAKKFndKAGGKYGFAY----DQT-NPYFSYPF 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 201 ATAAGGEE-EANNVwrfsEVNGINAESKEMQKDFNRL-DLLREPKAL--QNNWQGAGYNdtvvtFTKGDALIMPNGSWAM 276
Cdd:cd13586   160 LAAFGGYVfGENGG----DPTDIGLNNEGAVKGLKFIkDLKKKYKVLppDLDYDIADAL-----FKEGKAAMIINGPWDL 230

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 277 PMIHSQNPDFEVGtfPFPADEAGQSLTIGAGDLALSVSATSQHKEEAKRFVEYMTTPEAMQKYYDVDGAP 346
Cdd:cd13586   231 ADYKDAGINFGVA--PLPTLPGGKQAAPFVGVQGAFVSAYSKNKEAAVEFAEYLTSDEAQLLLFEKTGRI 298
bind_CPR_0540 TIGR03850
carbohydrate ABC transporter substrate-binding protein, CPR_0540 family; Members of this ...
 5-354 7.91e-25

carbohydrate ABC transporter substrate-binding protein, CPR_0540 family; Members of this protein are the substrate-binding protein of a predicted carbohydrate transporter operon, together with permease subunits of ABC transporter homology families. This substrate-binding protein frequently co-occurs in genomes with a family of disaccharide phosphorylases, TIGR02336, suggesting that the molecule transported will include beta-D-galactopyranosyl-(1->3)-N-acetyl-D-glucosamine and related carbohydrates. Members of this family are sporadically strain by strain, often in species with a human host association, including Propionibacterium acnes and Clostridium perfringens, and Bacillus cereus. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids]


Pssm-ID: 274815 [Multi-domain]  Cd Length: 437  Bit Score: 105.54  E-value: 7.91e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139   5 KKIILACIALGATISLTACGKNQEDASGKVEIEFFN----QKKEMTQTIQEIAKDFEAKNPDIHVKVVDVPNAGEVIKTR 80
Cdd:TIGR03850   2 KLLALALALAMAASSLAGCGSGTADGASTGEEVTLKvaafEGGYGTKMWEEVVEAFEKSHEGVKVELTVSKNLEDVITPQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  81 MLAGDVPDVInlypqsiELKEWAKAGYLEDLTEEPYLENI-----KNGYAQRFAIED------------------RVYSI 137
Cdd:TIGR03850  82 IQAGDYPDVV-------YLATGRESGLTETLIKDKALADLtdvldMKVPGEDVTVKDkilpgfvgssatnpygdgKTYLA 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 138 PLTANVYGFYYNKTAFEEMGIQAPETWAEFEKIVAEIKDQNKVPFAIAGAegwtlnGYHQ---LAIATAAGGEEEANNVW 214
Cdd:TIGR03850 155 PMFYSPTGLFYNKTLFEEKGWEVPTTWDEMFALGDKAKAEGISLFTYPTT------GYFDaffYALLAEAGGDDFFNKAM 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 215 RFSEVNGINAESKEMQKDFNRLDLLREPKALQN-NWQGAGYNDTVVTFTKgdALIMPNGSWAM-PMIHSQNPD-FEVGTF 291
Cdd:TIGR03850 229 NYEEGIWDTEEAKKAFDTVGKLATYTEPTTVANaNNQDFTKNQQLVLDNK--ALFMPNGTWVVgEMKDAPRADgFEWGMT 306

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1359100139 292 PFPADEAGQSLTIGAGDLALSVSATSQHKEEAKRFVEYMTTPEAMqKYYDVDGAPCAVEGVIE 354
Cdd:TIGR03850 307 ALPAVKEGGDRYSYTFFEQMWIPAAAKNKDLAKEFIAFLYSDEAA-KIFAKSGAVQPVKGIAD 368
PBP2_ABC_oligosaccharides cd13522
The periplasmic-binding component of ABC transport systems specific for maltose and related ...
 47-344 2.09e-20

The periplasmic-binding component of ABC transport systems specific for maltose and related oligosaccharides; possess type 2 periplasmic binding fold; This family represents the periplasmic binding component of ABC transport systems involved in uptake of oligosaccharides including maltose, trehalose, maltodextrin, and cyclodextrin. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270240 [Multi-domain]  Cd Length: 368  Bit Score: 92.09  E-value: 2.09e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  47 QTIQEIAKDFEAKNPDIHVKVVDVPNAG--EVIKTRMLAGDVPDVInlYPQSIELKEWAKAGYLEDLTEepYLEniKNGY 124
Cdd:cd13522    14 QAVNELIAKFEKAYPGITVEVTYQDTEArrQFFSTAAAGGKGPDVV--FGPSDSLGPFAAAGLLAPLDE--YVS--KSGK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 125 AQRFAIED-----RVYSIPLTANVYGFYYNKTAFEEmgiQAPETWAEFEKIVAEIKDQNKVPFAIAGAEGwtlngYHQLA 199
Cdd:cd13522    88 YAPNTIAAmklngKLYGVPVSVGAHLMYYNKKLVPK---NPPKTWQELIALAQGLKAKNVWGLVYNQNEP-----YFFAA 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 200 IATAAGGEE-EANNVwrfseVNGINAESKEMQKDFNRL-DLLREPKALQNNwqgAGYNDTVVTFTKGDALIMPNGSWAMP 277
Cdd:cd13522   160 WIGGFGGQVfKANNG-----KNNPTLDTPGAVEALQFLvDLKSKYKIMPPE---TDYSIADALFKAGKAAMIINGPWDLG 231

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1359100139 278 MIHSQ-NPDFevGTFPFPADEAGQSLTIGAGDLALSVSATSQHKEEAKRFVEYMTTPEAMQKYYDVDG 344
Cdd:cd13522   232 DYRQAlKINL--GVAPLPTFSGTKHAAPFVGGKGFGINKESQNKAAAVEFVKYLTSYQAQLVLFDDAG 297
PBP2_CMBP cd13658
The periplasmic binding component of ABC transport systems specific for cyclo/maltodextrin; ...
 49-341 3.95e-15

The periplasmic binding component of ABC transport systems specific for cyclo/maltodextrin; possess the type 2 periplasmic binding fold; This group includes the periplasmic cyclo/maltodextrin-binding protein of Thermoactinomyces vulgaris ATP-binding cassette transporter and related proteins. Cyclodextrins are a family of compounds composed of glucose units connected by 1, 4 glycosidic linkages to form a series of oligosaccharide rings, and their cavity is hydrophibic which allows cyclodextrins to accomodate hydrophobic molecules/moieties in the cavity. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270376 [Multi-domain]  Cd Length: 372  Bit Score: 76.37  E-value: 3.95e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  49 IQEIAKDFEAKNpDIHVKVVDVPNAGEVIKTRM--LAGDVPDVInLYPQSiELKEWAKAGYLEDLTEEpylENIKNGYA- 125
Cdd:cd13658    15 IKKIAKQYTKKT-GVKVKLVEVDQLDQLEKLSLdgPAGKGPDVM-VAPHD-RIGSAVLQGLLSPIKLS---KDKKKGFTd 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 126 ---QRFAIEDRVYSIPLTANVYGFYYNKTAFEemgiQAPETWAEFEKIVAEIKDQNKVPFAIAGAegWTlNGYHQLAIAT 202
Cdd:cd13658    89 qalKALTYDGKLYGLPAAVETLALYYNKDLVK----NAPKTFDELEALAKDLTKEKGKQYGFLAD--AT-NFYYSYGLLA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 203 AAGGEEEANNVwRFSEVNGINAESKEMQKDFNRLDLLREPKALQNNWQGagynDTVVT-FTKGDALIMPNGSWAMPMIHS 281
Cdd:cd13658   162 GNGGYIFKKNG-SDLDINDIGLNSPGAVKAVKFLKKWYTEGYLPKGMTG----DVIQGlFKEGKAAAVIDGPWAIQEYQE 236

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 282 QNPDFevGTFPFPADEAGQSLTIGAGDLALSVSATSQHKEEAKRFVEYMTTPEAMQKYYD 341
Cdd:cd13658   237 AGVNY--GVAPLPTLPNGKPMAPFLGVKGWYLSAYSKHKEWAQKFMEFLTSKENLKKRYD 294
PBP2_AlgQ_like_1 cd13580
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ...
 49-414 5.34e-14

Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is 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. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270298 [Multi-domain]  Cd Length: 471  Bit Score: 73.52  E-value: 5.34e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  49 IQEIAKDFeakNPDIHVKVVDVPNAGEVIKTRMLAGDVPDVINLYPQSIeLKEWAKAGYLEDLTE--EPYLENIKNGYAQ 126
Cdd:cd13580    25 TKYLEEKT---NIDVKVKWVPDSSYDEKLNLALASGDLPDIVVVNDPQL-SITLVKQGALWDLTDylDKYYPNLKKIIEQ 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 127 ----RFAIEDRVYSIPLTANVY---GFYYNKTAFEEMGIQAPETWAEFEKIVAEIKDQN------KVPFAIAGAEGWTLN 193
Cdd:cd13580   101 egwdSASVDGKIYGIPRKRPLIgrnGLWIRKDWLDKLGLEVPKTLDELYEVAKAFTEKDpdgngkKDTYGLTDTKDLIGS 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 194 GYHQLAIATAAGGE---EEANNVWRFSevnGINAESKEMQKDFNRldlLREPKALQNNWqgAGYNDTVVT--FTKGDALI 268
Cdd:cd13580   181 GFTGLFGAFGAPPNnwwKDEDGKLVPG---SIQPEMKEALKFLKK---LYKEGLIDPEF--AVNDGTKANekFISGKAGI 252

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 269 MPNGSWAMP----MIHSQNPDFEVGTFPFPADEAGQSL--TIGAGDLALSVSATSQHKEEAKRFVEYMTTPEaMQKY--- 339
Cdd:cd13580   253 FVGNWWDPAwpqaSLKKNDPDAEWVAVPIPSGPDGKYGvwAESGVNGFFVIPKKSKKPEAILKLLDFLSDPE-VQKLldy 331

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 340 ------YDVDGAPCAvegVIENTQDSPLSGLTELAFTDRHLVWLAKDWNSENDFYTLTTNYLHNGNQKAMINALNAFFNP 413
Cdd:cd13580   332 giegvhYTVKDGGPV---NIIPPDKQEVGDATLDYFQGSLALEKYKLTNNGERKSDAKKEALDERVVNANDEENENIAVG 408


                  .
gi 1359100139 414 M 414
Cdd:cd13580   409 P 409
PBP2_Maltodextrin cd13657
The periplasmic binding component of ABC transport system specific for maltodextrin; This ...
 49-357 3.97e-13

The periplasmic binding component of ABC transport system specific for maltodextrin; This group includes the periplasmic maltodextrin-binding protein of a binding protein-dependent ATP-binding cassette transporter. Maltodextrin is a polysaccharide that is used as a food addtive and can be enzymatically produced from any starch . Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270375 [Multi-domain]  Cd Length: 368  Bit Score: 70.10  E-value: 3.97e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  49 IQEIAKDFEAKNPDIHVKVV--DVPNAGEVIKTRMLAGDVPDVInLYPQSiELKEWAKAGYLEDLTEEpYLENIKNGYAq 126
Cdd:cd13657    16 LQQIIDEFEAKYPVPNVKVPfeKKPDLQNKLLTAIPAGEGPDLF-IWAHD-WIGQFAEAGLLVPISDY-LSEDDFENYL- 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 127 RFAIE-----DRVYSIPLTANVYGFYYNKtafeEMGIQAPETWAEFEKIVAEIKDQNKVPFAIAGAEGwtlNGYHQLAIA 201
Cdd:cd13657    92 PTAVEavtykGKVYGLPEAYETVALIYNK----ALVDQPPETTDELLAIMKDHTDPAAGSYGLAYQVS---DAYFVSAWI 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 202 TAAGGE---EEANNVwrfsevnGINaeSKEMQKDFNRLDLLREPKALQNnwqgAGYNDTVVTFTKGDALIMPNGSWAMPM 278
Cdd:cd13657   165 FGFGGYyfdDETDKP-------GLD--TPETIKGIQFLKDFSWPYMPSD----PSYNTQTSLFNEGKAAMIINGPWFIGG 231

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1359100139 279 IHSQNPDFEVGTFPFPADEAGQSLTIGAGDLALSVSATSQHKEEAKRFVEYMTTPEAMQKYYDVDGAPCAVEGVIENTQ 357
Cdd:cd13657   232 IKAAGIDLGVAPLPTVDGTNPPRPYSGVEGIYVTKYAERKNKEAALDFAKFFTTAEASKILADENGYVPAATNAYDDAE 310
PBP2_AlgQ_like_4 cd13583
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ...
 51-335 4.04e-12

Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is 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. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270301 [Multi-domain]  Cd Length: 478  Bit Score: 67.77  E-value: 4.04e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  51 EIAKDFEAKNpDIHVKVVDVPNAGEVIKTRML--AGDVPDVIN-LYPQsiELKEWAKAGYLEDLTE-EPYLENIKNGYAQ 126
Cdd:cd13583    21 LIWKEIEEKT-NVKFKRTPIPSSDYETKRSLLiaSGDAPDIIPvLYPG--EENEFVASGALLPISDyLDYMPNYKKYVEK 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 127 ----------RFAiEDRVYSIPLTANV----YGFYYNKTAFEEMGIQAPETWAEFEKIVAEIKDQ--NKVPFAIAGAEGW 190
Cdd:cd13583    98 wglgkelatgRQS-DGKYYSLPGLHEDpgvqYSFLYRKDIFEKAGIKIPTTWDEFYAALKKLKEKypDSYPYSDRWNSNA 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 191 TLNGYHQLAIATAAGG------EEEANNVWRFsevnGINAESKEMQKDFNRL--DLLREPKALQNNwqgagyNDTVVT-F 261
Cdd:cd13583   177 LLLIAAPAFGTTAGWGfsnytyDPDTDKFVYG----ATTDEYKDMLQYFNKLyaEGLLDPESFTQT------DDQAKAkF 246

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 262 TKGDALIMPNGSWAM-----PMIHSQNPDFEVGTFPFPADEAGQSLTIGAGDL--ALSVSAT-SQHKEEAKRFVEYMTTP 333
Cdd:cd13583   247 LNGKSFVITTNPQTVdelqrNLRAADGGNYEVVSITPPAGPAGKAINGSRLENgfMISSKAKdSKNFEALLQFLDWLYSD 326


                  ..
gi 1359100139 334 EA 335
Cdd:cd13583   327 EG 328
PotD COG0687
Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism];
4-354 5.87e-12

Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism];


Pssm-ID: 440451 [Multi-domain]  Cd Length: 348  Bit Score: 66.47  E-value: 5.87e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139   4 SKKIILACIALGATISLTACGKNqedASGKVEIEFFNQKKEMTQtiqEIAKDFEAKNpDIHVKVVDVPNAGEVIkTRMLA 83
Cdd:COG0687     2 SRRSLLGLAAAALAAALAGGAPA---AAAEGTLNVYNWGGYIDP---DVLEPFEKET-GIKVVYDTYDSNEEML-AKLRA 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  84 GDVP-DVInlYPQSIELKEWAKAGYLEDLTEE--PYLENIKNGYAQRFAIEDRVYSIPLTANVYGFYYNKTAFEEmgiqA 160
Cdd:COG0687    74 GGSGyDVV--VPSDYFVARLIKAGLLQPLDKSklPNLANLDPRFKDPPFDPGNVYGVPYTWGTTGIAYNTDKVKE----P 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 161 PETWAEFekivaeIKDQNKVPFAIagaegwtLNGYHQLAIATAAggeeeannvwrfseVNGINAESKeMQKDFNRL-DLL 239
Cdd:COG0687   148 PTSWADL------WDPEYKGKVAL-------LDDPREVLGAALL--------------YLGYDPNST-DPADLDAAfELL 199

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 240 REpkaLQNNWqgAGYNDTVVT----FTKGDALIMPNGSWAMPMIHSQNPDFEVgTFPfpadEAGQSLTIGagdlALSVSA 315
Cdd:COG0687   200 IE---LKPNV--RAFWSDGAEyiqlLASGEVDLAVGWSGDALALRAEGPPIAY-VIP----KEGALLWFD----NMAIPK 265

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 1359100139 316 TSQHKEEAKRFVEYMTTPEAMQKYYDVDGAPCAVEGVIE 354
Cdd:COG0687   266 GAPNPDLAYAFINFMLSPEVAAALAEYVGYAPPNKAARE 304
PRK10974 PRK10974
sn-glycerol-3-phosphate ABC transporter substrate-binding protein UgpB;
8-344 1.35e-09

sn-glycerol-3-phosphate ABC transporter substrate-binding protein UgpB;


Pssm-ID: 182876 [Multi-domain]  Cd Length: 438  Bit Score: 59.81  E-value: 1.35e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139   8 ILACIALGATISLTACGKNqedasgkvEIEFFNQ-KKEMTQTIQEIAKDFEAKNPDIHVKVVDVPNAGEVIKTRMLA--- 83
Cdd:PRK10974    8 TALGLALGLALSGNAQAVT--------EIPFWHSmEGELGKEVDSLAQRFNASQPDYKIVPVYKGNYEQSLAAGIAAfrs 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  84 GDVPDVINLY--------------PQSIELKEwakAGylEDLTEEPYLENIKNGYAQrfAIEDRVYSIPLTANVYGFYYN 149
Cdd:PRK10974   80 GNAPAILQVYevgtatmmaskaikPVYDVFKD---AG--IPFDESQFVPTVAGYYSD--AKTGHLLSQPFNSSTPVLYYN 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 150 KTAFEEMGI---QAPETWAEFEKIVAEIKDQNKVPFAIAGAEGW----TLNGYHQLAIATAAGGEEEANNVWRFS---EV 219
Cdd:PRK10974  153 KDAFKKAGLdpeQPPKTWQDLAAYAAKLRAAGMKCGYASGWQGWiqleNFSAWHGLPFASKNNGFDGTDAVLEFNkpeQV 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 220 NGInAESKEMQKD-----FNRLDllrEPKAlqnnwqgagyndtvvTFTKGDALIMPNGSWAMPMI-HSQNPDFEVGTFPF 293
Cdd:PRK10974  233 KHI-ALLEEMNKKgdftyVGRKD---ESTE---------------KFYNGDCAITTASSGSLANIrKYAKFNYGVGMMPY 293

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1359100139 294 PADEAG--QSLTIGAGDL-ALSVSATSQHKEEAKrFVEYMTTPEAMQKYYDVDG 344
Cdd:PRK10974  294 DADVKGapQNAIIGGASLwVMQGKDKETYKGVAK-FLDFLAKPENAAEWHQKTG 346
AfuA COG1840
ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; ...
 52-352 1.75e-09

ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism];


Pssm-ID: 441445 [Multi-domain]  Cd Length: 286  Bit Score: 58.41  E-value: 1.75e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  52 IAKDFEAKNpDIHVKVVDvPNAGEVIkTRMLAGD---VPDVInLYPQSIELKEWAKAGYLEDLTEePYLENIKNGYAqrf 128
Cdd:COG1840     1 LLEAFEKKT-GIKVNVVR-GGSGELL-ARLKAEGgnpPADVV-WSGDADALEQLANEGLLQPYKS-PELDAIPAEFR--- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 129 aiEDRVYSIPLTANVYGFYYNKTAFEEMGiqAPETWAEFekivaeIKDQNKVPFAIAGAegwTLNGYHQLAIAT--AAGG 206
Cdd:COG1840    73 --DPDGYWFGFSVRARVIVYNTDLLKELG--VPKSWEDL------LDPEYKGKIAMADP---SSSGTGYLLVAAllQAFG 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 207 EEEAnnvwrfsevnginaeskemqkdfnrLDLLrepKALQNNwqGAGY----NDTVVTFTKGDALIMPNGSWAMPMIHSQ 282
Cdd:COG1840   140 EEKG-------------------------WEWL---KGLAAN--GARVtgssSAVAKAVASGEVAIGIVNSYYALRAKAK 189

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 283 NPDFEVGtfpFPADEAGQSLTIGAgdlalsVSATSQHKEEAKRFVEYMTTPEAMQKYYDVDGAPCAVEGV 352
Cdd:COG1840   190 GAPVEVV---FPEDGTLVNPSGAA------ILKGAPNPEAAKLFIDFLLSDEGQELLAEEGYEYPVRPDV 250
PBP2_oligosaccharide_1 cd13655
The periplasmic binding component of ABC tansport system specific for an unknown ...
 47-361 3.42e-08

The periplasmic binding component of ABC tansport system specific for an unknown oligosaccharide; possess the type 2 periplasmic binidng fold; This group represents an uncharacterized periplasmic-binding protein of an ATP-binding cassette transporter predicted to be involved in uptake of an unknown oligosaccharide molecule. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270373 [Multi-domain]  Cd Length: 363  Bit Score: 55.04  E-value: 3.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  47 QTIQEIAKDFEAKNPDIHVK----VVDVPNAG-EVIKTRMLAGDVpdviNLYPqSIELKEWAKAGYLEDLTEePYLENIK 121
Cdd:cd13655    12 EWLKEMVDAFKEKHPEWKITitigVVGEADAKdEVLKDPSAAADV----FAFA-NDQLGELVDAGAIYPLTG-SAVDKIK 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 122 N----GYAQRFAIEDRVYSIPLTANVYGFYYNKTAFEEmgiqapETWAEFEKIVAEIKDQN-KVPFAIAgaegwtlNGYH 196
Cdd:cd13655    86 NtnseATVDAVTYNGKLYGYPFTANTWFMYYDKSKLTE------DDVKSLDTMLAKAPDAKgKVSFDLS-------NSWY 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 197 QLAIATAAGGEEEANNVwrfSEVNGINAESKEMQKDFNRL-DLLREPKALQNNWQGAGyndTVVTFTKGDALImpNGSWA 275
Cdd:cd13655   153 LYAFFFGAGCKLFGNNG---GDTAGCDFNNEKGVAVTNYLvDLVANPKFVNDADGDAI---SGLKDGTLGAGV--SGPWD 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 276 MPMIHSQNPDfEVGTFPFP-ADEAGQSLTIG--AGDLALSVSATSQHKEEAKRFVEYMTTPEAMQKYYDVDG-APCAVE- 350
Cdd:cd13655   225 AANLKKALGD-NYAVAKLPtYTLGGKDVQMKsfAGYKAIGVNSNTKNPEAAMALADYLTNEESQLTRFEKRGiGPTNKEa 303

                         330
                  ....*....|.
gi 1359100139 351 GVIENTQDSPL 361
Cdd:cd13655   304 AESDAVKADPA 314
malE PRK09474
maltose/maltodextrin ABC transporter substrate-binding protein MalE;
49-338 6.60e-08

maltose/maltodextrin ABC transporter substrate-binding protein MalE;


Pssm-ID: 236533 [Multi-domain]  Cd Length: 396  Bit Score: 54.25  E-value: 6.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  49 IQEIAKDFEAknpDIHVKV-VDVPNAGEVIKTRMLA-GDVPDVInLYPQSiELKEWAKAGYLEDLTEEpylENIKNGYAq 126
Cdd:PRK09474   46 LAEVGKKFEK---DTGIKVtVEHPDKLEEKFPQVAAtGDGPDII-FWAHD-RFGGYAQSGLLAEVTPS---KAFKDKLV- 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 127 RFA-----IEDRVYSIPLTANVYGFYYNKTAFEEmgiqAPETWAEFEKIVAEIKDQNKVpfAIAgaegWTLNG-YHQLAI 200
Cdd:PRK09474  117 PFTwdavrYNGKLIGYPIAVEALSLIYNKDLVPT----PPKTWEEIPALDKELKAKGKS--AIM----WNLQEpYFTWPL 186

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 201 ATAAGGE--EEANNVWRFSEVnGINAESKemQKDFNRLDLLREPKALQnnwQGAGYNDTVVTFTKGDALIMPNGSWAMPM 278
Cdd:PRK09474  187 IAADGGYafKFENGGYDVKDV-GVNNAGA--KAGLQFLVDLVKNKHMN---ADTDYSIAEAAFNKGETAMTINGPWAWSN 260

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1359100139 279 IHSQNPDFEVGTFPFPADEAGQSLTigaGDLALSVSATSQHKEEAKRFVE-YMTTPEAMQK 338
Cdd:PRK09474  261 IDKSGINYGVTVLPTFNGKPSKPFV---GVLSAGINAASPNKELAKEFLEnYLLTDEGLET 318
PBP2_MBP cd13656
The periplasmic binding component of ABC tansport system specific for maltose; possess the ...
 49-337 8.95e-08

The periplasmic binding component of ABC tansport system specific for maltose; possess the type 2 periplasmic binidng fold; This group includes the periplasmic maltose-binding protein of an ATP-binding cassette transporter. Maltose is a disaccharide formed from two units of glucose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270374 [Multi-domain]  Cd Length: 364  Bit Score: 53.75  E-value: 8.95e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  49 IQEIAKDFEaKNPDIHVKVVDVPNAGEVIKTRMLAGDVPDVInLYPQSiELKEWAKAGYLEDLT-EEPYLENIKNGYAQR 127
Cdd:cd13656    16 LAEVGKKFE-KDTGIKVTVEHPDKLEEKFPQVAATGDGPDII-FWAHD-RFGGYAQSGLLAEITpDKAFQDKLYPFTWDA 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 128 FAIEDRVYSIPLTANVYGFYYNKtafeEMGIQAPETWAEFEKIVAEIKDQNKvpfaiaGAEGWTL-NGYHQLAIATAAGG 206
Cdd:cd13656    93 VRYNGKLIAYPIAVEALSLIYNK----DLLPNPPKTWEEIPALDKELKAKGK------SALMFNLqEPYFTWPLIAADGG 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 207 E--EEANNVWRFSEVNGINAESKEmqkdfnRLDLLREPKALQNNWQGAGYNDTVVTFTKGDALIMPNGSWAMPMIHSQNP 284
Cdd:cd13656   163 YafKYENGKYDIKDVGVDNAGAKA------GLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKV 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1359100139 285 DFEVGTFPFPADEAGQSLTigaGDLALSVSATSQHKEEAKRFVE-YMTTPEAMQ 337
Cdd:cd13656   237 NYGVTVLPTFKGQPSKPFV---GVLSAGINAASPNKELAKEFLEnYLLTDEGLE 287
PBP2_PotD_PotF_like cd13590
The periplasmic-binding component of ABC transporters involved in uptake of polyamines; ...
 50-351 8.99e-08

The periplasmic-binding component of ABC transporters involved in uptake of polyamines; possess the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding domain that functions as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270308 [Multi-domain]  Cd Length: 315  Bit Score: 53.39  E-value: 8.99e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  50 QEIAKDFEAKNpDIHVkVVDVPNAGEVIKTRMLAGDVP--DVInlYPQSIELKEWAKAGYLEDLTEEpYLENIKNGYAQR 127
Cdd:cd13590    13 PEVLKAFEKET-GVKV-NYDTYDSNEEMLAKLRAGGGSgyDLV--VPSDYMVERLIKQGLLEPLDHS-KLPNLKNLDPQF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 128 FAIE---DRVYSIPLTANVYGFYYNKTAFEEmgiqAPETWAEFekivaEIKDQNKVPFAIagaegwtLNGYHQ-LAIATA 203
Cdd:cd13590    88 LNPPydpGNRYSVPYQWGTTGIAYNKDKVKE----PPTSWDLD-----LWDPALKGRIAM-------LDDAREvLGAALL 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 204 AGGEeeannvwrfsEVNGINAEskEMQKDFNRLdllrepKALQNNWQGAGYNDTVVTFTKGDALIMPNGSWAMPMIHSQN 283
Cdd:cd13590   152 ALGY----------SPNTTDPA--ELAAAAELL------IKQKPNVRAFDSDSYVQDLASGEIWLAQAWSGDALQANREN 213

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1359100139 284 PDFEvgtFPFPADeaGQSLTIgagDLaLSVSATSQHKEEAKRFVEYMTTPEAMQKYYDVDGAPCAVEG 351
Cdd:cd13590   214 PNLK---FVIPKE--GGLLWV---DN-MAIPKGAPNPELAHAFINFLLDPEVAAKNAEYIGYATPNKA 272
PBP2_AlgQ_like cd13521
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ...
 40-208 1.75e-06

Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This family represents the periplasmic-binding component of high molecular weight (HMW) alginate uptake system found in gram-negative soil bacteria and related proteins. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. In Sphingomonas sp. A1, the transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins AlgQ1 and AlgQ2. Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is 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. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270239 [Multi-domain]  Cd Length: 483  Bit Score: 50.15  E-value: 1.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  40 NQKKEMTQTIQEIAKDfeaknPDIHVKVVDVPNAGEVIK--TRMLAGDVPDVINLYPQSIELKEWAKAGYLEDLTeePYL 117
Cdd:cd13521    14 WVDDENWPVAKEIEKL-----TNVKLEIVAVTAATSQQKlnLMLASGDLPDIVGADYLKDKFIAYGMEGAFLPLS--KYI 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 118 E---NIKNGYAQRFAIED-------RVYSIP----LTANVYGFYYNKTAFEEMGIQAPETWAEFEKIVAEIKDQ------ 177
Cdd:cd13521    87 DqypNLKAFFKQHPDVLRastasdgKIYLIPyeppKDVPNQGYFIRKDWLDKLNLKTPKTLDELYNVLKAFKEKdpngng 166

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1359100139 178 --NKVPFAIA-GAEGW--TLNGYhqlAIATAAGGEE 208
Cdd:cd13521   167 kaDEIPFIDRdPLYGAfrLINSW---GARSAGGSTD 199
PBP2_AlgQ_like_2 cd13581
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ...
 51-178 3.55e-06

Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is 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. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270299 [Multi-domain]  Cd Length: 490  Bit Score: 48.86  E-value: 3.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  51 EIAKDFEAKNpDIHVKVVDVPN-AGEVIKTRMLA-GDVPDVI-NLYPQSIELKEWAKAGYLEDLTE--EPYLENIKNGYA 125
Cdd:cd13581    21 LFFKRLEEKT-GIKIEWETVPEdAWAEKKNLMLAsGDLPDAFlGAGASDADLMTYGKQGLFLPLEDliDKYAPNLKALFD 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1359100139 126 Q----RFAIED---RVYSIP-LTANVYGFYYNKTAF-----EEMGIQAPETWAEFEKIVAEIKDQN 178
Cdd:cd13581   100 EnpdiKAAITApdgHIYALPsVNECYHCSYGQRMWInkkwlDKLGLEMPTTTDELYEVLKAFKEQD 165
PBP2_Fbp_like_1 cd13544
Substrate binding domain of a putative ferric iron transporter, a member of the type 2 ...
 49-343 1.11e-04

Substrate binding domain of a putative ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily; The substrate domain of this group shows a high homology to the periplasmic component of ferric iron transporter (Fbp), but its biochemical characterization has not been performed. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270262 [Multi-domain]  Cd Length: 292  Bit Score: 43.74  E-value: 1.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  49 IQEIAKDFEAKNPdIHVKVVDVPnAGEVIkTRMLA-GDVP--DVI------NLypqsIELKEwakagylEDLTEePY-LE 118
Cdd:cd13544    13 AKAILEAFKKDTG-IKVEFVRLS-TGEAL-ARLEAeKGNPqaDVWfggtadAH----IQAKK-------EGLLE-PYkSP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 119 NIKNGYAQrFAIEDRvYSIPLTANVYGFYYNKTAFEEMGIQAPETWAEFEKIvaEIKDQNKVPF-AIAGaegwTlnGYHQ 197
Cdd:cd13544    78 NADKIPAK-FKDPDG-YWTGIYLGPLGFGVNTDELKEKGLPVPKSWEDLLNP--EYKGEIVMPNpASSG----T--AYTF 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 198 LAIATAAGGEEEAnnvWRFsevnginaeskeMqkdfnrldllrepKALQNNwqgagyndtVVTFTK-----------GDA 266
Cdd:cd13544   148 LASLIQLMGEDEA---WEY------------L-------------KKLNKN---------VGQYTKsgsapaklvasGEA 190

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 267 LImpngswAMPMIHSQnPDFEVGTFP----FPADEAGqsLTIGagdlALSVSATSQHKEEAKRFVEYMTTPEAMQKYYDV 342
Cdd:cd13544   191 AI------GISFLHDA-LKLKEQGYPikiiFPKEGTG--YEIE----AVAIIKGAKNPEAAKAFIDWALSKEAQELLAKV 257


                  .
gi 1359100139 343 D 343
Cdd:cd13544   258 G 258
PBP2_Fbp_like_2 cd13547
Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 ...
 49-177 6.32e-03

Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily; The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic domain (Fbp) has high affinity for ferric iron and serves as the primary receptor for transport. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270265 [Multi-domain]  Cd Length: 259  Bit Score: 37.97  E-value: 6.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  49 IQEIAKDFEAKNPDIHVKVVDvPNAGEV---IKTRMLAGDV-PDVINLypqsielkewAKAGYLEDLTEEPYLENIKNGY 124
Cdd:cd13547    13 ANALVEAFEKKYPGVKVEVFR-AGTGKLmakLAAEAEAGNPqADVLWV----------ADPPTAEALKKEGLLLPYKSPE 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1359100139 125 AQRFAIEDRV---YSIPLTANVYGFYYNKTAFEEmgiQAPETWAEFEKivAEIKDQ 177
Cdd:cd13547    82 ADAIPAPFYDkdgYYYGTRLSAMGIAYNTDKVPE---EAPKSWADLTK--PKYKGQ 132
PBP2_AlgQ_like_3 cd13582
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ...
 34-190 6.46e-03

Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is 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. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270300 [Multi-domain]  Cd Length: 504  Bit Score: 38.84  E-value: 6.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139  34 VEIEFFNqkKEMTQTIQE----IAKDFEAKNpDIHVKVVDVPNAGEVIKTRMLA-GDVPDVINLYPQSIELKEwakAGY- 107
Cdd:cd13582     2 ITFTFFS--ADSNATPDDfktpVAKKITELT-GVTLEIEYLVGGEKQKIGLMIAsGDLPDLIYAKGDTDKLIE---AGAl 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359100139 108 --LEDLTEEpYLENIKNGY----AQRFAIED-RVYSIPLTAN-------VYGFYYNKTAFEEMGIQAPETWAEFEKIVAE 173
Cdd:cd13582    76 vpLDDLIEK-YGPNIKKWYgdylLKKLRSEDgHIYYLPNYRVedapwypNGGFWLQHDVLKELGYPKIKTLDDYENLIKD 154

                         170       180
                  ....*....|....*....|....
gi 1359100139 174 IKD-------QNKVPFAiAGAEGW 190
Cdd:cd13582   155 YKKkyptingQPTIGFT-ALTDDW 177
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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