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Conserved domains on  [gi|2486361625|ref|WP_279077010|]
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transporter substrate-binding domain-containing protein [Hafnia alvei]

Protein Classification

lysozyme family protein; bifunctional lytic transglycosylase/C40 family peptidase( domain architecture ID 13408976)

lysozyme family protein| bifunctional lytic transglycosylase/C40 family peptidase may catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), and/or cleave peptide cross-bridges between glycan chains

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
25-460 3.41e-146

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


:

Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 424.47  E-value: 3.41e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  25 TLALPTTINSVYGDFDAMQQRRIIRVLIPYSKTFYFLDNqGTPRGLMVELMQQFDKTLNNGIKpdkkihiVVIPTSRDRL 104
Cdd:COG4623     1 LLLLLPACSSEPGDLEQIKERGVLRVLTRNSPTTYFIYR-GGPMGFEYELAKAFADYLGVKLE-------IIVPDNLDEL 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 105 IPDLLAGKGDLIAANLTITPERQQQVDFTLPLASgVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQhli 184
Cdd:COG4623    73 LPALNAGEGDIAAAGLTITPERKKQVRFSPPYYS-VSQVLVYRKGSPRPKSLEDLAGKTVHVRAGSSYAERLKQLNQ--- 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 185 snKLAPVEvINAPGNLEPEDILEMVNANLAGYTVVDRYLALLWQKIYPNLVTydQFTLRTDGNIALAVRKNSPQLLAVLN 264
Cdd:COG4623   149 --EGPPLK-WEEDEDLETEDLLEMVAAGEIDYTVADSNIAALNQRYYPNLRV--AFDLSEPQPIAWAVRKNDPSLLAALN 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 265 PFCKAHKLGTsFGNQQVYKYLRSVKWVKSATSEKEIAKFNQLTTIFQKYGQEYSVDWLLMVSQGYQESQLDQRKRSHSGA 344
Cdd:COG4623   224 EFFAKIKKGG-TLARLYERYFGHVKRDTRAFLRRIEGRLPPYDPLFEKYAEEYGLDWRLLAALAYQESHWNPRARSPTGA 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 345 IGIMQILPSTGKELKVGDISLAEPNVNAGIKYIRFMQDRYfaDQPMDELNKMLFTFAAYNAGPAKIEKLRKQAKLMGLDP 424
Cdd:COG4623   303 RGLMQLMPATAKELGVDDRLDPEQSIRAGAKYLRWLYDRF--PEAIDEPDRWWFALAAYNAGPGHVQDARRLAKKQGLDP 380
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 2486361625 425 NRWFNNVERVAQL-----KIGNETVQYVSNIFKYYVAYTLI 460
Cdd:COG4623   381 DRWFDVEKSQPKYydtgyARGRETVNYVPNIRAYYDIYKRL 421
 
Name Accession Description Interval E-value
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
25-460 3.41e-146

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


Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 424.47  E-value: 3.41e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  25 TLALPTTINSVYGDFDAMQQRRIIRVLIPYSKTFYFLDNqGTPRGLMVELMQQFDKTLNNGIKpdkkihiVVIPTSRDRL 104
Cdd:COG4623     1 LLLLLPACSSEPGDLEQIKERGVLRVLTRNSPTTYFIYR-GGPMGFEYELAKAFADYLGVKLE-------IIVPDNLDEL 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 105 IPDLLAGKGDLIAANLTITPERQQQVDFTLPLASgVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQhli 184
Cdd:COG4623    73 LPALNAGEGDIAAAGLTITPERKKQVRFSPPYYS-VSQVLVYRKGSPRPKSLEDLAGKTVHVRAGSSYAERLKQLNQ--- 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 185 snKLAPVEvINAPGNLEPEDILEMVNANLAGYTVVDRYLALLWQKIYPNLVTydQFTLRTDGNIALAVRKNSPQLLAVLN 264
Cdd:COG4623   149 --EGPPLK-WEEDEDLETEDLLEMVAAGEIDYTVADSNIAALNQRYYPNLRV--AFDLSEPQPIAWAVRKNDPSLLAALN 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 265 PFCKAHKLGTsFGNQQVYKYLRSVKWVKSATSEKEIAKFNQLTTIFQKYGQEYSVDWLLMVSQGYQESQLDQRKRSHSGA 344
Cdd:COG4623   224 EFFAKIKKGG-TLARLYERYFGHVKRDTRAFLRRIEGRLPPYDPLFEKYAEEYGLDWRLLAALAYQESHWNPRARSPTGA 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 345 IGIMQILPSTGKELKVGDISLAEPNVNAGIKYIRFMQDRYfaDQPMDELNKMLFTFAAYNAGPAKIEKLRKQAKLMGLDP 424
Cdd:COG4623   303 RGLMQLMPATAKELGVDDRLDPEQSIRAGAKYLRWLYDRF--PEAIDEPDRWWFALAAYNAGPGHVQDARRLAKKQGLDP 380
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 2486361625 425 NRWFNNVERVAQL-----KIGNETVQYVSNIFKYYVAYTLI 460
Cdd:COG4623   381 DRWFDVEKSQPKYydtgyARGRETVNYVPNIRAYYDIYKRL 421
MLTF-like cd13403
membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins; This subfamily ...
310-457 1.68e-71

membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins; This subfamily includes membrane-bound lytic murein transglycosylase F (MltF, murein lyase F) that degrades murein glycan strands. It is responsible for catalyzing the release of 1,6-anhydromuropeptides from peptidoglycan. Lytic transglycosylase catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc) as do goose-type lysozymes. However, in addition, it also makes a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue.


Pssm-ID: 381606 [Multi-domain]  Cd Length: 161  Bit Score: 223.57  E-value: 1.68e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 310 FQKYGQEYSVDWLLMVSQGYQESQLDQRKRSHSGAIGIMQILPSTGKELKVGDISLAEPNVNAGIKYIRFMQDRYFADqp 389
Cdd:cd13403     1 FKKYAEKYGFDWRLLAAQAYQESRFNPNARSPAGARGLMQLMPSTARELGVNDRLDPEQNIHAGAKYLRYLRDRFPPD-- 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 390 MDELNKMLFTFAAYNAGPAKIEKLRKQAKLMGLDPNRWFNNVERVAQLK-------------IGNETVQYVSNIFKYYVA 456
Cdd:cd13403    79 IDEPDRLKFALAAYNAGPGHVRDARRLAKKYGLNPNVWFDNVEVLPLLKspyydpvvkygyaRGRETVNYVRNIRKYYDA 158

                  .
gi 2486361625 457 Y 457
Cdd:cd13403   159 Y 159
PRK10859 PRK10859
membrane-bound lytic murein transglycosylase MltF;
1-454 6.25e-57

membrane-bound lytic murein transglycosylase MltF;


Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 195.86  E-value: 6.25e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625   1 MVRCLFLLI--ALFFIGTASHAAPSKtlalpttinsvygdFDAMQQRRIIRVLIPYSKTFYFLDNQGtPRGLMVELMQQF 78
Cdd:PRK10859   10 FIGLLALLLaaALWPSIPWFSKEENQ--------------LEQIQERGELRVGTINSPLTYYIGNDG-PTGFEYELAKRF 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  79 DKTLnnGIKPDkkihiVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASgVHEVIVANKLQPSLTTRDD 158
Cdd:PRK10859   75 ADYL--GVKLE-----IKVRDNISQLFDALDKGKADLAAAGLTYTPERLKQFRFGPPYYS-VSQQLVYRKGQPRPRSLGD 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 159 LAGKSVFINPSTSYVQSIAQLNQHLISNKLAPVEvinapgNLEPEDILEMVNANLAGYTVVDRYLALLWQKIYPNLVTyd 238
Cdd:PRK10859  147 LKGGTLTVAAGSSHVETLQELKKKYPELSWEESD------DKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPELAV-- 218
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 239 QFTLRTDGNIALAVRKNS-PQLLAVLNPFC-KAHKLGT-------------SFGNQQVYKYLRSVKwvksatsekeiAKF 303
Cdd:PRK10859  219 AFDLTDEQPVAWALPPSGdDSLYAALLDFFnQIKEDGTlarleekyfghvdRFDYVDTRTFLRAID-----------NRL 287
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 304 NQLTTIFQKYGQEysVDWLLMVSQGYQESQLDQRKRSHSGAIGIMQILPSTGKELKVGDISLAEPNVNAGIKYIRFMQDR 383
Cdd:PRK10859  288 PKYQPLFEKYAGE--LDWRLLAAIAYQESHWNPQATSPTGVRGLMMLTRNTAQSMGVTDRLDPEQSIRGGARYLQDLMER 365
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 384 YFADQPMDElnKMLFTFAAYNAGPAKIEKLRKQAKLMGLDPNRWFnNVERV----------AQLKI----GNETVQYVSN 449
Cdd:PRK10859  366 LPESIPEPE--RIWFALAAYNIGYGHMLDARRLTKKQGGNPDSWA-DVKKRlpllsqkkyySKTRYgyarGHEAVHYVEN 442

                  ....*
gi 2486361625 450 IFKYY 454
Cdd:PRK10859  443 IRRYY 447
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
58-264 6.66e-30

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


Pssm-ID: 425719 [Multi-domain]  Cd Length: 221  Bit Score: 116.24  E-value: 6.66e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLnnGIKpdkkihIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLA 137
Cdd:pfam00497  12 FEYVDENGKLVGFDVDLAKAIAKRL--GVK------VEFVPVSWDGLIPALQSGKVDLIIAGMTITPERAKQVDFSDPYY 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 SgVHEVIVANK--LQPSLTTRDDLAGKSVFINPSTSYVQSIAQLnqhlisnKLAPVEVINAPGNlepEDILEMVNANLAG 215
Cdd:pfam00497  84 Y-SGQVILVRKkdSSKSIKSLADLKGKTVGVQKGSTAEELLKNL-------KLPGAEIVEYDDD---AEALQALANGRVD 152
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2486361625 216 YTVVDRYLALLWQKIYPNLVTYDQFTLRTDGNIALAVRKNSPQLLAVLN 264
Cdd:pfam00497 153 AVVADSPVAAYLIKKNPGLNLVVVGEPLSPEPYGIAVRKGDPELLAAVN 201
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
48-264 2.09e-27

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 109.34  E-value: 2.09e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625   48 IRVLI-PYSKTFYFLDNQGTPRGLMVELMQQFDKTLnnGIKpdkkihIVVIPTSRDRLIPDLLAGKGDLIAANLTITPER 126
Cdd:smart00062   2 LRVGTnGDYPPFSFADEDGELTGFDVDLAKAIAKEL--GLK------VEFVEVSFDSLLTALKSGKIDVVAAGMTITPER 73
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  127 QQQVDFTLPLASgVHEVIVANKlQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQHlisnklapVEVINAPGNlepEDIL 206
Cdd:smart00062  74 AKQVDFSDPYYR-SGQVILVRK-DSPIKSLEDLKGKKVAVVAGTTAEELLKKLYPE--------AKIVSYDSN---AEAL 140
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2486361625  207 EMVNANLAGYTVVDRYLALLWQKIYPNL---VTYDQFTlrTDGNIALAVRKNSPQLLAVLN 264
Cdd:smart00062 141 AALKAGRADAAVADAPLLAALVKQHGLPelkIVPDPLD--TPEGYAIAVRKGDPELLDKIN 199
3A0103s03R TIGR01096
lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino ...
75-178 5.58e-10

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


Pssm-ID: 273440 [Multi-domain]  Cd Length: 250  Bit Score: 59.68  E-value: 5.58e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  75 MQQFDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGvHEVIVANKLQPSLT 154
Cdd:TIGR01096  46 LVGFDVDLAKALCKRMKAKCKFVEQNFDGLIPSLKAKKVDAIMATMSITPKRQKQIDFSDPYYAT-GQGFVVKKGSDLAK 124
                          90       100
                  ....*....|....*....|....
gi 2486361625 155 TRDDLAGKSVFINPSTSYVQSIAQ 178
Cdd:TIGR01096 125 TLEDLDGKTVGVQSGTTHEQYLKD 148
 
Name Accession Description Interval E-value
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
25-460 3.41e-146

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


Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 424.47  E-value: 3.41e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  25 TLALPTTINSVYGDFDAMQQRRIIRVLIPYSKTFYFLDNqGTPRGLMVELMQQFDKTLNNGIKpdkkihiVVIPTSRDRL 104
Cdd:COG4623     1 LLLLLPACSSEPGDLEQIKERGVLRVLTRNSPTTYFIYR-GGPMGFEYELAKAFADYLGVKLE-------IIVPDNLDEL 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 105 IPDLLAGKGDLIAANLTITPERQQQVDFTLPLASgVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQhli 184
Cdd:COG4623    73 LPALNAGEGDIAAAGLTITPERKKQVRFSPPYYS-VSQVLVYRKGSPRPKSLEDLAGKTVHVRAGSSYAERLKQLNQ--- 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 185 snKLAPVEvINAPGNLEPEDILEMVNANLAGYTVVDRYLALLWQKIYPNLVTydQFTLRTDGNIALAVRKNSPQLLAVLN 264
Cdd:COG4623   149 --EGPPLK-WEEDEDLETEDLLEMVAAGEIDYTVADSNIAALNQRYYPNLRV--AFDLSEPQPIAWAVRKNDPSLLAALN 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 265 PFCKAHKLGTsFGNQQVYKYLRSVKWVKSATSEKEIAKFNQLTTIFQKYGQEYSVDWLLMVSQGYQESQLDQRKRSHSGA 344
Cdd:COG4623   224 EFFAKIKKGG-TLARLYERYFGHVKRDTRAFLRRIEGRLPPYDPLFEKYAEEYGLDWRLLAALAYQESHWNPRARSPTGA 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 345 IGIMQILPSTGKELKVGDISLAEPNVNAGIKYIRFMQDRYfaDQPMDELNKMLFTFAAYNAGPAKIEKLRKQAKLMGLDP 424
Cdd:COG4623   303 RGLMQLMPATAKELGVDDRLDPEQSIRAGAKYLRWLYDRF--PEAIDEPDRWWFALAAYNAGPGHVQDARRLAKKQGLDP 380
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 2486361625 425 NRWFNNVERVAQL-----KIGNETVQYVSNIFKYYVAYTLI 460
Cdd:COG4623   381 DRWFDVEKSQPKYydtgyARGRETVNYVPNIRAYYDIYKRL 421
MLTF-like cd13403
membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins; This subfamily ...
310-457 1.68e-71

membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins; This subfamily includes membrane-bound lytic murein transglycosylase F (MltF, murein lyase F) that degrades murein glycan strands. It is responsible for catalyzing the release of 1,6-anhydromuropeptides from peptidoglycan. Lytic transglycosylase catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc) as do goose-type lysozymes. However, in addition, it also makes a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue.


Pssm-ID: 381606 [Multi-domain]  Cd Length: 161  Bit Score: 223.57  E-value: 1.68e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 310 FQKYGQEYSVDWLLMVSQGYQESQLDQRKRSHSGAIGIMQILPSTGKELKVGDISLAEPNVNAGIKYIRFMQDRYFADqp 389
Cdd:cd13403     1 FKKYAEKYGFDWRLLAAQAYQESRFNPNARSPAGARGLMQLMPSTARELGVNDRLDPEQNIHAGAKYLRYLRDRFPPD-- 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 390 MDELNKMLFTFAAYNAGPAKIEKLRKQAKLMGLDPNRWFNNVERVAQLK-------------IGNETVQYVSNIFKYYVA 456
Cdd:cd13403    79 IDEPDRLKFALAAYNAGPGHVRDARRLAKKYGLNPNVWFDNVEVLPLLKspyydpvvkygyaRGRETVNYVRNIRKYYDA 158

                  .
gi 2486361625 457 Y 457
Cdd:cd13403   159 Y 159
PBP2_YfhD_N cd01009
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ...
46-285 4.98e-63

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


Pssm-ID: 270230 [Multi-domain]  Cd Length: 223  Bit Score: 203.98  E-value: 4.98e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  46 RIIRVLIPYSKTFYFLDNqGTPRGLMVELMQQFDKTLnngikpdkKIHIVVIPT-SRDRLIPDLLAGKGDLIAANLTITP 124
Cdd:cd01009     1 GELRVLTRNSPTTYYIDR-GGPRGFEYELAKAFADYL--------GVELEIVPAdNLEELLEALEEGKGDLAAAGLTITP 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 125 ERQQQVDFTLPLASGVhEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQhlisnKLAPVEVINAPgNLEPED 204
Cdd:cd01009    72 ERKKKVDFSFPYYYVV-QVLVYRKGSPRPRSLEDLSGKTIAVRKGSSYAETLQKLNK-----GGPPLTWEEVD-EALTEE 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 205 ILEMVNANLAGYTVVDRYLALLWQKIYPNLVTydQFTLRTDGNIALAVRKNSPQLLAVLNPFCKAHKlGTSFGNQQVYKY 284
Cdd:cd01009   145 LLEMVAAGEIDYTVADSNIAALWRRYYPELRV--AFDLSEPQPLAWAVRKNSPSLLAALNRFLAQIK-KDGTLARLYERY 221

                  .
gi 2486361625 285 L 285
Cdd:cd01009   222 Y 222
PRK10859 PRK10859
membrane-bound lytic murein transglycosylase MltF;
1-454 6.25e-57

membrane-bound lytic murein transglycosylase MltF;


Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 195.86  E-value: 6.25e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625   1 MVRCLFLLI--ALFFIGTASHAAPSKtlalpttinsvygdFDAMQQRRIIRVLIPYSKTFYFLDNQGtPRGLMVELMQQF 78
Cdd:PRK10859   10 FIGLLALLLaaALWPSIPWFSKEENQ--------------LEQIQERGELRVGTINSPLTYYIGNDG-PTGFEYELAKRF 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  79 DKTLnnGIKPDkkihiVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASgVHEVIVANKLQPSLTTRDD 158
Cdd:PRK10859   75 ADYL--GVKLE-----IKVRDNISQLFDALDKGKADLAAAGLTYTPERLKQFRFGPPYYS-VSQQLVYRKGQPRPRSLGD 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 159 LAGKSVFINPSTSYVQSIAQLNQHLISNKLAPVEvinapgNLEPEDILEMVNANLAGYTVVDRYLALLWQKIYPNLVTyd 238
Cdd:PRK10859  147 LKGGTLTVAAGSSHVETLQELKKKYPELSWEESD------DKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPELAV-- 218
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 239 QFTLRTDGNIALAVRKNS-PQLLAVLNPFC-KAHKLGT-------------SFGNQQVYKYLRSVKwvksatsekeiAKF 303
Cdd:PRK10859  219 AFDLTDEQPVAWALPPSGdDSLYAALLDFFnQIKEDGTlarleekyfghvdRFDYVDTRTFLRAID-----------NRL 287
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 304 NQLTTIFQKYGQEysVDWLLMVSQGYQESQLDQRKRSHSGAIGIMQILPSTGKELKVGDISLAEPNVNAGIKYIRFMQDR 383
Cdd:PRK10859  288 PKYQPLFEKYAGE--LDWRLLAAIAYQESHWNPQATSPTGVRGLMMLTRNTAQSMGVTDRLDPEQSIRGGARYLQDLMER 365
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 384 YFADQPMDElnKMLFTFAAYNAGPAKIEKLRKQAKLMGLDPNRWFnNVERV----------AQLKI----GNETVQYVSN 449
Cdd:PRK10859  366 LPESIPEPE--RIWFALAAYNIGYGHMLDARRLTKKQGGNPDSWA-DVKKRlpllsqkkyySKTRYgyarGHEAVHYVEN 442

                  ....*
gi 2486361625 450 IFKYY 454
Cdd:PRK10859  443 IRRYY 447
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
53-264 6.41e-30

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


Pssm-ID: 440596 [Multi-domain]  Cd Length: 223  Bit Score: 116.23  E-value: 6.41e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  53 PYSktfyFLDNQGTPRGLMVELMQQFDKTLNngikpdkkIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDF 132
Cdd:COG0834    11 PFS----FRDEDGKLVGFDVDLARAIAKRLG--------LKVEFVPVPWDRLIPALQSGKVDLIIAGMTITPEREKQVDF 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 133 TLPLASgVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQHlisnklapVEVINAPGNlepEDILEMVNAN 212
Cdd:COG0834    79 SDPYYT-SGQVLLVRKDNSGIKSLADLKGKTVGVQAGTTYEEYLKKLGPN--------AEIVEFDSY---AEALQALASG 146
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2486361625 213 LAGYTVVDRYLALLWQKIYPNL---VTYDQFtlrTDGNIALAVRKNSPQLLAVLN 264
Cdd:COG0834   147 RVDAVVTDEPVAAYLLAKNPGDdlkIVGEPL---SGEPYGIAVRKGDPELLEAVN 198
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
58-264 6.66e-30

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


Pssm-ID: 425719 [Multi-domain]  Cd Length: 221  Bit Score: 116.24  E-value: 6.66e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLnnGIKpdkkihIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLA 137
Cdd:pfam00497  12 FEYVDENGKLVGFDVDLAKAIAKRL--GVK------VEFVPVSWDGLIPALQSGKVDLIIAGMTITPERAKQVDFSDPYY 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 SgVHEVIVANK--LQPSLTTRDDLAGKSVFINPSTSYVQSIAQLnqhlisnKLAPVEVINAPGNlepEDILEMVNANLAG 215
Cdd:pfam00497  84 Y-SGQVILVRKkdSSKSIKSLADLKGKTVGVQKGSTAEELLKNL-------KLPGAEIVEYDDD---AEALQALANGRVD 152
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2486361625 216 YTVVDRYLALLWQKIYPNLVTYDQFTLRTDGNIALAVRKNSPQLLAVLN 264
Cdd:pfam00497 153 AVVADSPVAAYLIKKNPGLNLVVVGEPLSPEPYGIAVRKGDPELLAAVN 201
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
48-264 2.09e-27

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 109.34  E-value: 2.09e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625   48 IRVLI-PYSKTFYFLDNQGTPRGLMVELMQQFDKTLnnGIKpdkkihIVVIPTSRDRLIPDLLAGKGDLIAANLTITPER 126
Cdd:smart00062   2 LRVGTnGDYPPFSFADEDGELTGFDVDLAKAIAKEL--GLK------VEFVEVSFDSLLTALKSGKIDVVAAGMTITPER 73
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  127 QQQVDFTLPLASgVHEVIVANKlQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQHlisnklapVEVINAPGNlepEDIL 206
Cdd:smart00062  74 AKQVDFSDPYYR-SGQVILVRK-DSPIKSLEDLKGKKVAVVAGTTAEELLKKLYPE--------AKIVSYDSN---AEAL 140
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2486361625  207 EMVNANLAGYTVVDRYLALLWQKIYPNL---VTYDQFTlrTDGNIALAVRKNSPQLLAVLN 264
Cdd:smart00062 141 AALKAGRADAAVADAPLLAALVKQHGLPelkIVPDPLD--TPEGYAIAVRKGDPELLDKIN 199
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
58-264 4.13e-26

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


Pssm-ID: 270248 [Multi-domain]  Cd Length: 217  Bit Score: 105.41  E-value: 4.13e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLnnGIKpdkkihIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLA 137
Cdd:cd13530    13 FEYIDKNGKLVGFDVDLANAIAKRL--GVK------VEFVDTDFDGLIPALQSGKIDVAISGMTITPERAKVVDFSDPYY 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 SgVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQHlisnklapVEVINAPGNlepEDILEMVNANLAGYT 217
Cdd:cd13530    85 Y-TGQVLVVKKDSKITKTVADLKGKKVGVQAGTTGEDYAKKNLPN--------AEVVTYDNY---PEALQALKAGRIDAV 152
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2486361625 218 VVDRYLALLW-QKIYPNLVTYDQFTlrTDGNIALAVRKNSPQLLAVLN 264
Cdd:cd13530   153 ITDAPVAKYYvKKNGPDLKVVGEPL--TPEPYGIAVRKGNPELLDAIN 198
MltE COG0741
Soluble lytic murein transglycosylase or regulatory protein s ( may contain LysM/invasin ...
309-457 6.12e-22

Soluble lytic murein transglycosylase or regulatory protein s ( may contain LysM/invasin domain) [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440504 [Multi-domain]  Cd Length: 244  Bit Score: 94.68  E-value: 6.12e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 309 IFQKYGQEYSVDWLLMVSQGYQESQLDQRKRSHSGAIGIMQILPSTGKEL--KVGDIS----LAEP--NVNAGIKYIRFM 380
Cdd:COG0741   106 LIEEAAKKYGVDPALVLALIRQESAFNPNAVSPAGARGLMQLMPATARRLglKLGLGPspddLFDPetNIRAGAAYLREL 185
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2486361625 381 QDRYFADQPMdelnkmlfTFAAYNAGPAKIeklrkqaklmgldpNRWFNNVERVAQLKI-GNETVQYVSNIFKYYVAY 457
Cdd:COG0741   186 LDRFDGDLVL--------ALAAYNAGPGRV--------------RRWLRRNGDRDGEIIpYAETRNYVKKVLANYAIY 241
Slt70-like cd13401
70kDa soluble lytic transglycosylase (Slt70) and similar proteins; Catalytic domain of the ...
309-457 1.67e-20

70kDa soluble lytic transglycosylase (Slt70) and similar proteins; Catalytic domain of the 70kda soluble lytic transglycosylase (LT)-like proteins, which also have an N-terminal U-shaped U-domain and a linker L-domain. LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do "goose-type" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria and the LTs in bacteriophage lambda.


Pssm-ID: 381604 [Multi-domain]  Cd Length: 152  Bit Score: 87.92  E-value: 1.67e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 309 IFQKYGQEYSVDWLLMVSQGYQESQLDQRKRSHSGAIGIMQILPSTGKE----LKVGDIS---LAEPNVNA--GIKYIRF 379
Cdd:cd13401     9 LVERAAKKNGLDPALVYAIIRQESAFDPDAVSPAGALGLMQLMPATAKDvakkLGLPYYSprdLFDPEYNIrlGSAYLAE 88
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2486361625 380 MQDRYFADQPMdelnkmlfTFAAYNAGPAKIEKLRKQAKlmGLDPNRWfnnVERVAQlkigNETVQYVSNIFKYYVAY 457
Cdd:cd13401    89 LLDRFDGNPVL--------ALAAYNAGPGRVRRWLKRRG--DLDPDLW---IETIPF----SETRNYVKRVLENYVVY 149
PBP2_Dsm1740 cd13629
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ...
58-271 6.91e-20

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


Pssm-ID: 270347 [Multi-domain]  Cd Length: 221  Bit Score: 88.01  E-value: 6.91e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLNngikpdKKIHIVviPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLA 137
Cdd:cd13629    13 FEMTDKKGELIGFDVDLAKALAKDLG------VKVEFV--NTAWDGLIPALQTGKFDLIISGMTITPERNLKVNFSNPYL 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 SGVHEVIVANKLQPSLTTRDDLAGKSVFI---NPSTSyvqsiaqlnqHLISNKLAPveviNAPGNL---EPEDILEMVNA 211
Cdd:cd13629    85 VSGQTLLVNKKSAAGIKSLEDLNKPGVTIavkLGTTG----------DQAARKLFP----KATILVfddEAAAVLEVVNG 150
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2486361625 212 NlAGYTVVDR-YLALLWQKIYPNLVTYDQftLRTDGNIALAVRKNSPQLLAVLNPFCKAHK 271
Cdd:cd13629   151 K-ADAFIYDQpTPARFAKKNDPTLVALLE--PFTYEPLGFAIRKGDPDLLNWLNNFLKQIK 208
PBP2_MidA_like cd01004
Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 ...
53-263 9.35e-19

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


Pssm-ID: 270225 [Multi-domain]  Cd Length: 230  Bit Score: 84.99  E-value: 9.35e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  53 PYSktfyFLDNQGTPRGLMVELMQQFDKTLnnGIKPDkkihivVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDF 132
Cdd:cd01004    14 PYE----FVDEDGKLIGFDVDLAKAIAKRL--GLKVE------IVNVSFDGLIPALQSGRYDIIMSGITDTPERAKQVDF 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 133 TLPLASGVhEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQHLISNKLAPVEVINAPGNlepEDIL-----E 207
Cdd:cd01004    82 VDYMKDGL-GVLVAKGNPKKIKSPEDLCGKTVAVQTGTTQEQLLQAANKKCKAAGKPAIEIQTFPDQ---ADALqalrsG 157
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2486361625 208 MVNANLAGYTVVDRYlallwQKIYPNL--VTYDQFTLRTDgnIALAVRKNSPQLLAVL 263
Cdd:cd01004   158 RADAYLSDSPTAAYA-----VKQSPGKleLVGEVFGSPAP--IGIAVKKDDPALADAV 208
LT_Slt70-like cd16896
uncharacterized lytic transglycosylase subfamily with similarity to Slt70; Uncharacterized ...
311-454 1.01e-18

uncharacterized lytic transglycosylase subfamily with similarity to Slt70; Uncharacterized lytic transglycosylase (LT) with a conserved sequence pattern suggesting similarity to the Slt70, a 70kda soluble lytic transglycosylase which also has an N-terminal U-shaped U-domain and a linker L-domain. LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do "goose-type" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue.


Pssm-ID: 381617 [Multi-domain]  Cd Length: 146  Bit Score: 82.56  E-value: 1.01e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 311 QKYGQEYSVDWLLMVSQGYQESQLDQRKRSHSGAIGIMQILPSTGKEL--KVGDIS-----LAEP--NVNAGIKYIRFMQ 381
Cdd:cd16896     9 EKYAKEYGVDPLLVAAVIKVESNFNPNAVSSKGAIGLMQIMPETAEWIaeKLGLEDfseddLYDPetNIRLGTWYLSYLL 88
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2486361625 382 DRYFADqpmdeLNKMLftfAAYNAGPAKIEKlrkqaklmGLDPNRWFNNVERVAQLKIGnETVQYVSNIFKYY 454
Cdd:cd16896    89 KEFDGN-----LVLAL---AAYNAGPGNVDK--------WLKDGGWSGDGKTLDQIPFP-ETRHYVKKVLKNY 144
LT-like cd00254
lytic transglycosylase(LT)-like domain; Members include the soluble and insoluble ...
330-454 1.16e-18

lytic transglycosylase(LT)-like domain; Members include the soluble and insoluble membrane-bound LTs in bacteria and LTs in bacteriophage lambda. LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do "goose-type" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue.


Pssm-ID: 381594 [Multi-domain]  Cd Length: 111  Bit Score: 81.49  E-value: 1.16e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 330 QESQLDQRKRSHSGAIGIMQILPSTGKELKVGDIS-LAEP--NVNAGIKYIRFMQDRYFADQPMdelnkmlfTFAAYNAG 406
Cdd:cd00254    10 VESGFNPRAVSPAGARGLMQLMPGTARDLGRRGVDdLFDPeeNIRAGARYLRELLDRFGGDLEL--------ALAAYNAG 81
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2486361625 407 PAKIEKLRKQAKLMgldpnrwfnnvervaqlkiGNETVQYVSNIFKYY 454
Cdd:cd00254    82 PGAVDRWGGGEVPP-------------------YKETRNYVQRVLAYY 110
PBP2_Cystine_like cd13626
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ...
58-264 1.44e-18

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


Pssm-ID: 270344 [Multi-domain]  Cd Length: 219  Bit Score: 84.29  E-value: 1.44e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLnnGIKPDKKihivviPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLP-L 136
Cdd:cd13626    13 FTFKDEDGKLTGFDVEVGREIAKRL--GLKVEFK------ATEWDGLLPGLNSGKFDVIANQVTITPEREEKYLFSDPyL 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 137 ASGVheVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQhlisnklaPVEVINAPGNlepEDILEMVNANLAGY 216
Cdd:cd13626    85 VSGA--QIIVKKDNTIIKSLEDLKGKVVGVSLGSNYEEVARDLAN--------GAEVKAYGGA---NDALQDLANGRADA 151
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2486361625 217 TVVDRyLALLWQ--------KIYPNLVTYDQftlrtdgnIALAVRKNSPQLLAVLN 264
Cdd:cd13626   152 TLNDR-LAALYAlknsnlplKIVGDIVSTAK--------VGFAFRKDNPELRKKVN 198
PBP2_BvgS_D2 cd13707
The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
46-264 3.09e-18

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


Pssm-ID: 270425 [Multi-domain]  Cd Length: 221  Bit Score: 83.42  E-value: 3.09e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  46 RIIRVLI-----PYSktfyFLDNQGTPRGLMVELMQQFdkTLNNGIkpdkkiHIVVIPT-SRDRLIPDLLAGKGDLIAAn 119
Cdd:cd13707     2 PVVRVVVnpdlaPLS----FFDSNGQFRGISADLLELI--SLRTGL------RFEVVRAsSPAEMIEALRSGEADMIAA- 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 120 LTITPERQQQVDFTLPLASgVHEVIVANKLQPSLTTRDDLAGKSVFInPSTSYVQSiaqlnqhLISNKLAPVEVINAPGn 199
Cdd:cd13707    69 LTPSPEREDFLLFTRPYLT-SPFVLVTRKDAAAPSSLEDLAGKRVAI-PAGSALED-------LLRRRYPQIELVEVDN- 138
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2486361625 200 lePEDILEMVNANLAGYTVVD----RYLAllwQKIYPNLVtydQFTLRTDG---NIALAVRKNSPQLLAVLN 264
Cdd:cd13707   139 --TAEALALVASGKADATVASlisaRYLI---NHYFRDRL---KIAGILGEppaPIAFAVRRDQPELLSILD 202
PBP2_BvgS_HisK_like cd01007
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
58-264 8.98e-18

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


Pssm-ID: 270228 [Multi-domain]  Cd Length: 220  Bit Score: 81.81  E-value: 8.98e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLNngikpdkkIHIVVIPT-SRDRLIPDLLAGKGDLIAAnLTITPERQQQVDFTLPL 136
Cdd:cd01007    15 FEFIDEGGEPQGIAADYLKLIAKKLG--------LKFEYVPGdSWSELLEALKAGEIDLLSS-VSKTPEREKYLLFTKPY 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 137 ASGVHeVIVANKLQPSLTTRDDLAGKSVFINPSTSYvqsIAQLNQHLISNKLAPVEvinapgnlEPEDILEMVNANLAGY 216
Cdd:cd01007    86 LSSPL-VIVTRKDAPFINSLSDLAGKRVAVVKGYAL---EELLRERYPNINLVEVD--------STEEALEAVASGEADA 153
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2486361625 217 TVVDryLALLWQKI----YPNLVTYDQftLRTDGNIALAVRKNSPQLLAVLN 264
Cdd:cd01007   154 YIGN--LAVASYLIqkygLSNLKIAGL--TDYPQDLSFAVRKDWPELLSILN 201
PBP2_Cys_DEBP_like cd01000
Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ...
40-271 6.80e-16

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


Pssm-ID: 270221 [Multi-domain]  Cd Length: 228  Bit Score: 76.58  E-value: 6.80e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  40 DAMQQRRIIRVLIPYSKT-FYFLDNQGTPRGLMVELMQQFDKTLNNgikPDKKIHIVVIpTSRDRlIPDLLAGKGDLIAA 118
Cdd:cd01000     2 DDIKSRGVLIVGVKPDLPpFGARDANGKIQGFDVDVAKALAKDLLG---DPVKVKFVPV-TSANR-IPALQSGKVDLIIA 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 119 NLTITPERQQQVDFTLPLaSGVHEVIVANKLQPsLTTRDDLAGKSVFINPSTSYVQSIaqlnqhlisNKLAP-VEVINAP 197
Cdd:cd01000    77 TMTITPERAKEVDFSVPY-YADGQGLLVRKDSK-IKSLEDLKGKTILVLQGSTAEAAL---------RKAAPeAQLLEFD 145
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2486361625 198 GNLEPEDILEmvnANLAGYTVVDRYLALLWQKIYPnlvtyDQFTLR----TDGNIALAVRKNSPQLLAVLNPFCKAHK 271
Cdd:cd01000   146 DYAEAFQALE---SGRVDAMATDNSLLAGWAAENP-----DDYVILpkpfSQEPYGIAVRKGDTELLKAVNATIAKLK 215
PBP2_SMa0082_like cd01072
The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic ...
58-293 1.26e-15

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


Pssm-ID: 270233 [Multi-domain]  Cd Length: 238  Bit Score: 76.15  E-value: 1.26e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLnnGIKpdkkIHIV-VIPTSRdrlIPDLLAGKGDLIAANLTITPERQQQVDFTLPL 136
Cdd:cd01072    26 FGFVDASMQPQGYDVDVAKLLAKDL--GVK----LELVpVTGANR---IPYLQTGKVDMLIASLGITPERAKVVDFSQPY 96
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 137 AsgVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQlnqhlisnklapveviNAPGNLEP---EDILEMVNANL 213
Cdd:cd01072    97 A--AFYLGVYGPKDAKVKSPADLKGKTVGVTRGSTQDIALTK----------------AAPKGATIkrfDDDASTIQALL 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 214 AG---YTVVDRYLALLWQKIYPNLVTYDQFTLRTDgNIALAVRKNSPQLLAVLNPFCKAHKLGTSFGnqQVYKylrsvKW 290
Cdd:cd01072   159 SGqvdAIATGNAIAAQIAKANPDKKYELKFVLRTS-PNGIGVRKGEPELLKWVNTFIAKNKANGELN--ALSQ-----KW 230

                  ...
gi 2486361625 291 VKS 293
Cdd:cd01072   231 FGT 233
PBP2_ArtJ cd00999
The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold ...
58-264 1.73e-15

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


Pssm-ID: 270220 [Multi-domain]  Cd Length: 223  Bit Score: 75.44  E-value: 1.73e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLNngikpdKKIHIVviPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLA 137
Cdd:cd00999    17 FEFRDEKGELVGFDIDLAEAISEKLG------KKLEWR--DMAFDALIPNLLTGKIDAIAAGMSATPERAKRVAFSPPYG 88
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 SGVHEVIVANKlQPSLTTRDDLAGKSVFINPSTSyvqsiaqlnQHLISNKLAPVEVINAPGNLepeDILEMVNANLAGYT 217
Cdd:cd00999    89 ESVSAFVTVSD-NPIKPSLEDLKGKSVAVQTGTI---------QEVFLRSLPGVEVKSFQKTD---DCLREVVLGRSDAA 155
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2486361625 218 VVDRYLA--LLWQKIYPNLVTyDQFTLR-TDGNIALAVRKNSPQLLAVLN 264
Cdd:cd00999   156 VMDPTVAkvYLKSKDFPGKLA-TAFTLPeWGLGKALAVAKDDPALKEAVN 204
PBP2_Cysteine cd13694
Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein ...
40-264 5.44e-15

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


Pssm-ID: 270412 [Multi-domain]  Cd Length: 229  Bit Score: 74.31  E-value: 5.44e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  40 DAMQQRRIIRVLIPYSKT-FYFLDNQGTPRGLMVELMQQFDKTLNNgiKPDKKIHIVVIPTSRdrlIPDLLAGKGDLIAA 118
Cdd:cd13694     2 EQIKQSGVIRIGVFGDKPpFGYVDENGKFQGFDIDLAKQIAKDLFG--SGVKVEFVLVEAANR---VPYLTSGKVDLILA 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 119 NLTITPERQQQVDFTLP---LASGVheVIVANKLqpsLTTRDDLAGKSVFINPSTS---YVQSiaqlnqhlisnklapve 192
Cdd:cd13694    77 NFTVTPERAEVVDFANPymkVALGV--VSPKDSN---ITSVAQLDGKTLLVNKGTTaekYFTK----------------- 134
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2486361625 193 viNAPGnLEPE------DILEMVNANLAGYTVVDRYLALLWQKIYPNL-VTYDQftLRTDGNIALAVRKNSPQLLAVLN 264
Cdd:cd13694   135 --NHPE-IKLLkydqnaEAFQALKDGRADAYAHDNILVLAWAKSNPGFkVGIKN--LGDTDFIAPGVQKGNKELLEFIN 208
PBP2_Arg_Lys_His cd13624
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ...
58-264 7.96e-15

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


Pssm-ID: 270342 [Multi-domain]  Cd Length: 219  Bit Score: 73.30  E-value: 7.96e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLnnGIKpdkkihIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLA 137
Cdd:cd13624    13 FEFVDENGKIVGFDIDLIKAIAKEA--GFE------VEFKNMAFDGLIPALQSGKIDIIISGMTITEERKKSVDFSDPYY 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 SgVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSyvqsiaqlnQHLISNKLAPVEVINAPGNLePEDILEMVNANLAG-- 215
Cdd:cd13624    85 E-AGQAIVVRKDSTIIKSLDDLKGKKVGVQIGTT---------GAEAAEKILKGAKVKRFDTI-PLAFLELKNGGVDAvv 153
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2486361625 216 --YTVVDRYLAllwQKIYPNLVTYdqFTLRTDGNIALAVRKNSPQLLAVLN 264
Cdd:cd13624   154 ndNPVAAYYVK---QNPDKKLKIV--GDPLTSEYYGIAVRKGNKELLDKIN 199
PBP2_AA_binding_like_1 cd13625
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
58-274 9.00e-15

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


Pssm-ID: 270343 [Multi-domain]  Cd Length: 230  Bit Score: 73.56  E-value: 9.00e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQ---GTPRGLMVELMQQFdktlnnGIKPDKkihiVVIPTSRdrLIPDLLAGKGDLIAANLTITPERQQQVDFTL 134
Cdd:cd13625    18 FEFVENGkivGFDRDLLDEMAKKL------GVKVEQ----QDLPWSG--ILPGLLAGKFDMVATSVTITKERAKRFAFTL 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 135 PLASGVHEVIVaNKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQHL-ISNKLAPVEVINAPGNlePEDILEM----V 209
Cdd:cd13625    86 PIAEATAALLK-RAGDDSIKTIEDLAGKVVGVQAGSAQLAQLKEFNETLkKKGGNGFGEIKEYVSY--PQAYADLangrV 162
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2486361625 210 NANLAGYTVVDrYLALLWQKIYPNLVTYDQFTLrtdgnIALAVRKNSPQLLAVLNPFC-KAHKLGT 274
Cdd:cd13625   163 DAVANSLTNLA-YLIKQRPGVFALVGPVGGPTY-----FAWVIRKGDAELRKAINDALlALKKSGK 222
SLT pfam01464
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found ...
310-418 1.76e-14

Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found in phages, type II, type III and type IV secretion systems.


Pssm-ID: 396169 [Multi-domain]  Cd Length: 114  Bit Score: 69.64  E-value: 1.76e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 310 FQKYGQEYSVDWLLMVSQGYQESQLDQRKRSHSGAIGIMQILPSTGKELK---VGDISLA---EPNVNAGIKYIRFMQDR 383
Cdd:pfam01464   1 IIKAAQKYGVDPSLLLAIAQQESGFNPKAVSKSGAVGLMQIMPSTAKRLGlrvNPGVDDLfdpEKNIKAGTKYLKELYKQ 80
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2486361625 384 YfadqpmdeLNKMLFTFAAYNAGPAKIEKLRKQAK 418
Cdd:pfam01464  81 Y--------GGDLWLALAAYNAGPGRVRKWIKNAG 107
PBP2_mlr5654_like cd13702
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
58-264 2.00e-14

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


Pssm-ID: 270420 [Multi-domain]  Cd Length: 223  Bit Score: 72.35  E-value: 2.00e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGlmvelmqqFDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLA 137
Cdd:cd13702    15 FNYVDADGKLGG--------FDVDIANALCAEMKAKCEIVAQDWDGIIPALQAKKFDAIIASMSITPERKKQVDFTDPYY 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 SGVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQlnqhlisnKLAPVEVinapgNLEP---EDILEMVNANLA 214
Cdd:cd13702    87 TNPLVFVAPKDSTITDVTPDDLKGKVIGAQRSTTAAKYLEE--------NYPDAEV-----KLYDtqeEAYLDLASGRLD 153
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2486361625 215 GyTVVDRYLALLWQKIYPNlvtyDQFTLR-----TDGNIALAVRKNSPQLLAVLN 264
Cdd:cd13702   154 A-VLSDKFPLLDWLKSPAG----KCCELKgepiaDDDGIGIAVRKGDTELREKFN 203
PBP2_FliY cd13712
Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ...
58-264 2.61e-14

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


Pssm-ID: 270430 [Multi-domain]  Cd Length: 219  Bit Score: 72.03  E-value: 2.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLnnGIKPdkkihiVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLA 137
Cdd:cd13712    13 FNFKDETGQLTGFEVDVAKALAAKL--GVKP------EFVTTEWSGILAGLQAGKYDVIINQVGITPERQKKFDFSQPYT 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 SGVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYvqsiaqlNQHLISNkLAPVEVINAPGnlEPEdILEMVNANLAGYT 217
Cdd:cd13712    85 YSGIQLIVRKNDTRTFKSLADLKGKKVGVGLGTNY-------EQWLKSN-VPGIDVRTYPG--DPE-KLQDLAAGRIDAA 153
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2486361625 218 VVDRYLALLWQKIYPNLVTYDQFTLRTDGNIALavRKNSPQLLAVLN 264
Cdd:cd13712   154 LNDRLAANYLVKTSLELPPTGGAFARQKSGIPF--RKGNPKLKAAIN 198
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
58-264 3.36e-14

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


Pssm-ID: 270422 [Multi-domain]  Cd Length: 220  Bit Score: 71.46  E-value: 3.36e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLNngikpdKKIHIVviPTSRDRLIPDLLAGKGDLIaANLTITPERQQQVDFTLPLA 137
Cdd:cd13704    15 YEFLDENGNPTGFNVDLLRAIAEEMG------LKVEIR--LGPWSEVLQALENGEIDVL-IGMAYSEERAKLFDFSDPYL 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 SgVHEVIVANKLQPSLTTRDDLAGKSVfinpstsYVQ--SIAQ--LNQHLISNKLAPVEvinapgnlEPEDILEMVNANL 213
Cdd:cd13704    86 E-VSVSIFVRKGSSIINSLEDLKGKKV-------AVQrgDIMHeyLKERGLGINLVLVD--------SPEEALRLLASGK 149
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2486361625 214 AGYTVVDRYLALLWQKIYP--NLVTYDQFTLRTDgnIALAVRKNSPQLLAVLN 264
Cdd:cd13704   150 VDAAVVDRLVGLYLIKELGltNVKIVGPPLLPLK--YCFAVRKGNPELLAKLN 200
PBP2_HisJ_LAO_like cd01001
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and ...
58-264 4.40e-14

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


Pssm-ID: 270222 [Multi-domain]  Cd Length: 228  Bit Score: 71.56  E-value: 4.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLNngikpdKKIHIVVIPTsrDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLA 137
Cdd:cd01001    15 FNFLDADGKLVGFDIDLANALCKRMK------VKCEIVTQPW--DGLIPALKAGKYDAIIASMSITDKRRQQIDFTDPYY 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 SGVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYvqsiaqlnQHLISNKLAPVEVINAPGnlePEDILEMVNANLAGYT 217
Cdd:cd01001    87 RTPSRFVARKDSPITDTTPAKLKGKRVGVQAGTTH--------EAYLRDRFPEADLVEYDT---PEEAYKDLAAGRLDAV 155
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2486361625 218 VVDRYLALLWQKIYPNLVTYDQF-------TLRTDGnIALAVRKNSPQLLAVLN 264
Cdd:cd01001   156 FGDKVALSEWLKKTKSGGCCKFVgpavpdpKYFGDG-VGIAVRKDDDALRAKLD 208
PBP2_polar_AA cd13693
Substrate binding domain of polar amino-acid uptake ABC transporter; the type 2 periplasmic ...
40-274 6.18e-13

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


Pssm-ID: 270411 [Multi-domain]  Cd Length: 228  Bit Score: 68.11  E-value: 6.18e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  40 DAMQQRRIIRVLIPYS-KTFYFLDNQGTPRGLMVELMQQFDKTLnnGIKPDKkihIVVIPTSRdrlIPDLLAGKGDLIAA 118
Cdd:cd13693     2 DRIKARGKLIVGVKNDyPPFGFLDPSGEIVGFEVDLAKDIAKRL--GVKLEL---VPVTPSNR---IQFLQQGKVDLLIA 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 119 NLTITPERQQQVDFTLP--LASGVheVIVANKLQPsLTTRDDLAGKSVFINPSTSYvqsiaqlNQHLISNKLApvEVINA 196
Cdd:cd13693    74 TMGDTPERRKVVDFVEPyyYRSGG--ALLAAKDSG-INDWEDLKGKPVCGSQGSYY-------NKPLIEKYGA--QLVAF 141
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 197 PGNLEPEDILEmvNANLAGYTVVDRYLALL------WQKIYPNLVTYdqftlrTDGNIALAVRKNSPQLLAVLNPFCK-A 269
Cdd:cd13693   142 KGTPEALLALR--DGRCVAFVYDDSTLQLLlqedgeWKDYEIPLPTI------EPSPWVIAVRKGETAFQNALDEIIKdW 213

                  ....*
gi 2486361625 270 HKLGT 274
Cdd:cd13693   214 HRTGK 218
PBP2_BsGlnH cd13689
Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ...
40-264 8.50e-13

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


Pssm-ID: 270407 [Multi-domain]  Cd Length: 229  Bit Score: 67.64  E-value: 8.50e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  40 DAMQQRRIIRV-----LIPYSktfyFLDNQ-GTPRGLMVELMQQFDKTLnnGIKPDKKihiVVIPTSRdrlIPDLLAGKG 113
Cdd:cd13689     2 DDIKARGVLRCgvfddVPPFG----FIDPKtREIVGFDVDLCKAIAKKL--GVKLELK---PVNPAAR---IPELQNGRV 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 114 DLIAANLTITPERQQQVDFTLP-LASGvHEVIVanKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQhlisnklapve 192
Cdd:cd13689    70 DLVAANLTYTPERAEQIDFSDPyFVTG-QKLLV--KKGSGIKSLKDLAGKRVGAVKGSTSEAAIREKLP----------- 135
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 193 vinapgnlepedilemvNANLAGY-TVVDRYLALLWQKIypNLVTYDQFTLR-------------------TDGNIALAV 252
Cdd:cd13689   136 -----------------KASVVTFdDTAQAFLALQQGKV--DAITTDETILAgllakapdpgnyeilgealSYEPYGIGV 196
                         250
                  ....*....|..
gi 2486361625 253 RKNSPQLLAVLN 264
Cdd:cd13689   197 PKGESALRDFVN 208
PBP2_Cystine_like_1 cd13713
Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ...
56-264 5.60e-12

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


Pssm-ID: 270431 [Multi-domain]  Cd Length: 218  Bit Score: 65.00  E-value: 5.60e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  56 KTFYFLDNQGTPRGLMVELMQQFDKTLnnGIKPdkkihiVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLP 135
Cdd:cd13713    11 PPFNFLDEDNQLVGFDVDVAKAIAKRL--GVKV------EPVTTAWDGIIAGLWAGRYDIIIGSMTITEERLKVVDFSNP 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 136 -LASGVheVIVANKlQPSLTTRDDLAGKSVFINPSTSYVQsiaQLNQHLISNKLAPVEviNAPGNLepediLEMVNANLA 214
Cdd:cd13713    83 yYYSGA--QIFVRK-DSTITSLADLKGKKVGVVTGTTYEA---YARKYLPGAEIKTYD--SDVLAL-----QDLALGRLD 149
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2486361625 215 GyTVVDRYLALlwqkiypNLVTYDQFTLRTDG------NIALAVRKNSPQLLAVLN 264
Cdd:cd13713   150 A-VITDRVTGL-------NAIKEGGLPIKIVGkplyyePMAIAIRKGDPELRAAVN 197
PBP2_Atu4678_like cd13696
The substrate binding domain of putative amino acid transporter; the type 2 periplasmic ...
58-266 6.51e-12

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


Pssm-ID: 270414 [Multi-domain]  Cd Length: 227  Bit Score: 65.09  E-value: 6.51e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLnnGIKPDkkihIVVIPtSRDRlIPDLLAGKGDLIAANLTITPERQQQVDFTLPLA 137
Cdd:cd13696    21 FGFRDAAGNPVGYDVDYAKDLAKAL--GVKPE----IVETP-SPNR-IPALVSGRVDVVVANTTRTLERAKTVAFSIPYV 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 SGVhEVIVANKLQPsLTTRDDLAGKSVFInpstsyvqSIAQLNQHLISNKLAPVEVInaPGNLEPEDILEmVNANLAGYT 217
Cdd:cd13696    93 VAG-MVVLTRKDSG-IKSFDDLKGKTVGV--------VKGSTNEAAVRALLPDAKIQ--EYDTSADAILA-LKQGQADAM 159
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2486361625 218 VVDRYLALLWQKIypnlvtyDQF-TLRTDGN-------IALAVRKNSPQLLAVLNPF 266
Cdd:cd13696   160 VEDNTVANYKASS-------GQFpSLEIAGEapypldyVAIGVRKGDYDWLRYLNLF 209
PBP2_Ngo0372_TcyA cd13711
Substrate binding domain of ABC transporters involved in cystine import; the type 2 ...
53-271 7.01e-12

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


Pssm-ID: 270429 [Multi-domain]  Cd Length: 222  Bit Score: 65.01  E-value: 7.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  53 PYSktfyFLDNQGTPRGLMVELMQQFDKTLnnGIKPDkkihivVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDF 132
Cdd:cd13711    13 PFT----YHDKSGKLTGFDVEVARAVAKKL--GVKVE------FVETQWDSMIAGLDAGRFDVVANQVGITDERKKKYDF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 133 TLPLASgVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQhlisnKLAPVEVINAPgnlepediLEMVNAN 212
Cdd:cd13711    81 STPYIY-SRAVLIVRKDNSDIKSFADLKGKKSAQSLTSNWGKIAKKYGA-----QVVGVDGFAQA--------VELITQG 146
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2486361625 213 LAGYTVVDRYLALLWQKIYPNLVTYDQFTLRTDGNIALAVRKNSPQLLAVLNPFCKAHK 271
Cdd:cd13711   147 RADATINDSLAFLDYKKQHPDAPVKIAAETDDASESAFLVRKGNDELVAAINKALKELK 205
MltD-like cd16894
Membrane-bound lytic murein transglycosylase D and similar proteins; Lytic transglycosylases ...
330-451 8.37e-12

Membrane-bound lytic murein transglycosylase D and similar proteins; Lytic transglycosylases (LT) catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc). Membrane-bound lytic murein transglycosylase D protein (MltD) family members may have one or more small LysM domains, which may contribute to peptidoglycan binding. Unlike the similar "goose-type" lysozymes, LTs also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as the eukaryotic "goose-type" lysozymes (goose egg-white lysozyme; GEWL).


Pssm-ID: 381615 [Multi-domain]  Cd Length: 129  Bit Score: 62.15  E-value: 8.37e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 330 QESQLDQRKRSHSGAIGIMQILPSTGKE--LKVG-------DISLAepnVNAGIKYIRFMQDRYfadqpmdelNKMLFTF 400
Cdd:cd16894    16 VESGFNPDAVSSAGAAGLWQFMPATAREygLRVDswvderrDPEKS---TRAAARYLKDLYKRF---------GDWLLAL 83
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2486361625 401 AAYNAGPAKIEKLRKQAklmGLDPNRWFNnvervaQLKIGNETVQYVSNIF 451
Cdd:cd16894    84 AAYNAGEGRVRRAIKRA---GTDKWEDYY------RLYLPAETRRYVPKFL 125
PBP2_GltI_DEBP cd13688
Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic ...
58-264 9.50e-12

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


Pssm-ID: 270406 [Multi-domain]  Cd Length: 238  Bit Score: 64.97  E-value: 9.50e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLNNGIKpDKKIHIVVIP-TSRDRlIPDLLAGKGDLIAANLTITPERQQQVDFTLP- 135
Cdd:cd13688    21 FSYLDDNGKPVGYSVDLCNAIADALKKKLA-LPDLKVRYVPvTPQDR-IPALTSGTIDLECGATTNTLERRKLVDFSIPi 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 136 LASGVheVIVANKlQPSLTTRDDLAGKSVFINPSTSYVQSIAQLN-QHLISNKLAPVevinapgnLEPEDILEMVNANLA 214
Cdd:cd13688    99 FVAGT--RLLVRK-DSGLNSLEDLAGKTVGVTAGTTTEDALRTVNpLAGLQASVVPV--------KDHAEGFAALETGKA 167
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2486361625 215 GYTVVDRYLALLWQKIYPNLVTY----DQFTLRTdgnIALAVRKNSPQLLAVLN 264
Cdd:cd13688   168 DAFAGDDILLAGLAARSKNPDDLalipRPLSYEP---YGLMLRKDDPDFRLLVD 218
PRK11260 PRK11260
cystine ABC transporter substrate-binding protein;
58-264 3.01e-11

cystine ABC transporter substrate-binding protein;


Pssm-ID: 183061 [Multi-domain]  Cd Length: 266  Bit Score: 63.59  E-value: 3.01e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLnnGIKPDKKihivviPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLA 137
Cdd:PRK11260   54 FSFQGEDGKLTGFEVEFAEALAKHL--GVKASLK------PTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYT 125
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 138 -SGVhEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQlnqhlisnklapveviNAPG------NLEPEDILEM-- 208
Cdd:PRK11260  126 vSGI-QALVKKGNEGTIKTAADLKGKKVGVGLGTNYEQWLRQ----------------NVQGvdvrtyDDDPTKYQDLrv 188
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 209 --VNANLagytvVDRYLALLWQKIYPN--LVTYDQFTLRTDGniaLAVRKNSPQLLAVLN 264
Cdd:PRK11260  189 grIDAIL-----VDRLAALDLVKKTNDtlAVAGEAFSRQESG---VALRKGNPDLLKAVN 240
PBP2_GltS cd13620
Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 ...
78-264 3.56e-11

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


Pssm-ID: 270338 [Multi-domain]  Cd Length: 227  Bit Score: 62.74  E-value: 3.56e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  78 FDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGVHEVIVANKLQPSLTTRD 157
Cdd:cd13620    32 ADIDIAKAIAKELGVKLEIKSMDFDNLLASLQSGKVDMAISGMTPTPERKKSVDFSDVYYEAKQSLLVKKADLDKYKSLD 111
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 158 DLAGKSVFINPSTSyvqsiaqlnQHLISNKLAPVEVINAPGNLePEDILEMVNANLAGyTVVDRYLALLWQKIYPNLVTY 237
Cdd:cd13620   112 DLKGKKIGAQKGST---------QETIAKDQLKNAKLKSLTKV-GDLILELKSGKVDG-VIMEEPVAKGYANNNSDLAIA 180
                         170       180
                  ....*....|....*....|....*...
gi 2486361625 238 D-QFTLRTDGNIALAVRKNSPQLLAVLN 264
Cdd:cd13620   181 DvNLENKPDDGSAVAIKKGSKDLLDAVN 208
PBP2_PheC cd01069
Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein ...
38-234 6.47e-11

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


Pssm-ID: 270231 [Multi-domain]  Cd Length: 232  Bit Score: 62.36  E-value: 6.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  38 DFDAMQQRRIIRVLIP--YsKTFYFLDNQGTPRGLMVELMQQFDKTLnnGIKpdkkihIVVIPTSRDRLIPDLLAGKGDL 115
Cdd:cd01069     2 RLDKILERGVLRVGTTgdY-KPFTYRDNQGQYEGYDIDMAEALAKSL--GVK------VEFVPTSWPTLMDDLAADKFDI 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 116 IAANLTITPERQQQVDFTLPLASGVHEVIV----ANKLQpsltTRDDL--AGKSVFINPSTSyvqsiaqlNQHLISNKLA 189
Cdd:cd01069    73 AMGGISITLERQRQAFFSAPYLRFGKTPLVrcadVDRFQ----TLEAInrPGVRVIVNPGGT--------NEKFVRANLK 140
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2486361625 190 PVEVINAPGNLepeDILEMVNANLAGYTVVDRYLALLWQKIYPNL 234
Cdd:cd01069   141 QATITVHPDNL---TIFQAIADGKADVMITDAVEARYYQKLDPRL 182
PBP2_Ala cd13628
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ...
75-181 3.68e-10

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


Pssm-ID: 270346 [Multi-domain]  Cd Length: 219  Bit Score: 59.79  E-value: 3.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  75 MQQFDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGVHEVI-VANKLQPSL 153
Cdd:cd13628    23 IVGFDIELAKTIAKKLGLKLQIQEYDFNGLIPALASGQADLALAGITPTPERKKVVDFSEPYYEASDTIVs*KDRKIKQL 102
                          90       100
                  ....*....|....*....|....*...
gi 2486361625 154 ttrDDLAGKSVFINPSTSYVQSIAQLNQ 181
Cdd:cd13628   103 ---QDLNGKSLGVQLGTIQEQLIKELSQ 127
3A0103s03R TIGR01096
lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino ...
75-178 5.58e-10

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


Pssm-ID: 273440 [Multi-domain]  Cd Length: 250  Bit Score: 59.68  E-value: 5.58e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  75 MQQFDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGvHEVIVANKLQPSLT 154
Cdd:TIGR01096  46 LVGFDVDLAKALCKRMKAKCKFVEQNFDGLIPSLKAKKVDAIMATMSITPKRQKQIDFSDPYYAT-GQGFVVKKGSDLAK 124
                          90       100
                  ....*....|....*....|....
gi 2486361625 155 TRDDLAGKSVFINPSTSYVQSIAQ 178
Cdd:TIGR01096 125 TLEDLDGKTVGVQSGTTHEQYLKD 148
PBP2_AA_binding_like_2 cd13627
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
87-264 9.83e-10

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


Pssm-ID: 270345 [Multi-domain]  Cd Length: 243  Bit Score: 58.95  E-value: 9.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  87 KPDKKIHIVVIptSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGvHEVIVANKLQP--SLTTRDDLAGKSV 164
Cdd:cd13627    49 KLDMKLVIKKI--EWNGLIPALNSGDIDLIIAGMSKTPEREKTIDFSDPYYIS-NIVMVVKKDSAyaNATNLSDFKGATI 125
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 165 FINPSTSYVQSIAQLnqhlisnklaPVEVINAPGNLEPEDILEMVNANLAGYTvVDRYLALLWQKIYPNLVtYDQFTLRT 244
Cdd:cd13627   126 TGQLGTMYDDVIDQI----------PDVVHTTPYDTFPTMVAALQAGTIDGFT-VELPSAISALETNPDLV-IIKFEQGK 193
                         170       180
                  ....*....|....*....|....*..
gi 2486361625 245 -------DGNIALAVRKNSPQLLAVLN 264
Cdd:cd13627   194 gfmqdkeDTNVAIGCRKGNDKLKDKIN 220
PBP2_AatB_like cd00996
Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong ...
60-264 1.53e-09

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


Pssm-ID: 270217 [Multi-domain]  Cd Length: 227  Bit Score: 57.97  E-value: 1.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  60 FLDNQGTPRGLMVELMQQFDKTLnnGIKPDKKihivviPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASG 139
Cdd:cd00996    19 FRDENGEIVGFDIDLAKEVAKRL--GVEVEFQ------PIDWDMKETELNSGNIDLIWNGLTITDERKKKVAFSKPYLEN 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 140 vHEVIVANKLQPSlTTRDDLAGKSVFINPSTSYVQSIAQLNQHLISNKlapvEVINAPGNLepeDILEMVNANLAGYTVV 219
Cdd:cd00996    91 -RQIIVVKKDSPI-NSKADLKGKTVGVQSGSSGEDALNADPNLLKKNK----EVKLYDDNN---DAFMDLEAGRIDAVVV 161
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2486361625 220 DRYLAllwqKIYPNLVTYDQFTLrTDGNI-----ALAVRKNSPQLLAVLN 264
Cdd:cd00996   162 DEVYA----RYYIKKKPLDDYKI-LDESFgseeyGVGFRKEDTELKEKIN 206
PBP2_TcyK cd13710
Substrate binding domain of an ABC transporter TcyJKLMN; the type 2 periplasmic binding ...
55-193 1.99e-09

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


Pssm-ID: 270428 [Multi-domain]  Cd Length: 233  Bit Score: 57.69  E-value: 1.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  55 SKTFYFLDNQGTPRGLMVELMQQFDKTLnngikPDKKIHIVVIPTSRdrLIPDLLAGKGDLIAANLTITPERQQQVDFT- 133
Cdd:cd13710    11 TPPFSYEDKKGELTGYDIEVLKAIDKKL-----PQYKFKFKVTEFSS--ILTGLDSGKYDMAANNFSKTKERAKKFLFSk 83
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 134 LPLASGVHeVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQHlisNKLAPVEV 193
Cdd:cd13710    84 VPYGYSPL-VLVVKKDSNDINSLDDLAGKTTIVVAGTNYAKVLEAWNKK---NPDNPIKI 139
PBP2_HisJ_LAO cd13703
Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; ...
58-164 3.15e-09

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


Pssm-ID: 270421 [Multi-domain]  Cd Length: 229  Bit Score: 57.26  E-value: 3.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGlmvelmqqFDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPL- 136
Cdd:cd13703    15 FESKDADGELTG--------FDIDLGNALCAEMKVKCTWVEQDFDGLIPGLLARKFDAIISSMSITEERKKVVDFTDKYy 86
                          90       100
                  ....*....|....*....|....*...
gi 2486361625 137 ASGVHevIVANKLQPSLTTRDDLAGKSV 164
Cdd:cd13703    87 HTPSR--LVARKGSGIDPTPASLKGKRV 112
Slt35-like cd13399
Slt35-like lytic transglycosylase; Lytic transglycosylase similar to Escherichia coli lytic ...
317-408 6.07e-09

Slt35-like lytic transglycosylase; Lytic transglycosylase similar to Escherichia coli lytic transglycosylase Slt35 and Pseudomonas aeruginosa Sltb1. Lytic transglycosylase (LT) catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc) as do "goose-type" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Proteins similar to this this family include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as the eukaryotic "goose-type" lysozymes (goose egg-white lysozyme; GEWL).


Pssm-ID: 381602 [Multi-domain]  Cd Length: 108  Bit Score: 53.47  E-value: 6.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 317 YSVDWLLMVSQGYQESQLDQRK-RSHSGAIGIMQILPSTGKELKV---GDISLAEPNVNAGIKYI-RFMQdRYFADQPMD 391
Cdd:cd13399     1 YGVPPGILAAILGVESGFGPNAgGSPAGAQGIAQFMPSTWKAYGVdgnGDGKADPFNPEDAIASAaNYLC-RHGWDLNAF 79
                          90
                  ....*....|....*..
gi 2486361625 392 ELNKMLFTFAAYNAGPA 408
Cdd:cd13399    80 LGEDNFLALAAYNAGPG 96
LT_MltC_MltE cd16893
membrane-bound lytic murein transglycosylases MltC and MltE, and similar proteins; MltC and ...
311-407 8.24e-09

membrane-bound lytic murein transglycosylases MltC and MltE, and similar proteins; MltC and MltE are periplasmic, outer membrane attached lytic transglycosylases (LTs), which cleave beta-1,4-glycosidic bonds joining N-acetylmuramic acid and N-acetylglucosamine in the cell wall peptidoglycan, yielding 1,6-anhydromuropeptides. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria and the LTs in bacteriophage lambda


Pssm-ID: 381614 [Multi-domain]  Cd Length: 162  Bit Score: 54.49  E-value: 8.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 311 QKYGQEYSVDWLLMVSQGYQESQLDQRKRSHSGAIGIMQILPST-GKEL------KVGDIS---LAEP--NVNAGIKYIR 378
Cdd:cd16893     4 EKYAKKYGVDPALILAIIETESSFNPYAVSHSPAYGLMQIVPSTaGRDVyrllggKGGLPSksyLFDPenNIDIGTAYLH 83
                          90       100
                  ....*....|....*....|....*....
gi 2486361625 379 FMQDRYFADqPMDELNKMLFTFAAYNAGP 407
Cdd:cd16893    84 ILQNRYLKG-IKNPKSREYCAIAAYNGGA 111
PBP2_GlnP cd13619
Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold ...
58-171 1.09e-08

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


Pssm-ID: 270337 [Multi-domain]  Cd Length: 220  Bit Score: 55.40  E-value: 1.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKtlNNGIKPDKKihivviPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLP-L 136
Cdd:cd13619    13 FEFQNDDGKYVGIDVDLLNAIAK--DQGFKVELK------PMGFDAAIQAVQSGQADGVIAGMSITDERKKTFDFSDPyY 84
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2486361625 137 ASGVheVIVANKLQPSLTTRDDLAGKSVFINPSTS 171
Cdd:cd13619    85 DSGL--VIAVKKDNTSIKSYEDLKGKTVAVKNGTA 117
PBP2_Ehub_like cd01002
Substrate binding domain of ectoine/hydroxyectoine specific ABC transport system; the type 2 ...
40-163 1.32e-08

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


Pssm-ID: 270223 [Multi-domain]  Cd Length: 242  Bit Score: 55.36  E-value: 1.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  40 DAMQQRRIIRVLIPYSKTFYFLDNQGTPRGLMVELMQQFDKTLnnGIKpdkkiHIVVIPTSRDRLIPDLLAGKGDLIAAN 119
Cdd:cd01002     4 ERLKEQGTIRIGYANEPPYAYIDADGEVTGESPEVARAVLKRL--GVD-----DVEGVLTEFGSLIPGLQAGRFDVIAAG 76
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2486361625 120 LTITPERQQQVDFTLPLASgVHEVIVANKLQP-SLTTRDDLAGKS 163
Cdd:cd01002    77 MFITPERCEQVAFSEPTYQ-VGEAFLVPKGNPkGLHSYADVAKNP 120
PBP2_YxeM cd13709
Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein ...
55-174 2.15e-08

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


Pssm-ID: 270427 [Multi-domain]  Cd Length: 227  Bit Score: 54.66  E-value: 2.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  55 SKTFYFLDNqGTPRGLMVELMQQFDKtlNNGIKPDkkihivVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTL 134
Cdd:cd13709    11 SYPFTFKEN-GKLKGFEVDVWNAIGK--RTGYKVE------FVTADFSGLFGMLDSGKVDTIANQITITPERQEKYDFSE 81
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2486361625 135 PLASgVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQ 174
Cdd:cd13709    82 PYVY-DGAQIVVKKDNNSIKSLEDLKGKTVAVNLGSNYEK 120
PBP2_ml15202_like cd13701
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
53-174 2.16e-08

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


Pssm-ID: 270419 [Multi-domain]  Cd Length: 227  Bit Score: 54.78  E-value: 2.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  53 PYSKtFYFLDNQGTPRGLMVELMQQFDKTLNngikpdkkIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDF 132
Cdd:cd13701    12 PYPP-FTSKDASGKWSGWEIDLIDALCARLD--------ARCEITPVAWDGIIPALQSGKIDMIWNSMSITDERKKVIDF 82
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2486361625 133 TLPLASgVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQ 174
Cdd:cd13701    83 SDPYYE-TPTAIVGAKSDDRRVTPEDLKGKVIGVQGSTNNAT 123
PBP2_GluR0 cd00997
Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ...
105-193 3.91e-08

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


Pssm-ID: 270218 [Multi-domain]  Cd Length: 218  Bit Score: 53.88  E-value: 3.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 105 IPDLLA----GKGDLIAANLTITPERQQQVDFTLPLASGVHEVIVANklQPSLTTRDDLAGKSV-FINPSTsyvqSIAQL 179
Cdd:cd00997    50 VSALLAavaeGEADIAIAAISITAEREAEFDFSQPIFESGLQILVPN--TPLINSVNDLYGKRVaTVAGST----AADYL 123
                          90
                  ....*....|....
gi 2486361625 180 NQHLISnklaPVEV 193
Cdd:cd00997   124 RRHDID----VVEV 133
PRK15437 PRK15437
histidine ABC transporter substrate-binding protein HisJ; Provisional
25-164 5.28e-08

histidine ABC transporter substrate-binding protein HisJ; Provisional


Pssm-ID: 185334 [Multi-domain]  Cd Length: 259  Bit Score: 53.88  E-value: 5.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  25 TLALPTTINSVYGDFDAMQQRriIRVLI-PYSKTFYFLDNQGTPRGLMVELMQQFDKTLNngikpdkkIHIVVIPTSRDR 103
Cdd:PRK15437    7 SLSLVLAFSSATAAFAAIPQN--IRIGTdPTYAPFESKNSQGELVGFDIDLAKELCKRIN--------TQCTFVENPLDA 76
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2486361625 104 LIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGVHEVIVAN--KLQPSLTTrddLAGKSV 164
Cdd:PRK15437   77 LIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKnsDIQPTVES---LKGKRV 136
PBP2_OccT_like cd13699
Substrate binding domain of ABC-type octopine transporter-like; the type 2 periplasmic-binding ...
78-146 1.34e-07

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


Pssm-ID: 270417 [Multi-domain]  Cd Length: 211  Bit Score: 51.99  E-value: 1.34e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2486361625  78 FDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGVHEVIVA 146
Cdd:cd13699    27 FEIDLANVLCERMKVKCTFVVQDWDGMIPALNAGKFDVIMDAMSITAERKKVIDFSTPYAATPNSFAVV 95
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
331-457 1.61e-07

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 53.59  E-value: 1.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 331 ESQLDQRKRSHSGAIGIMQILPSTGKelkvgdislaepnvNAGIKyirfmQDRYF------------ADQPMDELNKM-- 396
Cdd:PRK10783  128 ESAFDPHATSGANAAGIWQIIPSTGR--------------NYGLK-----QTRWYdarrdvvasttaALDMMQRLNKMfd 188
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 397 ---LFTFAAYNAGPAKIEKLRKQAKLMGLDPNRWfnnvervaQLKIGNETVQYV------SNIFKYYVAY 457
Cdd:PRK10783  189 gdwLLTVAAYNSGEGRVMKAIKANKAKGKPTDFW--------SLSLPRETKIYVpkmlalSDILKNSKRY 250
PBP2_GluB cd13690
Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein ...
65-181 2.13e-07

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


Pssm-ID: 270408 [Multi-domain]  Cd Length: 231  Bit Score: 51.89  E-value: 2.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  65 GTPRGLMVELMQQFDKTLnnGIKPDKkihIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASgVHEVI 144
Cdd:cd13690    29 GEFEGFDVDIARAVARAI--GGDEPK---VEFREVTSAEREALLQNGTVDLVVATYSITPERRKQVDFAGPYYT-AGQRL 102
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2486361625 145 VANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQ 181
Cdd:cd13690   103 LVRAGSKIITSPEDLNGKTVCTAAGSTSADNLKKNAP 139
PBP2_Arg_STM4351 cd13700
Substrate binding domain of arginine-specific ABC transporter; type 2 periplasmic-binding ...
78-290 5.92e-07

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


Pssm-ID: 270418 [Multi-domain]  Cd Length: 222  Bit Score: 50.14  E-value: 5.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  78 FDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGVHEVIVANKlqpSLTTRD 157
Cdd:cd13700    27 FDIDLANALCKQMQAECTFTNQAFDSLIPSLKFKKFDAVISGMDITPEREKQVSFSTPYYENSAVVIAKKD---TYKTFA 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 158 DLAGKSVFINPSTSYvqsiaqlnQHLISNKLAPVEVINAPGnlEPEDILEMVNANLAGyTVVDRYLALLWQKIYPNLVTY 237
Cdd:cd13700   104 DLKGKKIGVQNGTTH--------QKYLQDKHKEITTVSYDS--YQNAFLDLKNGRIDG-VFGDTAVVAEWLKTNPDLAFV 172
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2486361625 238 DQFTlrTDGN-----IALAVRKNSPQLLAVLNPFCKAHKLGTSFgnQQVYKylrsvKW 290
Cdd:cd13700   173 GEKV--TDPNyfgtgLGIAVRKDNQALLEKLNAALAAIKANGEY--QKIYD-----KW 221
PRK11619 PRK11619
lytic murein transglycosylase; Provisional
325-457 6.37e-07

lytic murein transglycosylase; Provisional


Pssm-ID: 183236 [Multi-domain]  Cd Length: 644  Bit Score: 51.99  E-value: 6.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 325 VSQGY------QESQLDQRKRSHSGAIGIMQILPSTGKE-LKVGDIS-------LAEP--NVNAGIKYI-----RFMQDR 383
Cdd:PRK11619  492 IPQSYamaiarQESAWNPKARSPVGASGLMQIMPGTATHtVKMFSIPgyssssqLLDPetNINIGTSYLeyvyqQFGNNR 571
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 384 YFADqpmdelnkmlftfAAYNAGPAKIeklrkqaklmgldpNRWFNN----VERVAQLK-IG-NETVQYVSNIFKYYVAY 457
Cdd:PRK11619  572 ILAS-------------AAYNAGPGRV--------------RTWLGNsagrIDAVAFVEsIPfSETRGYVKNVLAYDAYY 624
PBP2_GlnH cd00994
Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; ...
78-164 7.40e-07

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


Pssm-ID: 270216 [Multi-domain]  Cd Length: 218  Bit Score: 49.97  E-value: 7.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  78 FDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLP-LASGVheVIVANKLQPSLTTR 156
Cdd:cd00994    24 FDIDLWEAIAKEAGFKYELQPMDFKGIIPALQTGRIDIAIAGITITEERKKVVDFSDPyYDSGL--AVMVKADNNSIKSI 101

                  ....*...
gi 2486361625 157 DDLAGKSV 164
Cdd:cd00994   102 DDLAGKTV 109
PBP2_HisK_like_1 cd13706
Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein; This ...
53-264 1.15e-06

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


Pssm-ID: 270424 [Multi-domain]  Cd Length: 219  Bit Score: 49.48  E-value: 1.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  53 PYSktfyFLDNQGTPRGLMVELMQQFDKTlnNGIKpdkkihIVVIPTSRDRLIPDLLAGKGDLIAAnLTITPERQQQVDF 132
Cdd:cd13706    14 PFS----FLDEDGEPQGILVDLWRLWSEK--TGIP------VEFVLLDWNESLEAVRQGEADVHDG-LFKSPEREKYLDF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 133 TLPLASgVHEVIVANKLQPSLTTRDDLAGKSVFInPSTSYvqSIAQLNQHLISNKLAPvevinAPGNlepEDILEMVNAN 212
Cdd:cd13706    81 SQPIAT-IDTYLYFHKDLSGITNLSDLKGFRVGV-VKGDA--EEEFLRAHGPILSLVY-----YDNY---EAMIEAAKAG 148
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2486361625 213 -----LAGYTVVDRYLAL--LWQKIYPNLVTYdQFTLRTdgnialAVRKNSPQLLAVLN 264
Cdd:cd13706   149 eidvfVADEPVANYYLYKygLPDEFRPAFRLY-SGQLHP------AVAKGNSALLDLIN 200
PRK15010 PRK15010
lysine/arginine/ornithine ABC transporter substrate-binding protein ArgT;
78-189 1.44e-06

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


Pssm-ID: 184972 [Multi-domain]  Cd Length: 260  Bit Score: 49.62  E-value: 1.44e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  78 FDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGVHEVIVA--NKLQPSLtt 155
Cdd:PRK15010   51 FDIDLGNEMCKRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAkgSPIQPTL-- 128
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2486361625 156 rDDLAGKSVFI------------NPSTSYVQSIAQLNQHLISNKLA 189
Cdd:PRK15010  129 -DSLKGKHVGVlqgstqeayaneTWRSKGVDVVAYANQDLVYSDLA 173
Lig_chan-Glu_bd pfam10613
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
104-135 1.64e-05

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


Pssm-ID: 463166 [Multi-domain]  Cd Length: 111  Bit Score: 43.66  E-value: 1.64e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2486361625 104 LIPDLLAGKGDLIAANLTITPERQQQVDFTLP 135
Cdd:pfam10613  68 MIGELIDGKADLAVAPLTITSEREKVVDFTKP 99
orph_peri_GRRM TIGR04262
extracellular substrate-binding orphan protein, GRRM family; This subfamily belongs to ...
58-177 2.09e-05

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


Pssm-ID: 275088 [Multi-domain]  Cd Length: 257  Bit Score: 46.20  E-value: 2.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTpRGLMVELMQQFDKTLNNGIKPDKKIHIVVIPTSRDRLiPDLLAGKGDlIAANLTITPERQQQVDFTLPLA 137
Cdd:TIGR04262  14 LYQKDDAGY-DGLSFDVLELIRDQLQAELGKPITIQFVVVNSVQEGL-PKLRSGKAD-IACGVAFTWERQMFVDYSLPFA 90
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2486361625 138 SGVHEVIVANKlqpSLTTRDDLAGKSVFINPSTSYVQSIA 177
Cdd:TIGR04262  91 VSGIRLLAPKG---NDGTPESLEGKTVGVVKDSVAAAVLA 127
ectoine_ehuB TIGR02995
ectoine/hydroxyectoine ABC transporter solute-binding protein; Members of this family are the ...
1-160 2.58e-05

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


Pssm-ID: 132040 [Multi-domain]  Cd Length: 275  Bit Score: 46.07  E-value: 2.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625   1 MVRCLFLLIALFFIGTASHAApsktlalpTTINSVygdfdamQQRRIIRVLIPYSKTFYFLDNQGTPRGLMVELMQQFDK 80
Cdd:TIGR02995   3 MAAGLTALMAIAAATPAAADA--------NTLEEL-------KEQGFARIAIANEPPFTYVGADGKVSGAAPDVARAIFK 67
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  81 TLnnGIKpdkkiHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASgVHEVIVANKLQP-SLTTRDDL 159
Cdd:TIGR02995  68 RL--GIA-----DVNASITEYGALIPGLQAGRFDAIAAGLFIKPERCKQVAFTQPILC-DAEALLVKKGNPkGLKSYKDI 139

                  .
gi 2486361625 160 A 160
Cdd:TIGR02995 140 A 140
PBP2_iGluR_NMDA cd13687
The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate ...
104-135 3.94e-05

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


Pssm-ID: 270405 [Multi-domain]  Cd Length: 239  Bit Score: 44.94  E-value: 3.94e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2486361625 104 LIPDLLAGKGDLIAANLTITPERQQQVDFTLP 135
Cdd:cd13687    63 MIGELVSGRADMAVASLTINPERSEVIDFSKP 94
PBP2_iGluR_NMDA_Nr1 cd13719
The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
104-135 6.31e-05

The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains the ligand binding domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site.


Pssm-ID: 270437 [Multi-domain]  Cd Length: 277  Bit Score: 44.66  E-value: 6.31e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2486361625 104 LIPDLLAGKGDLIAANLTITPERQQQVDFTLP 135
Cdd:cd13719    95 MMGELVSGRADMIVAPLTINPERAQYIEFSKP 126
PBP2_Mlr3796_like cd13695
The substrate-binding domain of putative amino aicd transporter; the type 2 periplasmic ...
58-135 1.03e-04

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


Pssm-ID: 270413 [Multi-domain]  Cd Length: 232  Bit Score: 43.70  E-value: 1.03e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLNNgiKPDKkIHIVVIptSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLP 135
Cdd:cd13695    21 WHFKSADGELQGFDIDMGRIIAKALFG--DPQK-VEFVNQ--SSDARIPNLTTDKVDITCQFMTVTAERAQQVAFTIP 93
PBP2_Arg_3 cd13622
Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding ...
68-264 1.21e-04

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


Pssm-ID: 270340 [Multi-domain]  Cd Length: 222  Bit Score: 43.44  E-value: 1.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  68 RGLMVELMQQFDKTLNNGIKpdkkihivVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGVHEVIVaN 147
Cdd:cd13622    25 FGFDIDLMNEICKRIQRTCQ--------YKPMRFDDLLAALNNGKVDVAISSISITPERSKNFIFSLPYLLSYSQFLT-N 95
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 148 KLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQhlISNKLAPVEvinapgnlEPEDILEMVNANLAGYTVVDRYLALLW 227
Cdd:cd13622    96 KDNNISSFLEDLKGKRIGILKGTIYKDYLLQMFV--INPKIIEYD--------RLVDLLEALNNNEIDAILLDNPIAKYW 165
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2486361625 228 QKIYPN--LVTYDQFtlrTDGN-IALAVRKNSPQLLAVLN 264
Cdd:cd13622   166 ASNSSDkfKLIGKPI---PIGNgLGIAVNKDNAALLTKIN 202
PRK15007 PRK15007
arginine ABC transporter substrate-binding protein;
78-264 1.94e-04

arginine ABC transporter substrate-binding protein;


Pssm-ID: 184969 [Multi-domain]  Cd Length: 243  Bit Score: 43.10  E-value: 1.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  78 FDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGVHEVIvanKLQPSLTTRD 157
Cdd:PRK15007   46 FDVDLAQALCKEIDATCTFSNQAFDSLIPSLKFRRVEAVMAGMDITPEREKQVLFTTPYYDNSALFV---GQQGKYTSVD 122
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 158 DLAGKSVFINPSTSYvqsiaqlnQHLISNKLApvEVINAPGNLEPEDILEMVNANLAGyTVVDRYLALLWQKIYPNLVTY 237
Cdd:PRK15007  123 QLKGKKVGVQNGTTH--------QKFIMDKHP--EITTVPYDSYQNAKLDLQNGRIDA-VFGDTAVVTEWLKDNPKLAAV 191
                         170       180       190
                  ....*....|....*....|....*....|
gi 2486361625 238 -DQFTLRT--DGNIALAVRKNSPQLLAVLN 264
Cdd:PRK15007  192 gDKVTDKDyfGTGLGIAVRQGNTELQQKLN 221
PHA00658 PHA00658
putative lysin
340-418 2.15e-04

putative lysin


Pssm-ID: 106967 [Multi-domain]  Cd Length: 720  Bit Score: 44.04  E-value: 2.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 340 SHSGAIGIMQILPSTGKEL-KVGDISLAEPNVNAGIKYIRFMQDRYFADQPMDELNKMLFTFAAYNAGPAKIEKLRKQAK 418
Cdd:PHA00658  326 SPKGAVGIAQVMPDTAPEAaKLAGLPWDENRYRNDAAYNRALGMAYFQKQLRDFGGDLPKAYAAYNAGPGALQSALKDAK 405
PBP2_ArtJ_like cd13697
Putative substrate-binding domain of ABC arginine transporter; the type 2 periplasmic-binding ...
85-148 2.34e-04

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


Pssm-ID: 270415 [Multi-domain]  Cd Length: 228  Bit Score: 42.52  E-value: 2.34e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2486361625  85 GIKPDkkihiVVIPTSRDRlIPDLLAGKGDLIAANLTITPERQQQVDFTLPLASGVHEVIVANK 148
Cdd:cd13697    46 GVKLE-----LVPVSSADR-VPFLMAGKIDAVLGGLTRTPDRAKVIDFSDPVNTEVLGILTTAV 103
PBP2_BvgS_like_1 cd13708
Putative sensor domain similar to BvgS; the type 2 periplasmic binding protein domain; BvgS is ...
58-264 4.16e-04

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


Pssm-ID: 270426 [Multi-domain]  Cd Length: 220  Bit Score: 41.73  E-value: 4.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  58 FYFLDNQGTPRGLMVELMQQFDKTLNngikpdkkIHIVVIPTS--RDRLipDLL-AGKGDLIAAnLTITPERQQQVDFTL 134
Cdd:cd13708    15 YEGIDEGGKHVGIAADYLKLIAERLG--------IPIELVPTKswSESL--EAAkEGKCDILSL-LNQTPEREEYLNFTK 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625 135 PLASgVHEVIVANKLQPSLTTRDDLAGKSVFINPSTSYVQSIAQLNQHLisnKLAPVEVInapgnlepEDILEMV-NANL 213
Cdd:cd13708    84 PYLS-DPNVLVTREDHPFIADLSDLGDKTIGVVKGYAIEEILRQKYPNL---NIVEVDSE--------EEGLKKVsNGEL 151
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2486361625 214 AGYTvvdRYLALLWQKI----YPNLVTYDQFTLrtDGNIALAVRKNSPQLLAVLN 264
Cdd:cd13708   152 FGFI---DSLPVAAYTIqkegLFNLKISGKLDE--DNELRIGVRKDEPLLLSILN 201
PBP2_iGluR_Kainate cd13714
Kainate receptor of the type 2 periplasmic-binding fold superfamily; This group contains ...
104-135 4.37e-04

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


Pssm-ID: 270432 [Multi-domain]  Cd Length: 251  Bit Score: 41.75  E-value: 4.37e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2486361625 104 LIPDLLAGKGDLIAANLTITPERQQQVDFTLP 135
Cdd:cd13714    72 MVRELIDGRADLAVADLTITYERESVVDFTKP 103
PBP2_iGluR_non_NMDA_like cd13685
The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate ...
104-135 1.07e-03

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


Pssm-ID: 270403 [Multi-domain]  Cd Length: 252  Bit Score: 40.63  E-value: 1.07e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2486361625 104 LIPDLLAGKGDLIAANLTITPERQQQVDFTLP 135
Cdd:cd13685    69 MIGELVRGEADIAVAPLTITAEREEVVDFTKP 100
PBP2_AA_binding_like_3 cd13621
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
40-136 2.52e-03

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


Pssm-ID: 270339 [Multi-domain]  Cd Length: 229  Bit Score: 39.34  E-value: 2.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  40 DAMQQRRIIRVLIPYSKTFYFLDN--QGTPRGLMVELMQQFDKTLnnGIKPdkkihiVVIPTSRDRLIPDLLAGKGDLIA 117
Cdd:cd13621     2 DRVKKRGVLRIGVALGEDPYFKKDpsTGEWTGFGIDMAEDIAKDL--GVKV------EPVETTWGNAVLDLQAGKIDVAF 73
                          90
                  ....*....|....*....
gi 2486361625 118 AnLTITPERQQQVDFTLPL 136
Cdd:cd13621    74 A-LDATPERALAIDFSTPL 91
PBP2_iGluR_ligand_binding cd00998
The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic ...
102-135 2.91e-03

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


Pssm-ID: 270219 [Multi-domain]  Cd Length: 243  Bit Score: 39.28  E-value: 2.91e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2486361625 102 DRLIPDLLAGKGDLIAANLTITPERQQQVDFTLP 135
Cdd:cd00998    67 NGMVGEVVRGEADLAVGPITITSERSVVIDFTQP 100
glnH PRK09495
glutamine ABC transporter periplasmic protein; Reviewed
78-173 2.92e-03

glutamine ABC transporter periplasmic protein; Reviewed


Pssm-ID: 236540 [Multi-domain]  Cd Length: 247  Bit Score: 39.34  E-value: 2.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486361625  78 FDKTLNNGIKPDKKIHIVVIPTSRDRLIPDLLAGKGDLIAANLTITPERQQQVDFTLP-LASGVHEVIVANklQPSLTTR 156
Cdd:PRK09495   49 FDIDLWAAIAKELKLDYTLKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGyYKSGLLVMVKAN--NNDIKSV 126
                          90
                  ....*....|....*..
gi 2486361625 157 DDLAGKSVFINPSTSYV 173
Cdd:PRK09495  127 KDLDGKVVAVKSGTGSV 143
PBP2_HisGluGlnArgOpine cd13698
Substrate binding domain of ABC-type histidine/glutamate/glutamine/arginine/opine transporter; ...
102-133 4.01e-03

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


Pssm-ID: 270416 [Multi-domain]  Cd Length: 214  Bit Score: 38.82  E-value: 4.01e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2486361625 102 DRLIPDLLAGKGDLIAANLTITPERQQQVDFT 133
Cdd:cd13698    51 DSIIPNLVSGNYDTIIAGMSITDERDEVIDFT 82
 
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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