NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1222442805|ref|WP_090494231|]
View 

MULTISPECIES: membrane-bound lytic murein transglycosylase MltF [unclassified Pseudoalteromonas]

Protein Classification

membrane-bound lytic murein transglycosylase F( domain architecture ID 11484996)

membrane-bound lytic murein transglycosylase F (MltF) cleaves the glycosidic bond between N-acetylmuramic acid and N-acetylglucosamin to allow for the regular growth and maintenance of the murein sacculus

CATH:  3.40.190.10
EC:  4.2.2.-
Gene Ontology:  GO:0000270|GO:0016837|GO:0008933|GO:0016829|GO:0016020
PubMed:  17468031|18234673

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK10859 PRK10859
membrane-bound lytic murein transglycosylase MltF;
2-467 0e+00

membrane-bound lytic murein transglycosylase MltF;


:

Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 710.49  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805   2 LKIKLITIITLVILLCAC------NTQEQSTQLAQIKSENKIRIGTLASASNYYQAVQGEQGFEFELSQAFADYLGVELE 75
Cdd:PRK10859    4 LKINYLFIGLLALLLAAAlwpsipWFSKEENQLEQIQERGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADYLGVKLE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  76 IVPFFNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYGPTYRTISQKLVFKQGRERPRDFDDLTG-NFTVIAKSSHSLT 154
Cdd:PRK10859   84 IKVRDNISQLFDALDKGKADLAAAGLTYTPERLKQFRFGPPYYSVSQQLVYRKGQPRPRSLGDLKGgTLTVAAGSSHVET 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 155 LEEIQQTNPNLSWNETEEFDEEELLQAVIDGEIDYTLADSHTLALFRRYHPNLSIGFSVTRNDSIAWILRKSNDDSLYAL 234
Cdd:PRK10859  164 LQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPELAVAFDLTDEQPVAWALPPSGDDSLYAA 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 235 LVPFFGEAKQNNQLYVLEEKYFGHVRQFNYVNTLAYIDAIKETLPKYQPWFMQYAGSLDWRLLAALSYQESMWNPRAKSP 314
Cdd:PRK10859  244 LLDFFNQIKEDGTLARLEEKYFGHVDRFDYVDTRTFLRAIDNRLPKYQPLFEKYAGELDWRLLAAIAYQESHWNPQATSP 323

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 315 TGVRGIMMLTRRTAKQVGVTNRLEPEQNIRGGAQYLAKLIKRVPDRIPQPDRTWLALAAYNVGWGHVNDARIITEQQGAS 394
Cdd:PRK10859  324 TGVRGLMMLTRNTAQSMGVTDRLDPEQSIRGGARYLQDLMERLPESIPEPERIWFALAAYNIGYGHMLDARRLTKKQGGN 403

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1222442805 395 PDKWADVKKRLPLLIKKRHYRNTRYGYARGDVAVTYVDNIRRYYDALVWLD---ENNAMAPITSTNETEEKIVKPD 467
Cdd:PRK10859  404 PDSWADVKKRLPLLSQKKYYSKTRYGYARGHEAVHYVENIRRYYDSLVGYLqekEKQAAEEAPQLAQDYPAVSPAE 479
 
Name Accession Description Interval E-value
PRK10859 PRK10859
membrane-bound lytic murein transglycosylase MltF;
2-467 0e+00

membrane-bound lytic murein transglycosylase MltF;


Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 710.49  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805   2 LKIKLITIITLVILLCAC------NTQEQSTQLAQIKSENKIRIGTLASASNYYQAVQGEQGFEFELSQAFADYLGVELE 75
Cdd:PRK10859    4 LKINYLFIGLLALLLAAAlwpsipWFSKEENQLEQIQERGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADYLGVKLE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  76 IVPFFNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYGPTYRTISQKLVFKQGRERPRDFDDLTG-NFTVIAKSSHSLT 154
Cdd:PRK10859   84 IKVRDNISQLFDALDKGKADLAAAGLTYTPERLKQFRFGPPYYSVSQQLVYRKGQPRPRSLGDLKGgTLTVAAGSSHVET 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 155 LEEIQQTNPNLSWNETEEFDEEELLQAVIDGEIDYTLADSHTLALFRRYHPNLSIGFSVTRNDSIAWILRKSNDDSLYAL 234
Cdd:PRK10859  164 LQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPELAVAFDLTDEQPVAWALPPSGDDSLYAA 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 235 LVPFFGEAKQNNQLYVLEEKYFGHVRQFNYVNTLAYIDAIKETLPKYQPWFMQYAGSLDWRLLAALSYQESMWNPRAKSP 314
Cdd:PRK10859  244 LLDFFNQIKEDGTLARLEEKYFGHVDRFDYVDTRTFLRAIDNRLPKYQPLFEKYAGELDWRLLAAIAYQESHWNPQATSP 323

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 315 TGVRGIMMLTRRTAKQVGVTNRLEPEQNIRGGAQYLAKLIKRVPDRIPQPDRTWLALAAYNVGWGHVNDARIITEQQGAS 394
Cdd:PRK10859  324 TGVRGLMMLTRNTAQSMGVTDRLDPEQSIRGGARYLQDLMERLPESIPEPERIWFALAAYNIGYGHMLDARRLTKKQGGN 403

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1222442805 395 PDKWADVKKRLPLLIKKRHYRNTRYGYARGDVAVTYVDNIRRYYDALVWLD---ENNAMAPITSTNETEEKIVKPD 467
Cdd:PRK10859  404 PDSWADVKKRLPLLSQKKYYSKTRYGYARGHEAVHYVENIRRYYDSLVGYLqekEKQAAEEAPQLAQDYPAVSPAE 479
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
 12-444 7.59e-175

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


Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 497.28  E-value: 7.59e-175
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  12 LVILLCACntQEQSTQLAQIKSENKIRIGTLASASNYYQAVQGEQGFEFELSQAFADYLGVELEIVPFFNLSEMFARLDS 91
Cdd:COG4623     1 LLLLLPAC--SSEPGDLEQIKERGVLRVLTRNSPTTYFIYRGGPMGFEYELAKAFADYLGVKLEIIVPDNLDELLPALNA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  92 GDLDLIASGLTYNKVRAERYRYGPTYRTISQKLVFKQGRERPRDFDDLTG-NFTVIAKSSHSLTLEEIQQTNPNLSWNET 170
Cdd:COG4623    79 GEGDIAAAGLTITPERKKQVRFSPPYYSVSQVLVYRKGSPRPKSLEDLAGkTVHVRAGSSYAERLKQLNQEGPPLKWEED 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 171 EEFDEEELLQAVIDGEIDYTLADSHTLALFRRYHPNLSIGFSVTRNDSIAWILRKsNDDSLYALLVPFFGEAKQNNQLYV 250
Cdd:COG4623   159 EDLETEDLLEMVAAGEIDYTVADSNIAALNQRYYPNLRVAFDLSEPQPIAWAVRK-NDPSLLAALNEFFAKIKKGGTLAR 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 251 LEEKYFGHVRQFNYvntlAYIDAIKETLPKYQPWFMQYAGS--LDWRLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTA 328
Cdd:COG4623   238 LYERYFGHVKRDTR----AFLRRIEGRLPPYDPLFEKYAEEygLDWRLLAALAYQESHWNPRARSPTGARGLMQLMPATA 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 329 KQVGVTNRLEPEQNIRGGAQYLAKLIKRVPDRIPQPDRTWLALAAYNVGWGHVNDARIITEQQGASPDKWADVKKRlpll 408
Cdd:COG4623   314 KELGVDDRLDPEQSIRAGAKYLRWLYDRFPEAIDEPDRWWFALAAYNAGPGHVQDARRLAKKQGLDPDRWFDVEKS---- 389

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 1222442805 409 iKKRHYRNtryGYARGDVAVTYVDNIRRYYDALVWL 444
Cdd:COG4623   390 -QPKYYDT---GYARGRETVNYVPNIRAYYDIYKRL 421
MLTF-like cd13403
membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins; This subfamily ...
 285-443 9.07e-83

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: 252.84  E-value: 9.07e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 285 FMQYAGS--LDWRLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTAKQVGVTNRLEPEQNIRGGAQYLAKLIKRVPDRIP 362
Cdd:cd13403     1 FKKYAEKygFDWRLLAAQAYQESRFNPNARSPAGARGLMQLMPSTARELGVNDRLDPEQNIHAGAKYLRYLRDRFPPDID 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 363 QPDRTWLALAAYNVGWGHVNDARIITEQQGASPDKWADVKKRLPLLIKKRHYRNTRYGYARGDVAVTYVDNIRRYYDALV 442
Cdd:cd13403    81 EPDRLKFALAAYNAGPGHVRDARRLAKKYGLNPNVWFDNVEVLPLLKSPYYDPVVKYGYARGRETVNYVRNIRKYYDAYK 160


                  .
gi 1222442805 443 W 443
Cdd:cd13403   161 Q 161
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
 37-256 3.14e-29

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: 114.31  E-value: 3.14e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  37 IRIGTLASAS--NYYQAVQGEQGFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYG 114
Cdd:pfam00497   1 LRVGTDGDYPpfEYVDENGKLVGFDVDLAKAIAKRLGVKVEFVPV-SWDGLIPALQSGKVDLIIAGMTITPERAKQVDFS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 115 PTYRTISQKLVFKQGRERP--RDFDDLTGNFTVIAKSShslTLEEIQQTNPNLSWNETEEFDEEELLQAVIDGEIDYTLA 192
Cdd:pfam00497  80 DPYYYSGQVILVRKKDSSKsiKSLADLKGKTVGVQKGS---TAEELLKNLKLPGAEIVEYDDDAEALQALANGRVDAVVA 156

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1222442805 193 DSHTLALFRRYHPNLSI--GFSVTRNDSIAWILRKSNDDsLYALLVPFFGEAKQNNQLYVLEEKYF 256
Cdd:pfam00497 157 DSPVAAYLIKKNPGLNLvvVGEPLSPEPYGIAVRKGDPE-LLAAVNKALAELKADGTLAKIYEKWF 221
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
 36-256 4.35e-25

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 102.79  E-value: 4.35e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805   36 KIRIGTLASASN--YYQAVQGEQGFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIASGLTYNKVRAERYRY 113
Cdd:smart00062   1 TLRVGTNGDYPPfsFADEDGELTGFDVDLAKAIAKELGLKVEFVEV-SFDSLLTALKSGKIDVVAAGMTITPERAKQVDF 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  114 GPTYRTISQKLVFKQGrERPRDFDDLTGnfTVIAKSSHSLTLEEIQQTNPNLSWneTEEFDEEELLQAVIDGEIDYTLAD 193
Cdd:smart00062  80 SDPYYRSGQVILVRKD-SPIKSLEDLKG--KKVAVVAGTTAEELLKKLYPEAKI--VSYDSNAEALAALKAGRADAAVAD 154

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1222442805  194 SHTLALFRRYHPNL---SIGFSVTRNDSIAWILRKSNDDsLYALLVPFFGEAKQNNQLYVLEEKYF 256
Cdd:smart00062 155 APLLAALVKQHGLPelkIVPDPLDTPEGYAIAVRKGDPE-LLDKINKALKELKADGTLKKISEKWF 219
 
Name Accession Description Interval E-value
PRK10859 PRK10859
membrane-bound lytic murein transglycosylase MltF;
2-467 0e+00

membrane-bound lytic murein transglycosylase MltF;


Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 710.49  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805   2 LKIKLITIITLVILLCAC------NTQEQSTQLAQIKSENKIRIGTLASASNYYQAVQGEQGFEFELSQAFADYLGVELE 75
Cdd:PRK10859    4 LKINYLFIGLLALLLAAAlwpsipWFSKEENQLEQIQERGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADYLGVKLE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  76 IVPFFNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYGPTYRTISQKLVFKQGRERPRDFDDLTG-NFTVIAKSSHSLT 154
Cdd:PRK10859   84 IKVRDNISQLFDALDKGKADLAAAGLTYTPERLKQFRFGPPYYSVSQQLVYRKGQPRPRSLGDLKGgTLTVAAGSSHVET 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 155 LEEIQQTNPNLSWNETEEFDEEELLQAVIDGEIDYTLADSHTLALFRRYHPNLSIGFSVTRNDSIAWILRKSNDDSLYAL 234
Cdd:PRK10859  164 LQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPELAVAFDLTDEQPVAWALPPSGDDSLYAA 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 235 LVPFFGEAKQNNQLYVLEEKYFGHVRQFNYVNTLAYIDAIKETLPKYQPWFMQYAGSLDWRLLAALSYQESMWNPRAKSP 314
Cdd:PRK10859  244 LLDFFNQIKEDGTLARLEEKYFGHVDRFDYVDTRTFLRAIDNRLPKYQPLFEKYAGELDWRLLAAIAYQESHWNPQATSP 323

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 315 TGVRGIMMLTRRTAKQVGVTNRLEPEQNIRGGAQYLAKLIKRVPDRIPQPDRTWLALAAYNVGWGHVNDARIITEQQGAS 394
Cdd:PRK10859  324 TGVRGLMMLTRNTAQSMGVTDRLDPEQSIRGGARYLQDLMERLPESIPEPERIWFALAAYNIGYGHMLDARRLTKKQGGN 403

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1222442805 395 PDKWADVKKRLPLLIKKRHYRNTRYGYARGDVAVTYVDNIRRYYDALVWLD---ENNAMAPITSTNETEEKIVKPD 467
Cdd:PRK10859  404 PDSWADVKKRLPLLSQKKYYSKTRYGYARGHEAVHYVENIRRYYDSLVGYLqekEKQAAEEAPQLAQDYPAVSPAE 479
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
 12-444 7.59e-175

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


Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 497.28  E-value: 7.59e-175
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  12 LVILLCACntQEQSTQLAQIKSENKIRIGTLASASNYYQAVQGEQGFEFELSQAFADYLGVELEIVPFFNLSEMFARLDS 91
Cdd:COG4623     1 LLLLLPAC--SSEPGDLEQIKERGVLRVLTRNSPTTYFIYRGGPMGFEYELAKAFADYLGVKLEIIVPDNLDELLPALNA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  92 GDLDLIASGLTYNKVRAERYRYGPTYRTISQKLVFKQGRERPRDFDDLTG-NFTVIAKSSHSLTLEEIQQTNPNLSWNET 170
Cdd:COG4623    79 GEGDIAAAGLTITPERKKQVRFSPPYYSVSQVLVYRKGSPRPKSLEDLAGkTVHVRAGSSYAERLKQLNQEGPPLKWEED 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 171 EEFDEEELLQAVIDGEIDYTLADSHTLALFRRYHPNLSIGFSVTRNDSIAWILRKsNDDSLYALLVPFFGEAKQNNQLYV 250
Cdd:COG4623   159 EDLETEDLLEMVAAGEIDYTVADSNIAALNQRYYPNLRVAFDLSEPQPIAWAVRK-NDPSLLAALNEFFAKIKKGGTLAR 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 251 LEEKYFGHVRQFNYvntlAYIDAIKETLPKYQPWFMQYAGS--LDWRLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTA 328
Cdd:COG4623   238 LYERYFGHVKRDTR----AFLRRIEGRLPPYDPLFEKYAEEygLDWRLLAALAYQESHWNPRARSPTGARGLMQLMPATA 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 329 KQVGVTNRLEPEQNIRGGAQYLAKLIKRVPDRIPQPDRTWLALAAYNVGWGHVNDARIITEQQGASPDKWADVKKRlpll 408
Cdd:COG4623   314 KELGVDDRLDPEQSIRAGAKYLRWLYDRFPEAIDEPDRWWFALAAYNAGPGHVQDARRLAKKQGLDPDRWFDVEKS---- 389

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 1222442805 409 iKKRHYRNtryGYARGDVAVTYVDNIRRYYDALVWL 444
Cdd:COG4623   390 -QPKYYDT---GYARGRETVNYVPNIRAYYDIYKRL 421
MLTF-like cd13403
membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins; This subfamily ...
 285-443 9.07e-83

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: 252.84  E-value: 9.07e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 285 FMQYAGS--LDWRLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTAKQVGVTNRLEPEQNIRGGAQYLAKLIKRVPDRIP 362
Cdd:cd13403     1 FKKYAEKygFDWRLLAAQAYQESRFNPNARSPAGARGLMQLMPSTARELGVNDRLDPEQNIHAGAKYLRYLRDRFPPDID 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 363 QPDRTWLALAAYNVGWGHVNDARIITEQQGASPDKWADVKKRLPLLIKKRHYRNTRYGYARGDVAVTYVDNIRRYYDALV 442
Cdd:cd13403    81 EPDRLKFALAAYNAGPGHVRDARRLAKKYGLNPNVWFDNVEVLPLLKSPYYDPVVKYGYARGRETVNYVRNIRKYYDAYK 160


                  .
gi 1222442805 443 W 443
Cdd:cd13403   161 Q 161
PBP2_YfhD_N cd01009
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ...
 36-257 5.16e-73

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: 229.79  E-value: 5.16e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  36 KIRIGTLASASNYYQAVQGEQGFEFELSQAFADYLGVELEIVPFFNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYGP 115
Cdd:cd01009     2 ELRVLTRNSPTTYYIDRGGPRGFEYELAKAFADYLGVELEIVPADNLEELLEALEEGKGDLAAAGLTITPERKKKVDFSF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 116 TYRTISQKLVFKQGRERPRDFDDLTG-NFTVIAKSSHSLTLEEIQQTNPNLSWNETEEFDEEELLQAVIDGEIDYTLADS 194
Cdd:cd01009    82 PYYYVVQVLVYRKGSPRPRSLEDLSGkTIAVRKGSSYAETLQKLNKGGPPLTWEEVDEALTEELLEMVAAGEIDYTVADS 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1222442805 195 HTLALFRRYHPNLSIGFSVTRNDSIAWILRKsNDDSLYALLVPFFGEAKQNNQLYVLEEKYFG 257
Cdd:cd01009   162 NIAALWRRYYPELRVAFDLSEPQPLAWAVRK-NSPSLLAALNRFLAQIKKDGTLARLYERYYG 223
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
 37-256 3.14e-29

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: 114.31  E-value: 3.14e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  37 IRIGTLASAS--NYYQAVQGEQGFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYG 114
Cdd:pfam00497   1 LRVGTDGDYPpfEYVDENGKLVGFDVDLAKAIAKRLGVKVEFVPV-SWDGLIPALQSGKVDLIIAGMTITPERAKQVDFS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 115 PTYRTISQKLVFKQGRERP--RDFDDLTGNFTVIAKSShslTLEEIQQTNPNLSWNETEEFDEEELLQAVIDGEIDYTLA 192
Cdd:pfam00497  80 DPYYYSGQVILVRKKDSSKsiKSLADLKGKTVGVQKGS---TAEELLKNLKLPGAEIVEYDDDAEALQALANGRVDAVVA 156

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1222442805 193 DSHTLALFRRYHPNLSI--GFSVTRNDSIAWILRKSNDDsLYALLVPFFGEAKQNNQLYVLEEKYF 256
Cdd:pfam00497 157 DSPVAAYLIKKNPGLNLvvVGEPLSPEPYGIAVRKGDPE-LLAAVNKALAELKADGTLAKIYEKWF 221
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
 36-256 4.35e-25

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 102.79  E-value: 4.35e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805   36 KIRIGTLASASN--YYQAVQGEQGFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIASGLTYNKVRAERYRY 113
Cdd:smart00062   1 TLRVGTNGDYPPfsFADEDGELTGFDVDLAKAIAKELGLKVEFVEV-SFDSLLTALKSGKIDVVAAGMTITPERAKQVDF 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  114 GPTYRTISQKLVFKQGrERPRDFDDLTGnfTVIAKSSHSLTLEEIQQTNPNLSWneTEEFDEEELLQAVIDGEIDYTLAD 193
Cdd:smart00062  80 SDPYYRSGQVILVRKD-SPIKSLEDLKG--KKVAVVAGTTAEELLKKLYPEAKI--VSYDSNAEALAALKAGRADAAVAD 154

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1222442805  194 SHTLALFRRYHPNL---SIGFSVTRNDSIAWILRKSNDDsLYALLVPFFGEAKQNNQLYVLEEKYF 256
Cdd:smart00062 155 APLLAALVKQHGLPelkIVPDPLDTPEGYAIAVRKGDPE-LLDKINKALKELKADGTLKKISEKWF 219
SLT pfam01464
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found ...
 287-384 6.70e-24

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: 96.22  E-value: 6.70e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 287 QYAGSLDWRLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTAK------QVGVTNRLEPEQNIRGGAQYLAKLIKRVPDR 360
Cdd:pfam01464   5 AQKYGVDPSLLLAIAQQESGFNPKAVSKSGAVGLMQIMPSTAKrlglrvNPGVDDLFDPEKNIKAGTKYLKELYKQYGGD 84

                          90       100
                  ....*....|....*....|....
gi 1222442805 361 IpqpdrtWLALAAYNVGWGHVNDA 384
Cdd:pfam01464  85 L------WLALAAYNAGPGRVRKW 102
LT-like cd00254
lytic transglycosylase(LT)-like domain; Members include the soluble and insoluble ...
 295-385 9.88e-24

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: 95.36  E-value: 9.88e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 295 RLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTAKQVG---VTNRLEPEQNIRGGAQYLAKLIKRVPDRIpqpdrtWLAL 371
Cdd:cd00254     2 ALVLAVIRVESGFNPRAVSPAGARGLMQLMPGTARDLGrrgVDDLFDPEENIRAGARYLRELLDRFGGDL------ELAL 75

                          90
                  ....*....|....
gi 1222442805 372 AAYNVGWGHVNDAR 385
Cdd:cd00254    76 AAYNAGPGAVDRWG 89
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
 37-257 1.35e-23

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: 98.51  E-value: 1.35e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  37 IRIGTLASASNY-YQAVQGE-QGFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYG 114
Cdd:COG0834     1 LRVGVDPDYPPFsFRDEDGKlVGFDVDLARAIAKRLGLKVEFVPV-PWDRLIPALQSGKVDLIIAGMTITPEREKQVDFS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 115 PTYRTISQKLVFKQGRERPRDFDDLTGnfTVIAKSSHSLTLEEIQQTNPNLswNETEEFDEEELLQAVIDGEIDYTLADS 194
Cdd:COG0834    80 DPYYTSGQVLLVRKDNSGIKSLADLKG--KTVGVQAGTTYEEYLKKLGPNA--EIVEFDSYAEALQALASGRVDAVVTDE 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1222442805 195 HTLALFRRYHPNLSIGFSVTR--NDSIAWILRKSNDDslyalLVPFFGEA----KQNNQLYVLEEKYFG 257
Cdd:COG0834   156 PVAAYLLAKNPGDDLKIVGEPlsGEPYGIAVRKGDPE-----LLEAVNKAlaalKADGTLDKILEKWFG 219
MltE COG0741
Soluble lytic murein transglycosylase or regulatory protein s ( may contain LysM/invasin ...
 280-438 3.57e-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: 95.45  E-value: 3.57e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 280 KYQPWFMQYAG--SLDWRLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTAKQVGVT--------NRLEPEQNIRGGAQY 349
Cdd:COG0741   102 PYLPLIEEAAKkyGVDPALVLALIRQESAFNPNAVSPAGARGLMQLMPATARRLGLKlglgpspdDLFDPETNIRAGAAY 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 350 LAKLIKRVPDRIPqpdrtwLALAAYNVGWGHVNDARiiteqqgaSPDKWADvKKRLPllikkrhYRNTRygyargdvavT 429
Cdd:COG0741   182 LRELLDRFDGDLV------LALAAYNAGPGRVRRWL--------RRNGDRD-GEIIP-------YAETR----------N 229


                  ....*....
gi 1222442805 430 YVDNIRRYY 438
Cdd:COG0741   230 YVKKVLANY 238
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
 36-255 6.41e-21

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: 90.77  E-value: 6.41e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  36 KIRIGTLASAS--NYYQAVQGEQGFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIASGLTYNKVRAERYRY 113
Cdd:cd13530     1 TLRVGTDADYPpfEYIDKNGKLVGFDVDLANAIAKRLGVKVEFVDT-DFDGLIPALQSGKIDVAISGMTITPERAKVVDF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 114 GPTYRTISQKLVFKQGRERPRDFDDLTGnfTVIAKSSHSLTLEEIQQTNPNLswNETEEFDEEELLQAVIDGEIDYTLAD 193
Cdd:cd13530    80 SDPYYYTGQVLVVKKDSKITKTVADLKG--KKVGVQAGTTGEDYAKKNLPNA--EVVTYDNYPEALQALKAGRIDAVITD 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1222442805 194 SHTLALF-RRYHPNLSIGFSVTRNDSIAWILRKsNDDSLYALLVPFFGEAKQNNQLYVLEEKY 255
Cdd:cd13530   156 APVAKYYvKKNGPDLKVVGEPLTPEPYGIAVRK-GNPELLDAINKALAELKADGTLDKLLEKW 217
Slt70-like cd13401
70kDa soluble lytic transglycosylase (Slt70) and similar proteins; Catalytic domain of the ...
 281-382 1.03e-17

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: 79.83  E-value: 1.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 281 YQPWFMQYAG--SLDWRLLAALSYQESMWNPRAKSPTGVRGIMMLT----RRTAKQVGVTNR-----LEPEQNIRGGAQY 349
Cdd:cd13401     6 YRDLVERAAKknGLDPALVYAIIRQESAFDPDAVSPAGALGLMQLMpataKDVAKKLGLPYYsprdlFDPEYNIRLGSAY 85

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1222442805 350 LAKLIKRVPDRIPqpdrtwLALAAYNVGWGHVN 382
Cdd:cd13401    86 LAELLDRFDGNPV------LALAAYNAGPGRVR 112
LT_Slt70-like cd16896
uncharacterized lytic transglycosylase subfamily with similarity to Slt70; Uncharacterized ...
 292-382 1.78e-14

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: 70.62  E-value: 1.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 292 LDWRLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTA----KQVGVTNR-----LEPEQNIRGGAQYLAKLIKRVPDRIP 362
Cdd:cd16896    17 VDPLLVAAVIKVESNFNPNAVSSKGAIGLMQIMPETAewiaEKLGLEDFseddlYDPETNIRLGTWYLSYLLKEFDGNLV 96

                          90       100
                  ....*....|....*....|
gi 1222442805 363 qpdrtwLALAAYNVGWGHVN 382
Cdd:cd16896    97 ------LALAAYNAGPGNVD 110
PBP2_Cystine_like cd13626
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ...
 36-257 9.08e-14

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: 70.42  E-value: 9.08e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  36 KIRIGTLASASNY-YQAVQGE-QGFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIASGLTYNKVRAERYRY 113
Cdd:cd13626     1 KLTVGTEGTYPPFtFKDEDGKlTGFDVEVGREIAKRLGLKVEFKAT-EWDGLLPGLNSGKFDVIANQVTITPEREEKYLF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 114 GPTYRTISQKLVFKQGRERPRDFDDLTGNFT-VIAKSSHSLTLEEIqqtnpNLSWNETEEFDEEELLQAVIDGEIDYTLA 192
Cdd:cd13626    80 SDPYLVSGAQIIVKKDNTIIKSLEDLKGKVVgVSLGSNYEEVARDL-----ANGAEVKAYGGANDALQDLANGRADATLN 154

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1222442805 193 DSHTLALF-RRYHPNLSIGFSVTRNDSIAWILRKSNDDsLYALLVPFFGEAKQNNQLYVLEEKYFG 257
Cdd:cd13626   155 DRLAALYAlKNSNLPLKIVGDIVSTAKVGFAFRKDNPE-LRKKVNKALAEMKADGTLKKLSEKWFG 219
PBP2_AA_binding_like_1 cd13625
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
 31-255 9.37e-14

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: 70.48  E-value: 9.37e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  31 IKSENKIRIGTLASASNYYQAVQGEQ-GFEFELSQAFADYLGVELE--IVPFfnlSEMFARLDSGDLDLIASGLTYNKVR 107
Cdd:cd13625     1 IKKRGTITVATEADYAPFEFVENGKIvGFDRDLLDEMAKKLGVKVEqqDLPW---SGILPGLLAGKFDMVATSVTITKER 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 108 AERYRYGPTYRTISQKLVFKQGRERPRDFDDLTGNftVIAKSSHSLTLEEIQQTNPNLSWNETEEFDEEELLQ------- 180
Cdd:cd13625    78 AKRFAFTLPIAEATAALLKRAGDDSIKTIEDLAGK--VVGVQAGSAQLAQLKEFNETLKKKGGNGFGEIKEYVsypqaya 155

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1222442805 181 AVIDGEIDYTLADSHTLALFRRYHPN-LSIGFSVTRNDSIAWILRKsNDDSLYALLVPFFGEAKQNNQLYVLEEKY 255
Cdd:cd13625   156 DLANGRVDAVANSLTNLAYLIKQRPGvFALVGPVGGPTYFAWVIRK-GDAELRKAINDALLALKKSGKLAALQQKW 230
PBP2_Ngo0372_TcyA cd13711
Substrate binding domain of ABC transporters involved in cystine import; the type 2 ...
 37-257 6.45e-13

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: 68.09  E-value: 6.45e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  37 IRIGTLASASNY-YQAVQGE-QGFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYG 114
Cdd:cd13711     3 LTIGTEGTYAPFtYHDKSGKlTGFDVEVARAVAKKLGVKVEFVET-QWDSMIAGLDAGRFDVVANQVGITDERKKKYDFS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 115 PTYRTISQKLVFKQGRERPRDFDDLTGNftviaKSSHSLTleeiqqTNpnlsWNETEEFDEEEL---------LQAVIDG 185
Cdd:cd13711    82 TPYIYSRAVLIVRKDNSDIKSFADLKGK-----KSAQSLT------SN----WGKIAKKYGAQVvgvdgfaqaVELITQG 146

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1222442805 186 EIDYTLADSHTLALFRRYHPNLSIGFSVTRND--SIAWILRKSNDDsLYALLVPFFGEAKQNNQLYVLEEKYFG 257
Cdd:cd13711   147 RADATINDSLAFLDYKKQHPDAPVKIAAETDDasESAFLVRKGNDE-LVAAINKALKELKADGTLKKISEKYFG 219
PBP2_YxeM cd13709
Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein ...
 35-198 1.75e-12

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: 66.60  E-value: 1.75e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  35 NKIRIGTLASASNYYQAVQGE-QGFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIASGLTYNKVRAERYRY 113
Cdd:cd13709     1 KVIKVGSSGSSYPFTFKENGKlKGFEVDVWNAIGKRTGYKVEFVTA-DFSGLFGMLDSGKVDTIANQITITPERQEKYDF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 114 GPTYRTISQKLVFKQGRERPRDFDDLTGnFTViAKSSHSLTLEEIQQTNPNLSWNETEEFDEEELLQAVIDGEIDYTLAD 193
Cdd:cd13709    80 SEPYVYDGAQIVVKKDNNSIKSLEDLKG-KTV-AVNLGSNYEKILKAVDKDNKITIKTYDDDEGALQDVALGRVDAYVND 157


                  ....*
gi 1222442805 194 SHTLA 198
Cdd:cd13709   158 RVSLL 162
MltD-like cd16894
Membrane-bound lytic murein transglycosylase D and similar proteins; Lytic transglycosylases ...
 297-406 3.18e-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: 63.69  E-value: 3.18e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 297 LAALSYQESMWNPRAKSPTGVRGIMMLTRRTAKQVGVTN------RLEPEQNIRGGAQYLAKLIKRvpdripqpDRTW-L 369
Cdd:cd16894    10 LKYLALVESGFNPDAVSSAGAAGLWQFMPATAREYGLRVdswvdeRRDPEKSTRAAARYLKDLYKR--------FGDWlL 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1222442805 370 ALAAYNVGWGHVNDAriiTEQQGASPDKWADvKKRLP 406
Cdd:cd16894    82 ALAAYNAGEGRVRRA---IKRAGTDKWEDYY-RLYLP 114
PBP2_BvgS_HisK_like cd01007
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
 56-227 1.75e-11

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: 63.71  E-value: 1.75e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  56 QGFEFELSQAFADYLGVELEIVPFFNLSEMFARLDSGDLDLIASgLTYNKVRAERYRYGPTYRTISQKLVFKQGRERPRD 135
Cdd:cd01007    25 QGIAADYLKLIAKKLGLKFEYVPGDSWSELLEALKAGEIDLLSS-VSKTPEREKYLLFTKPYLSSPLVIVTRKDAPFINS 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 136 FDDLTGNftVIAKSSHSLTLEEIQQTNPNLswNETEEFDEEELLQAVIDGEIDYTLADSHTLA--LFRRYHPNLSIGFSV 213
Cdd:cd01007   104 LSDLAGK--RVAVVKGYALEELLRERYPNI--NLVEVDSTEEALEAVASGEADAYIGNLAVASylIQKYGLSNLKIAGLT 179

                         170
                  ....*....|....
gi 1222442805 214 TRNDSIAWILRKSN 227
Cdd:cd01007   180 DYPQDLSFAVRKDW 193
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
 48-197 4.38e-11

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: 62.60  E-value: 4.38e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  48 YYQAVQGE-QGFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIAsGLTYNKVRAERYRYGPTYRTISQKLVF 126
Cdd:cd13704    16 EFLDENGNpTGFNVDLLRAIAEEMGLKVEIRLG-PWSEVLQALENGEIDVLI-GMAYSEERAKLFDFSDPYLEVSVSIFV 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1222442805 127 KQGRERPRDFDDLTGNFTVIAKssHSLTLEEIQQTNPNLswNETEEFDEEELLQAVIDGEIDYTLADSHTL 197
Cdd:cd13704    94 RKGSSIINSLEDLKGKKVAVQR--GDIMHEYLKERGLGI--NLVLVDSPEEALRLLASGKVDAAVVDRLVG 160
PBP2_BsGlnH cd13689
Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ...
 28-257 5.36e-11

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: 62.25  E-value: 5.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  28 LAQIKSENKIRIGTLASAS--NYYQAVQGE-QGFEFELSQAFADYLGVELEIVPFFNLsemfAR---LDSGDLDLIASGL 101
Cdd:cd13689     1 LDDIKARGVLRCGVFDDVPpfGFIDPKTREiVGFDVDLCKAIAKKLGVKLELKPVNPA----ARipeLQNGRVDLVAANL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 102 TYNKVRAERYRYGPTYRTISQKLVFKQGReRPRDFDDLTGNFTVIAKSSHSltLEEIQQTNPNLswNETEEFDEEELLQA 181
Cdd:cd13689    77 TYTPERAEQIDFSDPYFVTGQKLLVKKGS-GIKSLKDLAGKRVGAVKGSTS--EAAIREKLPKA--SVVTFDDTAQAFLA 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 182 VIDGEIDYTLADSHTLALFRRYHPNLS----IGFSVTrNDSIAWILRKsNDDSLYALLVPFFGEAKQNNQLYVLEEKYFG 257
Cdd:cd13689   152 LQQGKVDAITTDETILAGLLAKAPDPGnyeiLGEALS-YEPYGIGVPK-GESALRDFVNETLADLEKDGEADKIYDKWFG 229
PBP2_FliY cd13712
Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ...
 49-257 1.39e-10

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: 60.86  E-value: 1.39e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  49 YQAVQGE-QGFEFELSQAFADYLGVELEIVPfFNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYGPTYrTIS--QKLV 125
Cdd:cd13712    15 FKDETGQlTGFEVDVAKALAAKLGVKPEFVT-TEWSGILAGLQAGKYDVIINQVGITPERQKKFDFSQPY-TYSgiQLIV 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 126 FKQGRERPRDFDDLTG---------NFTVIAKSshslTLEEIQ-QTNPNlswneteefdEEELLQAVIDGEIDYTLADSH 195
Cdd:cd13712    93 RKNDTRTFKSLADLKGkkvgvglgtNYEQWLKS----NVPGIDvRTYPG----------DPEKLQDLAAGRIDAALNDRL 158

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1222442805 196 TLALFRRYHPNLSIGFSVTRNDSIAWILRKSNDDsLYALLVPFFGEAKQNNQLYVLEEKYFG 257
Cdd:cd13712   159 AANYLVKTSLELPPTGGAFARQKSGIPFRKGNPK-LKAAINKAIEDLRADGTLAKLSEKWFG 219
Slt35-like cd13399
Slt35-like lytic transglycosylase; Lytic transglycosylase similar to Escherichia coli lytic ...
 292-380 2.43e-10

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: 57.70  E-value: 2.43e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 292 LDWRLLAALSYQESMWNPRA-KSPTGVRGIMMLTRRTAKQVGV-------TNRLEPEQNIRGGAQYLAKLIKRVPDRIPQ 363
Cdd:cd13399     3 VPPGILAAILGVESGFGPNAgGSPAGAQGIAQFMPSTWKAYGVdgngdgkADPFNPEDAIASAANYLCRHGWDLNAFLGE 82

                          90
                  ....*....|....*..
gi 1222442805 364 PDRtwLALAAYNVGWGH 380
Cdd:cd13399    83 DNF--LALAAYNAGPGA 97
PBP2_BvgS_D2 cd13707
The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
 67-217 1.35e-09

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: 58.00  E-value: 1.35e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  67 ADYL-------GVELEIVPFFNLSEMFARLDSGDLDLIAsGLTYNKVRAERYRYGPTYRTISQKLVFKQGRERPRDFDDL 139
Cdd:cd13707    29 ADLLelislrtGLRFEVVRASSPAEMIEALRSGEADMIA-ALTPSPEREDFLLFTRPYLTSPFVLVTRKDAAAPSSLEDL 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 140 TGNFTVIAKSSHSltLEEIQQTNPNLSWneTEEFDEEELLQAVIDGEIDYTLADSHTLA-LFRRYHPN------------ 206
Cdd:cd13707   108 AGKRVAIPAGSAL--EDLLRRRYPQIEL--VEVDNTAEALALVASGKADATVASLISARyLINHYFRDrlkiagilgepp 183

                         170
                  ....*....|.
gi 1222442805 207 LSIGFSVTRND 217
Cdd:cd13707   184 APIAFAVRRDQ 194
PBP2_Dsm1740 cd13629
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ...
 57-256 2.25e-09

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: 57.58  E-value: 2.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  57 GFEFELSQAFADYLGVELEIVPfFNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYGPTYRTISQK-LVFKQGRERPRD 135
Cdd:cd13629    24 GFDVDLAKALAKDLGVKVEFVN-TAWDGLIPALQTGKFDLIISGMTITPERNLKVNFSNPYLVSGQTlLVNKKSAAGIKS 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 136 FDDLTGNFTVIAKSSHSLTLEEIQQTNPNLSWNetEEFDEEELLQAVIDGEIDYTLADSHTLALF-RRYHPNL-SIGFSV 213
Cdd:cd13629   103 LEDLNKPGVTIAVKLGTTGDQAARKLFPKATIL--VFDDEAAAVLEVVNGKADAFIYDQPTPARFaKKNDPTLvALLEPF 180

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1222442805 214 TRnDSIAWILRKSNDDSLyALLVPFFGEAKQNNQLYVLEEKYF 256
Cdd:cd13629   181 TY-EPLGFAIRKGDPDLL-NWLNNFLKQIKGDGTLDELYDKWF 221
PHA00368 PHA00368
internal virion protein D
 285-356 2.76e-09

internal virion protein D


Pssm-ID: 222785 [Multi-domain]  Cd Length: 1315  Bit Score: 59.79  E-value: 2.76e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1222442805  285 FMQYAGS--LDWRLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTAKQVGV----TNRLEPEQNIRGGAQYLAKLIKR 356
Cdd:PHA00368    15 FQKAADAhgVSYDLLRKVGWDESRFNPTAKSPTGPKGLMQFTKATAKALGLivddDDRLDPELAIDAGARYLADLVGK 92
PRK11619 PRK11619
lytic murein transglycosylase; Provisional
 272-382 3.33e-09

lytic murein transglycosylase; Provisional


Pssm-ID: 183236 [Multi-domain]  Cd Length: 644  Bit Score: 59.30  E-value: 3.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 272 DAIKETLP-KYQPWFMQYAG--SLDWRLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTA----KQVGVTNR------LE 338
Cdd:PRK11619  469 DHLEERFPlAWNDEFRRYTSgkGIPQSYAMAIARQESAWNPKARSPVGASGLMQIMPGTAthtvKMFSIPGYssssqlLD 548

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1222442805 339 PEQNIRGGAQYLAKLIKRV-PDRIpqpdrtwLALAAYNVGWGHVN 382
Cdd:PRK11619  549 PETNINIGTSYLEYVYQQFgNNRI-------LASAAYNAGPGRVR 586
PRK11260 PRK11260
cystine ABC transporter substrate-binding protein;
13-141 4.62e-09

cystine ABC transporter substrate-binding protein;


Pssm-ID: 183061 [Multi-domain]  Cd Length: 266  Bit Score: 57.04  E-value: 4.62e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  13 VILLCACNTQEQS--TQLAQIKSENKIRIGTLASASNY-YQAVQGE-QGFEFELSQAFADYLGVELEIVPfFNLSEMFAR 88
Cdd:PRK11260   17 VALVAGMSVKSFAdeGLLNKVKERGTLLVGLEGTYPPFsFQGEDGKlTGFEVEFAEALAKHLGVKASLKP-TKWDGMLAS 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1222442805  89 LDSGDLDLIASGLTYNKVRAERYRYGPTYrTIS--QKLVFKQGRERPRDFDDLTG 141
Cdd:PRK11260   96 LDSKRIDVVINQVTISDERKKKYDFSTPY-TVSgiQALVKKGNEGTIKTAADLKG 149
PBP2_SMa0082_like cd01072
The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic ...
 27-257 1.04e-08

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: 55.73  E-value: 1.04e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  27 QLAQIKSENKIRIGTLASASNY-YQAVQGE-QGFEFELSQAFADYLGVELEIVPFFNLSEMfARLDSGDLDLIASGLTYN 104
Cdd:cd01072     5 TLDDIKKRGKLKVGVLVDAPPFgFVDASMQpQGYDVDVAKLLAKDLGVKLELVPVTGANRI-PYLQTGKVDMLIASLGIT 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 105 KVRAERYRYGPTYRTIsQKLVFKQGRERPRDFDDLTGNFTVIAKSShsltLEEIQQT--NPNLSwNETEEFDEEELLQAV 182
Cdd:cd01072    84 PERAKVVDFSQPYAAF-YLGVYGPKDAKVKSPADLKGKTVGVTRGS----TQDIALTkaAPKGA-TIKRFDDDASTIQAL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 183 IDGEIDYtLADSHTLA--LFRRY---HPNLSIGFSvTRNDSIAwiLRKSNDDsLYALLVPFFGEAKQNNQLYVLEEKYFG 257
Cdd:cd01072   158 LSGQVDA-IATGNAIAaqIAKANpdkKYELKFVLR-TSPNGIG--VRKGEPE-LLKWVNTFIAKNKANGELNALSQKWFG 232
PBP2_TcyK cd13710
Substrate binding domain of an ABC transporter TcyJKLMN; the type 2 periplasmic binding ...
 37-257 2.01e-08

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: 54.99  E-value: 2.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  37 IRIGTLASASNY-YQAVQGE-QGFEFELSQA----FADYlGVELEIVPFFNLsemFARLDSGDLDLIASGLTYNKVRAER 110
Cdd:cd13710     3 VKVATGADTPPFsYEDKKGElTGYDIEVLKAidkkLPQY-KFKFKVTEFSSI---LTGLDSGKYDMAANNFSKTKERAKK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 111 YRYGptYRTISQ---KLVFKQGRERPRDFDDLTG-NFTVIAKSSHSLTLEEIQQTNPNLSWNETEEFDEEEL-LQAVIDG 185
Cdd:cd13710    79 FLFS--KVPYGYsplVLVVKKDSNDINSLDDLAGkTTIVVAGTNYAKVLEAWNKKNPDNPIKIKYSGEGINDrLKQVESG 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1222442805 186 EIDYTLADSHTLALFRRYHP-NLS-IGFSVTRNDSIAWILRKSNDDslyalLVPFFGEA----KQNNQLYVLEEKYFG 257
Cdd:cd13710   157 RYDALILDKFSVDTIIKTQGdNLKvVDLPPVKKPYVYFLFNKDQQK-----LQKDIDKAlkelKKDGTLKKLSKKYFG 229
PBP2_polar_AA cd13693
Substrate binding domain of polar amino-acid uptake ABC transporter; the type 2 periplasmic ...
 28-117 2.36e-08

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: 54.63  E-value: 2.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  28 LAQIKSENKIRIGTLASAS--NYYQAVQGEQGFEFELSQAFADYLGVELEIVPFFNlSEMFARLDSGDLDLIASGLTYNK 105
Cdd:cd13693     1 LDRIKARGKLIVGVKNDYPpfGFLDPSGEIVGFEVDLAKDIAKRLGVKLELVPVTP-SNRIQFLQQGKVDLLIATMGDTP 79

                          90
                  ....*....|..
gi 1222442805 106 VRAERYRYGPTY 117
Cdd:cd13693    80 ERRKVVDFVEPY 91
PBP2_Cysteine cd13694
Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein ...
 28-231 2.44e-08

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: 54.67  E-value: 2.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  28 LAQIKSENKIRIGTLASASNY-YQAVQGE-QGFEFELSQAFADYL---GVELEIVpffnLSEMFAR---LDSGDLDLIAS 99
Cdd:cd13694     1 LEQIKQSGVIRIGVFGDKPPFgYVDENGKfQGFDIDLAKQIAKDLfgsGVKVEFV----LVEAANRvpyLTSGKVDLILA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 100 GLTYNKVRAERYRYGPTYRTISQKLVFKQGrERPRDFDDLTGNFTVIAKSShsLTLEEIQQTNPNLswNETEEFDEEELL 179
Cdd:cd13694    77 NFTVTPERAEVVDFANPYMKVALGVVSPKD-SNITSVAQLDGKTLLVNKGT--TAEKYFTKNHPEI--KLLKYDQNAEAF 151

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1222442805 180 QAVIDGEIDYTLADSHTLALFRRYHPNLSIGF-SVTRNDSIAWILRKSNDDSL 231
Cdd:cd13694   152 QALKDGRADAYAHDNILVLAWAKSNPGFKVGIkNLGDTDFIAPGVQKGNKELL 204
PBP2_MidA_like cd01004
Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 ...
 40-229 4.88e-08

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: 53.78  E-value: 4.88e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  40 GTLASASNY------YQAVQGE-QGFEFELSQAFADYLGVELEIVPfFNLSEMFARLDSGDLDLIASGLTYNKVRAERYR 112
Cdd:cd01004     2 GTLTVGTNPtyppyeFVDEDGKlIGFDVDLAKAIAKRLGLKVEIVN-VSFDGLIPALQSGRYDIIMSGITDTPERAKQVD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 113 YGPtYRTISQKLVFKQGRER-PRDFDDLTGnfTVIAKSSHSLTLEEIQQTNPNLS------WNETEEFDEEELLQAVIDG 185
Cdd:cd01004    81 FVD-YMKDGLGVLVAKGNPKkIKSPEDLCG--KTVAVQTGTTQEQLLQAANKKCKaagkpaIEIQTFPDQADALQALRSG 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1222442805 186 EIDYTLADSHTLALF-RRYHPNLSIGFSVTRND-SIAWILRKSNDD 229
Cdd:cd01004   158 RADAYLSDSPTAAYAvKQSPGKLELVGEVFGSPaPIGIAVKKDDPA 203
PBP2_GluB cd13690
Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein ...
 28-198 8.45e-08

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: 53.04  E-value: 8.45e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  28 LAQIKSENKIRIGTLASASN--YYQAVQGE-QGFEFELSQAFADYLGVELEIVPFFNLS--EMFARLDSGDLDLIASGLT 102
Cdd:cd13690     1 LAKIRKRGRLRVGVKFDQPGfsLRNPTTGEfEGFDVDIARAVARAIGGDEPKVEFREVTsaEREALLQNGTVDLVVATYS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 103 YNKVRAERYRYGPTYRTISQKLVFKQGRERPRDFDDLTGNFTVIAKSSHSLTleEIQQTNPNLswNETEEFDEEELLQAV 182
Cdd:cd13690    81 ITPERRKQVDFAGPYYTAGQRLLVRAGSKIITSPEDLNGKTVCTAAGSTSAD--NLKKNAPGA--TIVTRDNYSDCLVAL 156

                         170
                  ....*....|....*.
gi 1222442805 183 IDGEIDYTLADSHTLA 198
Cdd:cd13690   157 QQGRVDAVSTDDAILA 172
PBP2_Arg_Lys_His cd13624
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ...
 57-141 3.89e-07

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: 50.96  E-value: 3.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  57 GFEFELSQAFADYLGVELEIV--PFfnlSEMFARLDSGDLDLIASGLTYNKVRAERYRYGPTYRTISQKLVFKQGRERPR 134
Cdd:cd13624    24 GFDIDLIKAIAKEAGFEVEFKnmAF---DGLIPALQSGKIDIIISGMTITEERKKSVDFSDPYYEAGQAIVVRKDSTIIK 100


                  ....*..
gi 1222442805 135 DFDDLTG 141
Cdd:cd13624   101 SLDDLKG 107
LT_MltC_MltE cd16893
membrane-bound lytic murein transglycosylases MltC and MltE, and similar proteins; MltC and ...
 283-381 1.04e-06

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: 48.71  E-value: 1.04e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 283 PWFMQYAGS--LDWRLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTAkqvG--VTNRL-------------EPEQNIRG 345
Cdd:cd16893     1 PIVEKYAKKygVDPALILAIIETESSFNPYAVSHSPAYGLMQIVPSTA---GrdVYRLLggkgglpsksylfDPENNIDI 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1222442805 346 GAQYLAKLIKRVPDRIPQPD-RTWLALAAYNVGWGHV 381
Cdd:cd16893    78 GTAYLHILQNRYLKGIKNPKsREYCAIAAYNGGAGNV 114
PBP2_BvgS_D1 cd13705
The first of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
 67-228 1.34e-06

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


Pssm-ID: 270423 [Multi-domain]  Cd Length: 221  Bit Score: 49.13  E-value: 1.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  67 ADYLGVELEIVPFFNLSEMFARLDSGDLDLIASGLTYnkvraERYRYG-----PtYrTISQKLVFKQGRERPRDFDDLTG 141
Cdd:cd13705    37 ADALGVRVEVRRYPDREAALEALRNGEIDLLGTANGS-----EAGDGGlllsqP-Y-LPDQPVLVTRIGDSRQPPPDLAG 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 142 nfTVIAKSSHSLTLEEIQQTNPNLSWneTEEFDEEELLQAVIDGEIDYTLADSHTLA-LFRRYHP-NLSI-GFSVTRNDS 218
Cdd:cd13705   110 --KRVAVVPGYLPAEEIKQAYPDARI--VLYPSPLQALAAVAFGQADYFLGDAISANyLISRNYLnNLRIvRFAPLPSRG 185

                         170
                  ....*....|
gi 1222442805 219 IAWILRKSND 228
Cdd:cd13705   186 FGFAVRPDNT 195
PBP2_AA_hypothetical cd13623
Substrate-binding domain of putative amino-acid transport system; the type 2 periplasmic ...
 40-129 1.04e-05

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


Pssm-ID: 270341 [Multi-domain]  Cd Length: 220  Bit Score: 46.51  E-value: 1.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  40 GTLASA---SNYYQAVQGEQ----GFEFELSQAFADYLGVELEIVPFFNLSEMFARLDSGDLDLiaSGLTYNKVRAERYR 112
Cdd:cd13623     4 GTLRVAinlGNPVLAVEDATggprGVSVDLAKELAKRLGVPVELVVFPAAGAVVDAASDGEWDV--AFLAIDPARAETID 81

                          90
                  ....*....|....*..
gi 1222442805 113 YGPTYRTISQKLVFKQG 129
Cdd:cd13623    82 FTPPYVEIEGTYLVRAD 98
PBP2_GltS cd13620
Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 ...
 32-141 1.41e-05

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: 46.18  E-value: 1.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  32 KSENKIRIGTLASASNY-YQA-VQGEQ---GFEFELSQAFADYLGVELEIVPfFNLSEMFARLDSGDLDLIASGLTYNKV 106
Cdd:cd13620     1 KKKGKLVVGTSADYAPFeFQKmKDGKNqvvGADIDIAKAIAKELGVKLEIKS-MDFDNLLASLQSGKVDMAISGMTPTPE 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1222442805 107 RAERYRYGPTYRTISQKLVFKQG-RERPRDFDDLTG 141
Cdd:cd13620    80 RKKSVDFSDVYYEAKQSLLVKKAdLDKYKSLDDLKG 115
PBP2_ArtJ cd00999
The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold ...
 32-141 1.69e-05

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: 45.78  E-value: 1.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  32 KSENKIRIGTLASASNY-YQAVQGE-QGFEFELSQAFADYLGVELEIVPF-FNlsEMFARLDSGDLDLIASGLTYNKVRA 108
Cdd:cd00999     1 MDKDVIIVGTESTYPPFeFRDEKGElVGFDIDLAEAISEKLGKKLEWRDMaFD--ALIPNLLTGKIDAIAAGMSATPERA 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1222442805 109 ERYRYGPTYRTISQKLVFKQGRERPRDFDDLTG 141
Cdd:cd00999    79 KRVAFSPPYGESVSAFVTVSDNPIKPSLEDLKG 111
PBP2_AA_binding_like_2 cd13627
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
 41-228 5.68e-05

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: 44.70  E-value: 5.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  41 TLASASNYYQAVQGEQ-----GFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYGP 115
Cdd:cd13627    16 TQETASEYAIPIINGQggyadGYDVQIAKKLAEKLDMKLVIKKI-EWNGLIPALNSGDIDLIIAGMSKTPEREKTIDFSD 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 116 TYRTISQKLVFKQGR--ERPRDFDDLTG-NFTVIAKSSHSLTLEEIQ---QTNPnlswneteEFDEEELLQAVIDGEIDY 189
Cdd:cd13627    95 PYYISNIVMVVKKDSayANATNLSDFKGaTITGQLGTMYDDVIDQIPdvvHTTP--------YDTFPTMVAALQAGTIDG 166

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1222442805 190 TLADSHTLALFRRYHPNLSI-------GFSVTRNDSIAWI-LRKSND 228
Cdd:cd13627   167 FTVELPSAISALETNPDLVIikfeqgkGFMQDKEDTNVAIgCRKGND 213
PBP2_Cys_DEBP_like cd01000
Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ...
 28-205 1.04e-04

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: 43.45  E-value: 1.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  28 LAQIKSENKIRIGTLASASNY-YQAVQGE-QGFEFELSQAFADYL---GVELEIVPFfNLSEMFARLDSGDLDLIASGLT 102
Cdd:cd01000     1 LDDIKSRGVLIVGVKPDLPPFgARDANGKiQGFDVDVAKALAKDLlgdPVKVKFVPV-TSANRIPALQSGKVDLIIATMT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 103 YNKVRAERYRYGPTYRTISQKLVFKQGRERpRDFDDLTGnfTVIAKSSHSLTLEEIQQTNPNLswNETEEFDEEELLQAV 182
Cdd:cd01000    80 ITPERAKEVDFSVPYYADGQGLLVRKDSKI-KSLEDLKG--KTILVLQGSTAEAALRKAAPEA--QLLEFDDYAEAFQAL 154

                         170       180
                  ....*....|....*....|...
gi 1222442805 183 IDGEIDYTLADSHTLALFRRYHP 205
Cdd:cd01000   155 ESGRVDAMATDNSLLAGWAAENP 177
PBP2_GltI_DEBP cd13688
Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic ...
 28-256 1.91e-04

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: 43.01  E-value: 1.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  28 LAQIKSENKIRIGTL-ASASNYYQAVQGE-QGFEFELSQAFADYLGVEL-------EIVPFfNLSEMFARLDSGDLDLIA 98
Cdd:cd13688     1 LEKIRRTGTLTLGYReDSVPFSYLDDNGKpVGYSVDLCNAIADALKKKLalpdlkvRYVPV-TPQDRIPALTSGTIDLEC 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  99 SGLTYNKVRAERYRYGPTYRTISQKLVFKQGrERPRDFDDLTG-NFTVIAKSShslTLEEIQQTNP--NLSWNETEEFDE 175
Cdd:cd13688    80 GATTNTLERRKLVDFSIPIFVAGTRLLVRKD-SGLNSLEDLAGkTVGVTAGTT---TEDALRTVNPlaGLQASVVPVKDH 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 176 EELLQAVIDGEIDYTLADSHTLALFRRYHPN------LSIGFSVtrnDSIAWILRKsNDDSLYALLVPFFGEAKQNNQLY 249
Cdd:cd13688   156 AEGFAALETGKADAFAGDDILLAGLAARSKNpddlalIPRPLSY---EPYGLMLRK-DDPDFRLLVDRALAQLYQSGEIE 231


                  ....*..
gi 1222442805 250 VLEEKYF 256
Cdd:cd13688   232 KLYDKWF 238
PBP2_AatB_like cd00996
Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong ...
 57-166 4.23e-04

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: 41.79  E-value: 4.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  57 GFEFELSQAFADYLGVELEIVPF-FNLSEMfaRLDSGDLDLIASGLTYNKVRAERYRYGPTYRTISQKLVFKQGRErPRD 135
Cdd:cd00996    28 GFDIDLAKEVAKRLGVEVEFQPIdWDMKET--ELNSGNIDLIWNGLTITDERKKKVAFSKPYLENRQIIVVKKDSP-INS 104

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1222442805 136 FDDLTG-NFTVIAKSSHSLTLEEiqqtNPNLS 166
Cdd:cd00996   105 KADLKGkTVGVQSGSSGEDALNA----DPNLL 132
LT_IagB-like cd13400
Escherichia coli invasion protein IagB and similar proteins; Lytic transglycosylase-like ...
 295-384 1.24e-03

Escherichia coli invasion protein IagB and similar proteins; Lytic transglycosylase-like protein, similar to Escherichia coli invasion protein IagB. IagB is encoded within a pathogenicity island in Salmonella enterica and has been shown to degrade polymeric peptidoglycan. IagB-like invasion proteins are implicated in the invasion of eukaryotic host cells by bacteria. 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. Members of this family resemble the soluble and insoluble membrane-bound LTs in bacteria and the LTs in bacteriophage lambda.


Pssm-ID: 381603 [Multi-domain]  Cd Length: 109  Bit Score: 38.28  E-value: 1.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 295 RLLAALSYQESMWNPRAKSPTGVR----GIMML----TRRTAKQVGVTNRL--EPEQNIRGGAQYLAKLIKRVPDripqp 364
Cdd:cd13400     6 RLLRAIAKVESGFNPNAINRNKNGsydiGLMQInsiwLPELARYGITREELlnDPCTNIYVGAWILARNIKRYGN----- 80

                          90       100
                  ....*....|....*....|
gi 1222442805 365 drTWLALAAYNVGWGHVNDA 384
Cdd:cd13400    81 --TWKAVGAYNSGTPKKNDK 98
PBP2_Peb1a_like cd13691
Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 ...
 28-119 1.99e-03

Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 periplasmic-binding protein fold; This group includes periplasmic aspartate/glutamate binding domain Peb1a and its closely related protein. The Peb1a is an important virulence factor in the food-borne human pathogen Campylobacter jejuni, which has a major role in adherence and host colonization. The Peb1a domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270409 [Multi-domain]  Cd Length: 228  Bit Score: 39.74  E-value: 1.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  28 LAQIKSENKIRIGTLASASN--YYQAVQGE-QGFEFELSQAFADY-LGVELEIVPFfNLSEMFARLDSGDLDLIASGLTY 103
Cdd:cd13691     1 VGKIKKRGVLRVGVKNDVPGfgYQDPETGKyEGMEVDLARKLAKKgDGVKVEFTPV-TAKTRGPLLDNGDVDAVIATFTI 79

                          90
                  ....*....|....*.
gi 1222442805 104 NKVRAERYRYGPTYRT 119
Cdd:cd13691    80 TPERKKSYDFSTPYYT 95
Lyz-like cd00442
lysozyme-like domains; This family contains several members, including soluble lytic ...
 297-349 2.11e-03

lysozyme-like domains; This family contains several members, including soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, chitosanases, and pesticin. Typical members are involved in the hydrolysis of beta-1,4- linked polysaccharides.


Pssm-ID: 381596 [Multi-domain]  Cd Length: 59  Bit Score: 36.23  E-value: 2.11e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1222442805 297 LAALSYQESMWNP--RAKSPTGVRGIMMLTRRTAKQVGVT---NRLEPEQNIRGGAQY 349
Cdd:cd00442     2 LAAIIGQESGGNKpaNAGSGSGAAGLFQFMPGTWKAYGKNsssDLNDPEASIEAAAKY 59
PBP2_Ala cd13628
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ...
 48-218 4.05e-03

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: 38.60  E-value: 4.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  48 YYQAVQGE-QGFEFELSQAFADYLGVELEIVPF-FNlsEMFARLDSGDLDLIASGLTYNKVRAERYRYGPTYRTISQKLV 125
Cdd:cd13628    15 FKIGDRGKiVGFDIELAKTIAKKLGLKLQIQEYdFN--GLIPALASGQADLALAGITPTPERKKVVDFSEPYYEASDTIV 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 126 FKQGRERPRdFDDLTG-NFTVIAKSSHSLTLEEIQQTNPNLswNETEEFDEEELLQAVIDGEIDYTLADSHTLALFRRYH 204
Cdd:cd13628    93 S*KDRKIKQ-LQDLNGkSLGVQLGTIQEQLIKELSQPYPGL--KTKLYNRVNELVQALKSGRVDAAIVEDIVAETFAQKK 169

                         170
                  ....*....|....
gi 1222442805 205 PNLSIGFSVTRNDS 218
Cdd:cd13628   170 N*LLESRYIPKEAD 183
mltC PRK11671
membrane-bound lytic murein transglycosylase MltC;
280-381 4.32e-03

membrane-bound lytic murein transglycosylase MltC;


Pssm-ID: 183271 [Multi-domain]  Cd Length: 359  Bit Score: 39.26  E-value: 4.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805 280 KYQPWFMQYAG--SLDWRLLAALSYQESMWNPRAKSPTGVRGIMMLTRRTA-KQV-------GVTNR---LEPEQNIRGG 346
Cdd:PRK11671  191 KYLPMVRKASRkyGVDESLILAIMQTESSFNPYAVSRSDALGLMQVVQHTAgKDVfrmkgksGQPSRsylFDPANNIDTG 270

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1222442805 347 AQYLAKLIKRVPDRIPQP-DRTWLALAAYNVGWGHV 381
Cdd:PRK11671  271 TAYLAILQNVYLGGITNPtSRRYAVITAYNGGAGSV 306
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
 10-102 5.01e-03

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


Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 38.83  E-value: 5.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  10 ITLVILLCACNTQEQSTQlaqiksENKIRIGTLASASN--YYQAVqgEQGFefelsqaFADYlGVELEIVPFFNLSEMFA 87
Cdd:COG0715     3 ALAALALAACSAAAAAAE------KVTLRLGWLPNTDHapLYVAK--EKGY-------FKKE-GLDVELVEFAGGAAALE 66

                          90
                  ....*....|....*
gi 1222442805  88 RLDSGDLDLIASGLT 102
Cdd:COG0715    67 ALAAGQADFGVAGAP 81
PBP2_ml15202_like cd13701
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
 57-200 7.94e-03

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: 37.83  E-value: 7.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1222442805  57 GFEFELSQAFADYLGVELEIVPFfNLSEMFARLDSGDLDLIASGLTYNKVRAERYRYGPTYRTISQKLVFKQGRERPRDF 136
Cdd:cd13701    27 GWEIDLIDALCARLDARCEITPV-AWDGIIPALQSGKIDMIWNSMSITDERKKVIDFSDPYYETPTAIVGAKSDDRRVTP 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1222442805 137 DDLTG---------NFTVIAKSSH--SLTLEEIQQTNpnlswneteefdeeELLQAVIDGEIDYTLADSHTLALF 200
Cdd:cd13701   106 EDLKGkvigvqgstNNATFARKHFadDAELKVYDTQD--------------EALADLVAGRVDAVLADSLAFTEF 166
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH