NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2461897830|ref|WP_275929182|]
View 

lytic transglycosylase F [Aeromonas sp. 1HA1]

Protein Classification

lytic transglycosylase F( domain architecture ID 10099052)

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
 28-455 1.32e-116

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


:

Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 348.98  E-value: 1.32e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  28 PQPGDLEHILQKKELRALVVYERGFFFLDKGTQHGILVNQLQGFERWLNqtylakekIKLKIIyIPVRQDKLLDYLSEGR 107
Cdd:COG4623    10 SEPGDLEQIKERGVLRVLTRNSPTTYFIYRGGPMGFEYELAKAFADYLG--------VKLEII-VPDNLDELLPALNAGE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 108 GDLVAANMTVTPTRREQVTFSDPvIAPIEEWVVSQYSLPTFNRITQLSGRRIWVRASSSYYESLRQLNWlfrelGLPPIY 187
Cdd:COG4623    81 GDIAAAGLTITPERKKQVRFSPP-YYSVSQVLVYRKGSPRPKSLEDLAGKTVHVRAGSSYAERLKQLNQ-----EGPPLK 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 188 IEtVPEYLQDGDLLEMVAAGIIQLTVTDSFKGRIWLGMISGLRAHKliPLRDKGRSAWALRNNSPKLLKAVNGYLADAGK 267
Cdd:COG4623   155 WE-EDEDLETEDLLEMVAAGEIDYTVADSNIAALNQRYYPNLRVAF--DLSEPQPIAWAVRKNDPSLLAALNEFFAKIKK 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 268 RTLYSDMTLRgLLARSDQMSNILAPDPLGRLATIRKVLEQQADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLP 347
Cdd:COG4623   232 GGTLARLYER-YFGHVKRDTRAFLRRIEGRLPPYDPLFEKYAEEYGLDWRLLAALAYQESHWNPRARSPTGARGLMQLMP 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 348 STGGEVGIRGaRLaSLEGNVEAACRYMRLILDTYfnDPGLDVLNRHLFALAAYNAGPNRVQAIRAKAEAAGLDPNVWFGN 427
Cdd:COG4623   311 ATAKELGVDD-RL-DPEQSIRAGAKYLRWLYDRF--PEAIDEPDRWWFALAAYNAGPGHVQDARRLAKKQGLDPDRWFDV 386

                         410       420       430
                  ....*....|....*....|....*....|...
gi 2461897830 428 VEQL-----VANEVGQGPINYVSTIYKYYVAYR 455
Cdd:COG4623   387 EKSQpkyydTGYARGRETVNYVPNIRAYYDIYK 419
 
Name Accession Description Interval E-value
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
 28-455 1.32e-116

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


Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 348.98  E-value: 1.32e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  28 PQPGDLEHILQKKELRALVVYERGFFFLDKGTQHGILVNQLQGFERWLNqtylakekIKLKIIyIPVRQDKLLDYLSEGR 107
Cdd:COG4623    10 SEPGDLEQIKERGVLRVLTRNSPTTYFIYRGGPMGFEYELAKAFADYLG--------VKLEII-VPDNLDELLPALNAGE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 108 GDLVAANMTVTPTRREQVTFSDPvIAPIEEWVVSQYSLPTFNRITQLSGRRIWVRASSSYYESLRQLNWlfrelGLPPIY 187
Cdd:COG4623    81 GDIAAAGLTITPERKKQVRFSPP-YYSVSQVLVYRKGSPRPKSLEDLAGKTVHVRAGSSYAERLKQLNQ-----EGPPLK 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 188 IEtVPEYLQDGDLLEMVAAGIIQLTVTDSFKGRIWLGMISGLRAHKliPLRDKGRSAWALRNNSPKLLKAVNGYLADAGK 267
Cdd:COG4623   155 WE-EDEDLETEDLLEMVAAGEIDYTVADSNIAALNQRYYPNLRVAF--DLSEPQPIAWAVRKNDPSLLAALNEFFAKIKK 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 268 RTLYSDMTLRgLLARSDQMSNILAPDPLGRLATIRKVLEQQADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLP 347
Cdd:COG4623   232 GGTLARLYER-YFGHVKRDTRAFLRRIEGRLPPYDPLFEKYAEEYGLDWRLLAALAYQESHWNPRARSPTGARGLMQLMP 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 348 STGGEVGIRGaRLaSLEGNVEAACRYMRLILDTYfnDPGLDVLNRHLFALAAYNAGPNRVQAIRAKAEAAGLDPNVWFGN 427
Cdd:COG4623   311 ATAKELGVDD-RL-DPEQSIRAGAKYLRWLYDRF--PEAIDEPDRWWFALAAYNAGPGHVQDARRLAKKQGLDPDRWFDV 386

                         410       420       430
                  ....*....|....*....|....*....|...
gi 2461897830 428 VEQL-----VANEVGQGPINYVSTIYKYYVAYR 455
Cdd:COG4623   387 EKSQpkyydTGYARGRETVNYVPNIRAYYDIYK 419
PBP2_YfhD_N cd01009
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ...
 40-271 5.24e-64

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: 206.29  E-value: 5.24e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  40 KELRALVVYERGFFFLDKGTQHGILVNQLQGFERWLnqtylakekiKLKIIYIPV-RQDKLLDYLSEGRGDLVAANMTVT 118
Cdd:cd01009     1 GELRVLTRNSPTTYYIDRGGPRGFEYELAKAFADYL----------GVELEIVPAdNLEELLEALEEGKGDLAAAGLTIT 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 119 PTRREQVTFSDPvIAPIEEWVVSQYSLPTFNRITQLSGRRIWVRASSSYYESLRQLNWlfrelGLPPIYIETVPEYLQDg 198
Cdd:cd01009    71 PERKKKVDFSFP-YYYVVQVLVYRKGSPRPRSLEDLSGKTIAVRKGSSYAETLQKLNK-----GGPPLTWEEVDEALTE- 143

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2461897830 199 DLLEMVAAGIIQLTVTDSFKGRIWLGMISGLraHKLIPLRDKGRSAWALRNNSPKLLKAVNGYLADAGKRTLY 271
Cdd:cd01009   144 ELLEMVAAGEIDYTVADSNIAALWRRYYPEL--RVAFDLSEPQPLAWAVRKNSPSLLAALNRFLAQIKKDGTL 214
PRK10859 PRK10859
membrane-bound lytic murein transglycosylase MltF;
29-451 4.59e-35

membrane-bound lytic murein transglycosylase MltF;


Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 136.54  E-value: 4.59e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  29 QPGDLEHILQKKELRALVVYERGFFFLDKGTQHGILVNQLQGFERWLNqtylakekIKLKIIYIPvRQDKLLDYLSEGRG 108
Cdd:PRK10859   32 EENQLEQIQERGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADYLG--------VKLEIKVRD-NISQLFDALDKGKA 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 109 DLVAANMTVTPTRREQVTFSDPVIApieewvVSQY-------SLPTfnRITQLSGRRIWVRASSSYYESLRQLNWLFREL 181
Cdd:PRK10859  103 DLAAAGLTYTPERLKQFRFGPPYYS------VSQQlvyrkgqPRPR--SLGDLKGGTLTVAAGSSHVETLQELKKKYPEL 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 182 GlppiyIETVPEYLQDgDLLEMVAAGIIQLTVTDS--------FKGRIWLGMisglrahkliPLRDKGRSAWAL-RNNSP 252
Cdd:PRK10859  175 S-----WEESDDKDSE-ELLEQVAEGKIDYTIADSveislnqrYHPELAVAF----------DLTDEQPVAWALpPSGDD 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 253 KLLKAVNGYLadagkrtlySDMTLRGLLAR--------------SDQMSNILAPDplGRLATIRKVLEQQADkyGLDWLM 318
Cdd:PRK10859  239 SLYAALLDFF---------NQIKEDGTLARleekyfghvdrfdyVDTRTFLRAID--NRLPKYQPLFEKYAG--ELDWRL 305

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 319 LAALAYKESGLNAGVRSERGAVGIMQLLPSTGGEVGIRGaRLaSLEGNVEAACRYMRLILDTyFND--PGLDvlnRHLFA 396
Cdd:PRK10859  306 LAAIAYQESHWNPQATSPTGVRGLMMLTRNTAQSMGVTD-RL-DPEQSIRGGARYLQDLMER-LPEsiPEPE---RIWFA 379

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2461897830 397 LAAYNAGPNRVQAIRAKAEAAGLDPNVWfGNVEQ---LVANEV-----------GQGPINYVSTIYKYY 451
Cdd:PRK10859  380 LAAYNIGYGHMLDARRLTKKQGGNPDSW-ADVKKrlpLLSQKKyysktrygyarGHEAVHYVENIRRYY 447
SLT pfam01464
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found ...
 309-424 3.45e-19

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: 82.74  E-value: 3.45e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 309 ADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLPSTGGEVGIRGARLASL----EGNVEAACRYMRLILDTYfnd 384
Cdd:pfam01464   5 AQKYGVDPSLLLAIAQQESGFNPKAVSKSGAVGLMQIMPSTAKRLGLRVNPGVDDlfdpEKNIKAGTKYLKELYKQY--- 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2461897830 385 pgldvLNRHLFALAAYNAGPNRVqaIRAKAEAAGLDPNVW 424
Cdd:pfam01464  82 -----GGDLWLALAAYNAGPGRV--RKWIKNAGAKDKKLL 114
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
 66-263 2.82e-15

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 74.67  E-value: 2.82e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830   66 NQLQGFERWLNQtYLAKEkIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQYSL 145
Cdd:smart00062  20 GELTGFDVDLAK-AIAKE-LGLKVEFVEVSFDSLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYRSGQVILVRKDSP 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  146 PTfnRITQLSGRRIWVRASSSYYESLRQLNwlfrelglPPIYIETVPeylQDGDLLEMVAAGIIQLTVTDSFKGRIWLgM 225
Cdd:smart00062  98 IK--SLEDLKGKKVAVVAGTTAEELLKKLY--------PEAKIVSYD---SNAEALAALKAGRADAAVADAPLLAALV-K 163

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 2461897830  226 ISGLRAHKLIPLR--DKGRSAWALRNNSPKLLKAVNGYLA 263
Cdd:smart00062 164 QHGLPELKIVPDPldTPEGYAIAVRKGDPELLDKINKALK 203
 
Name Accession Description Interval E-value
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
 28-455 1.32e-116

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


Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 348.98  E-value: 1.32e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  28 PQPGDLEHILQKKELRALVVYERGFFFLDKGTQHGILVNQLQGFERWLNqtylakekIKLKIIyIPVRQDKLLDYLSEGR 107
Cdd:COG4623    10 SEPGDLEQIKERGVLRVLTRNSPTTYFIYRGGPMGFEYELAKAFADYLG--------VKLEII-VPDNLDELLPALNAGE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 108 GDLVAANMTVTPTRREQVTFSDPvIAPIEEWVVSQYSLPTFNRITQLSGRRIWVRASSSYYESLRQLNWlfrelGLPPIY 187
Cdd:COG4623    81 GDIAAAGLTITPERKKQVRFSPP-YYSVSQVLVYRKGSPRPKSLEDLAGKTVHVRAGSSYAERLKQLNQ-----EGPPLK 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 188 IEtVPEYLQDGDLLEMVAAGIIQLTVTDSFKGRIWLGMISGLRAHKliPLRDKGRSAWALRNNSPKLLKAVNGYLADAGK 267
Cdd:COG4623   155 WE-EDEDLETEDLLEMVAAGEIDYTVADSNIAALNQRYYPNLRVAF--DLSEPQPIAWAVRKNDPSLLAALNEFFAKIKK 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 268 RTLYSDMTLRgLLARSDQMSNILAPDPLGRLATIRKVLEQQADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLP 347
Cdd:COG4623   232 GGTLARLYER-YFGHVKRDTRAFLRRIEGRLPPYDPLFEKYAEEYGLDWRLLAALAYQESHWNPRARSPTGARGLMQLMP 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 348 STGGEVGIRGaRLaSLEGNVEAACRYMRLILDTYfnDPGLDVLNRHLFALAAYNAGPNRVQAIRAKAEAAGLDPNVWFGN 427
Cdd:COG4623   311 ATAKELGVDD-RL-DPEQSIRAGAKYLRWLYDRF--PEAIDEPDRWWFALAAYNAGPGHVQDARRLAKKQGLDPDRWFDV 386

                         410       420       430
                  ....*....|....*....|....*....|...
gi 2461897830 428 VEQL-----VANEVGQGPINYVSTIYKYYVAYR 455
Cdd:COG4623   387 EKSQpkyydTGYARGRETVNYVPNIRAYYDIYK 419
PBP2_YfhD_N cd01009
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ...
 40-271 5.24e-64

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: 206.29  E-value: 5.24e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  40 KELRALVVYERGFFFLDKGTQHGILVNQLQGFERWLnqtylakekiKLKIIYIPV-RQDKLLDYLSEGRGDLVAANMTVT 118
Cdd:cd01009     1 GELRVLTRNSPTTYYIDRGGPRGFEYELAKAFADYL----------GVELEIVPAdNLEELLEALEEGKGDLAAAGLTIT 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 119 PTRREQVTFSDPvIAPIEEWVVSQYSLPTFNRITQLSGRRIWVRASSSYYESLRQLNWlfrelGLPPIYIETVPEYLQDg 198
Cdd:cd01009    71 PERKKKVDFSFP-YYYVVQVLVYRKGSPRPRSLEDLSGKTIAVRKGSSYAETLQKLNK-----GGPPLTWEEVDEALTE- 143

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2461897830 199 DLLEMVAAGIIQLTVTDSFKGRIWLGMISGLraHKLIPLRDKGRSAWALRNNSPKLLKAVNGYLADAGKRTLY 271
Cdd:cd01009   144 ELLEMVAAGEIDYTVADSNIAALWRRYYPEL--RVAFDLSEPQPLAWAVRKNSPSLLAALNRFLAQIKKDGTL 214
MLTF-like cd13403
membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins; This subfamily ...
 306-455 4.55e-56

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: 183.51  E-value: 4.55e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 306 EQQADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLPSTGGEVGIRgaRLASLEGNVEAACRYMRLILDTYfnDP 385
Cdd:cd13403     2 KKYAEKYGFDWRLLAAQAYQESRFNPNARSPAGARGLMQLMPSTARELGVN--DRLDPEQNIHAGAKYLRYLRDRF--PP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 386 GLDVLNRHLFALAAYNAGPNRVQAIRAKAEAAGLDPNVWFGNVEQLV-------------ANEVGQGPINYVSTIYKYYV 452
Cdd:cd13403    78 DIDEPDRLKFALAAYNAGPGHVRDARRLAKKYGLNPNVWFDNVEVLPllkspyydpvvkyGYARGRETVNYVRNIRKYYD 157


                  ...
gi 2461897830 453 AYR 455
Cdd:cd13403   158 AYK 160
PRK10859 PRK10859
membrane-bound lytic murein transglycosylase MltF;
29-451 4.59e-35

membrane-bound lytic murein transglycosylase MltF;


Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 136.54  E-value: 4.59e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  29 QPGDLEHILQKKELRALVVYERGFFFLDKGTQHGILVNQLQGFERWLNqtylakekIKLKIIYIPvRQDKLLDYLSEGRG 108
Cdd:PRK10859   32 EENQLEQIQERGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADYLG--------VKLEIKVRD-NISQLFDALDKGKA 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 109 DLVAANMTVTPTRREQVTFSDPVIApieewvVSQY-------SLPTfnRITQLSGRRIWVRASSSYYESLRQLNWLFREL 181
Cdd:PRK10859  103 DLAAAGLTYTPERLKQFRFGPPYYS------VSQQlvyrkgqPRPR--SLGDLKGGTLTVAAGSSHVETLQELKKKYPEL 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 182 GlppiyIETVPEYLQDgDLLEMVAAGIIQLTVTDS--------FKGRIWLGMisglrahkliPLRDKGRSAWAL-RNNSP 252
Cdd:PRK10859  175 S-----WEESDDKDSE-ELLEQVAEGKIDYTIADSveislnqrYHPELAVAF----------DLTDEQPVAWALpPSGDD 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 253 KLLKAVNGYLadagkrtlySDMTLRGLLAR--------------SDQMSNILAPDplGRLATIRKVLEQQADkyGLDWLM 318
Cdd:PRK10859  239 SLYAALLDFF---------NQIKEDGTLARleekyfghvdrfdyVDTRTFLRAID--NRLPKYQPLFEKYAG--ELDWRL 305

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 319 LAALAYKESGLNAGVRSERGAVGIMQLLPSTGGEVGIRGaRLaSLEGNVEAACRYMRLILDTyFND--PGLDvlnRHLFA 396
Cdd:PRK10859  306 LAAIAYQESHWNPQATSPTGVRGLMMLTRNTAQSMGVTD-RL-DPEQSIRGGARYLQDLMER-LPEsiPEPE---RIWFA 379

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2461897830 397 LAAYNAGPNRVQAIRAKAEAAGLDPNVWfGNVEQ---LVANEV-----------GQGPINYVSTIYKYY 451
Cdd:PRK10859  380 LAAYNIGYGHMLDARRLTKKQGGNPDSW-ADVKKrlpLLSQKKyysktrygyarGHEAVHYVENIRRYY 447
MltE COG0741
Soluble lytic murein transglycosylase or regulatory protein s ( may contain LysM/invasin ...
 220-455 6.69e-23

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: 97.37  E-value: 6.69e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 220 RIWLGMISGLRAHKLIPLRDKGRSAWALRNNSPKLLKAVNGYLADAGKRTLYSDMTLRGLLARSDQMSNILAPDPLGRLA 299
Cdd:COG0741    21 LALALLAAAAAAAALAAAAAALAAAAAAAAGAAAAAASAAAGGPALAAALAAADALAAFAAIAALAAELLALAALLLRRP 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 300 T-IRKVLEQQADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLPSTGGEVGIRGARLASLEG------NVEAACR 372
Cdd:COG0741   101 LpYLPLIEEAAKKYGVDPALVLALIRQESAFNPNAVSPAGARGLMQLMPATARRLGLKLGLGPSPDDlfdpetNIRAGAA 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 373 YMRLILDTYFNDPGLdvlnrhlfALAAYNAGPNRVQaiRAKAEAAGLDPnvwfgnvEQLVANEvgqgPINYVSTIYKYYV 452
Cdd:COG0741   181 YLRELLDRFDGDLVL--------ALAAYNAGPGRVR--RWLRRNGDRDG-------EIIPYAE----TRNYVKKVLANYA 239


                  ...
gi 2461897830 453 AYR 455
Cdd:COG0741   240 IYR 242
Slt70-like cd13401
70kDa soluble lytic transglycosylase (Slt70) and similar proteins; Catalytic domain of the ...
 302-455 1.02e-20

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


Pssm-ID: 381604 [Multi-domain]  Cd Length: 152  Bit Score: 88.30  E-value: 1.02e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 302 RKVLEQQADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLPSTGGEV----GIRGARLASL---EGNVEAACRYM 374
Cdd:cd13401     7 RDLVERAAKKNGLDPALVYAIIRQESAFDPDAVSPAGALGLMQLMPATAKDVakklGLPYYSPRDLfdpEYNIRLGSAYL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 375 RLILDTYFNDPgldvlnrhLFALAAYNAGPNRVQaiRAKAEAAGLDPNVWfgnVEQLvanevgqgPI----NYVSTIYKY 450
Cdd:cd13401    87 AELLDRFDGNP--------VLALAAYNAGPGRVR--RWLKRRGDLDPDLW---IETI--------PFsetrNYVKRVLEN 145


                  ....*
gi 2461897830 451 YVAYR 455
Cdd:cd13401   146 YVVYR 150
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
 52-264 6.45e-20

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: 88.11  E-value: 6.45e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  52 FFFLDKGtqhgilvNQLQGFErwlnqTYLAKE---KIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFS 128
Cdd:COG0834    12 FSFRDED-------GKLVGFD-----VDLARAiakRLGLKVEFVPVPWDRLIPALQSGKVDLIIAGMTITPEREKQVDFS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 129 DPvIAPIEEWVVSQYSLPTFNRITQLSGRRIWVRASSSYYESLRQLNwlfrelglPPIYIETVPEYlqdGDLLEMVAAGI 208
Cdd:COG0834    80 DP-YYTSGQVLLVRKDNSGIKSLADLKGKTVGVQAGTTYEEYLKKLG--------PNAEIVEFDSY---AEALQALASGR 147

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2461897830 209 IQLTVTDSFKGRIWLGMISGLRAHKLIPLRDKGRSAWALRNNSPKLLKAVNGYLAD 264
Cdd:COG0834   148 VDAVVTDEPVAAYLLAKNPGDDLKIVGEPLSGEPYGIAVRKGDPELLEAVNKALAA 203
SLT pfam01464
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found ...
 309-424 3.45e-19

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: 82.74  E-value: 3.45e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 309 ADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLPSTGGEVGIRGARLASL----EGNVEAACRYMRLILDTYfnd 384
Cdd:pfam01464   5 AQKYGVDPSLLLAIAQQESGFNPKAVSKSGAVGLMQIMPSTAKRLGLRVNPGVDDlfdpEKNIKAGTKYLKELYKQY--- 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2461897830 385 pgldvLNRHLFALAAYNAGPNRVqaIRAKAEAAGLDPNVW 424
Cdd:pfam01464  82 -----GGDLWLALAAYNAGPGRV--RKWIKNAGAKDKKLL 114
LT-like cd00254
lytic transglycosylase(LT)-like domain; Members include the soluble and insoluble ...
 318-414 3.89e-19

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: 82.65  E-value: 3.89e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 318 MLAALAYKESGLNAGVRSERGAVGIMQLLPSTGGEVGIRGAR-LASLEGNVEAACRYMRLILDTYFNDPGLdvlnrhlfA 396
Cdd:cd00254     3 LVLAVIRVESGFNPRAVSPAGARGLMQLMPGTARDLGRRGVDdLFDPEENIRAGARYLRELLDRFGGDLEL--------A 74

                          90
                  ....*....|....*...
gi 2461897830 397 LAAYNAGPNRVQAIRAKA 414
Cdd:cd00254    75 LAAYNAGPGAVDRWGGGE 92
LT_Slt70-like cd16896
uncharacterized lytic transglycosylase subfamily with similarity to Slt70; Uncharacterized ...
 302-408 1.26e-18

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


Pssm-ID: 381617 [Multi-domain]  Cd Length: 146  Bit Score: 82.17  E-value: 1.26e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 302 RKVLEQQADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLPSTG----GEVGIRGARLASL---EGNVEAACRYM 374
Cdd:cd16896     5 REYIEKYAKEYGVDPLLVAAVIKVESNFNPNAVSSKGAIGLMQIMPETAewiaEKLGLEDFSEDDLydpETNIRLGTWYL 84

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2461897830 375 RLILDTYFNDPGLdvlnrhlfALAAYNAGPNRVQ 408
Cdd:cd16896    85 SYLLKEFDGNLVL--------ALAAYNAGPGNVD 110
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
 66-282 2.43e-18

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: 83.49  E-value: 2.43e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  66 NQLQGFErwlnqtY-LAKE---KIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVV- 140
Cdd:pfam00497  19 GKLVGFD------VdLAKAiakRLGVKVEFVPVSWDGLIPALQSGKVDLIIAGMTITPERAKQVDFSDPYYYSGQVILVr 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 141 SQYSLPTFNRITQLSGRRIWVRASSSYYESLRQLnwlfRELGLPPIYIETVPEYLQDgdllemVAAGIIQLTVTDSFKGR 220
Cdd:pfam00497  93 KKDSSKSIKSLADLKGKTVGVQKGSTAEELLKNL----KLPGAEIVEYDDDAEALQA------LANGRVDAVVADSPVAA 162

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2461897830 221 IWLGMISGLRAHKLIPLRDKGRSAWALRNNSPKLLKAVNGYLADagkrtLYSDMTLRGLLAR 282
Cdd:pfam00497 163 YLIKKNPGLNLVVVGEPLSPEPYGIAVRKGDPELLAAVNKALAE-----LKADGTLAKIYEK 219
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
 52-264 5.09e-16

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: 76.91  E-value: 5.09e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  52 FFFLDKgtqhgilVNQLQGFE----RWLnqtylAKeKIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTF 127
Cdd:cd13530    13 FEYIDK-------NGKLVGFDvdlaNAI-----AK-RLGVKVEFVDTDFDGLIPALQSGKIDVAISGMTITPERAKVVDF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 128 SDPVIApIEEWVVSQYSLPTFNRITQLSGRRIWVRASSSYYESLRQLnwlfrelgLPPIyieTVPEYLQDGDLLEMVAAG 207
Cdd:cd13530    80 SDPYYY-TGQVLVVKKDSKITKTVADLKGKKVGVQAGTTGEDYAKKN--------LPNA---EVVTYDNYPEALQALKAG 147

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2461897830 208 IIQLTVTDSFKGRIWLGMiSGLRAHKLIPLRDKGRSAWALRNNSPKLLKAVNGYLAD 264
Cdd:cd13530   148 RIDAVITDAPVAKYYVKK-NGPDLKVVGEPLTPEPYGIAVRKGNPELLDAINKALAE 203
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
 66-263 2.82e-15

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 74.67  E-value: 2.82e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830   66 NQLQGFERWLNQtYLAKEkIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQYSL 145
Cdd:smart00062  20 GELTGFDVDLAK-AIAKE-LGLKVEFVEVSFDSLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYRSGQVILVRKDSP 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  146 PTfnRITQLSGRRIWVRASSSYYESLRQLNwlfrelglPPIYIETVPeylQDGDLLEMVAAGIIQLTVTDSFKGRIWLgM 225
Cdd:smart00062  98 IK--SLEDLKGKKVAVVAGTTAEELLKKLY--------PEAKIVSYD---SNAEALAALKAGRADAAVADAPLLAALV-K 163

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 2461897830  226 ISGLRAHKLIPLR--DKGRSAWALRNNSPKLLKAVNGYLA 263
Cdd:smart00062 164 QHGLPELKIVPDPldTPEGYAIAVRKGDPELLDKINKALK 203
PBP2_Cystine_like cd13626
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ...
 66-264 2.74e-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: 71.97  E-value: 2.74e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  66 NQLQGFE-RWLNQtyLAKeKIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQYS 144
Cdd:cd13626    20 GKLTGFDvEVGRE--IAK-RLGLKVEFKATEWDGLLPGLNSGKFDVIANQVTITPEREEKYLFSDPYLVSGAQIIVKKDN 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 145 lPTFNRITQLSGRRIWVRASSSYYESLRQLNWLFRElglppIYIETVPEYLQDgdllemVAAGIIQLTVTDSFkGRIWL- 223
Cdd:cd13626    97 -TIIKSLEDLKGKVVGVSLGSNYEEVARDLANGAEV-----KAYGGANDALQD------LANGRADATLNDRL-AALYAl 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2461897830 224 -GMISGLRAHKLIPLRDKgrSAWALRNNSPKLLKAVNGYLAD 264
Cdd:cd13626   164 kNSNLPLKIVGDIVSTAK--VGFAFRKDNPELRKKVNKALAE 203
MltD-like cd16894
Membrane-bound lytic murein transglycosylase D and similar proteins; Lytic transglycosylases ...
 319-412 2.06e-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: 64.08  E-value: 2.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 319 LAALAYKESGLNAGVRSERGAVGIMQLLPSTGGEVGIRGA-----RLaSLEGNVEAACRYMRlILDTYFNDPgldvlnrh 393
Cdd:cd16894    10 LKYLALVESGFNPDAVSSAGAAGLWQFMPATAREYGLRVDswvdeRR-DPEKSTRAAARYLK-DLYKRFGDW-------- 79

                          90       100
                  ....*....|....*....|
gi 2461897830 394 LFALAAYNAGPNRVQ-AIRA 412
Cdd:cd16894    80 LLALAAYNAGEGRVRrAIKR 99
PBP2_FliY cd13712
Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ...
 52-279 5.83e-11

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: 62.02  E-value: 5.83e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  52 FFFLDKGtqhgilvNQLQGFErwlnqTYLAK---EKIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFS 128
Cdd:cd13712    13 FNFKDET-------GQLTGFE-----VDVAKalaAKLGVKPEFVTTEWSGILAGLQAGKYDVIINQVGITPERQKKFDFS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 129 DPVIAPIEEWVVSQYSLPTFNRITQLSGRRIWVRASSSYYESLRQLnwlfrelgLPPIYIETV---PEYLQDGDLLEMVA 205
Cdd:cd13712    81 QPYTYSGIQLIVRKNDTRTFKSLADLKGKKVGVGLGTNYEQWLKSN--------VPGIDVRTYpgdPEKLQDLAAGRIDA 152

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2461897830 206 AGIIQLTVTDSFKGRIWLGMISGLRAHKliplrdkgRSAWALRNNSPKLLKAVNGYLADagkrtLYSDMTLRGL 279
Cdd:cd13712   153 ALNDRLAANYLVKTSLELPPTGGAFARQ--------KSGIPFRKGNPKLKAAINKAIED-----LRADGTLAKL 213
PBP2_BsGlnH cd13689
Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ...
 33-173 6.11e-10

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: 59.17  E-value: 6.11e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  33 LEHILQKKELRALVVYE-RGFFFLDKGTqhgilvNQLQGFERWLNQtYLAKeKIKLKIIYIPVRQDKLLDYLSEGRGDLV 111
Cdd:cd13689     1 LDDIKARGVLRCGVFDDvPPFGFIDPKT------REIVGFDVDLCK-AIAK-KLGVKLELKPVNPAARIPELQNGRVDLV 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2461897830 112 AANMTVTPTRREQVTFSDPVIAPIEEWVVSQYSLptFNRITQLSGRRIWVRASSSYYESLRQ 173
Cdd:cd13689    73 AANLTYTPERAEQIDFSDPYFVTGQKLLVKKGSG--IKSLKDLAGKRVGAVKGSTSEAAIRE 132
Slt35-like cd13399
Slt35-like lytic transglycosylase; Lytic transglycosylase similar to Escherichia coli lytic ...
 312-416 1.06e-09

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


Pssm-ID: 381602 [Multi-domain]  Cd Length: 108  Bit Score: 55.78  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 312 YGLDWLMLAALAYKESGLNAG-VRSERGAVGIMQLLPSTGGEVGIRG-----ARLASLEGNVEAACRYMRLILDTYFNDP 385
Cdd:cd13399     1 YGVPPGILAAILGVESGFGPNaGGSPAGAQGIAQFMPSTWKAYGVDGngdgkADPFNPEDAIASAANYLCRHGWDLNAFL 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2461897830 386 GLDVLNrhlfALAAYNAGP-NRVQAIRAKAEA 416
Cdd:cd13399    81 GEDNFL----ALAAYNAGPgAYANAVLELAAT 108
PBP2_Cystine_like_1 cd13713
Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ...
 103-264 2.34e-08

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


Pssm-ID: 270431 [Multi-domain]  Cd Length: 218  Bit Score: 54.21  E-value: 2.34e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 103 LSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQYSlpTFNRITQLSGRRIWVRASSSYYESLRQlnwlfrelg 182
Cdd:cd13713    55 LWAGRYDIIIGSMTITEERLKVVDFSNPYYYSGAQIFVRKDS--TITSLADLKGKKVGVVTGTTYEAYARK--------- 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 183 lppiYIET--VPEYLQDGDLLEMVAAGIIQLTVTDSFKGriwLGMIS--GLRAHKLIPLRDKGRSAWALRNNSPKLLKAV 258
Cdd:cd13713   124 ----YLPGaeIKTYDSDVLALQDLALGRLDAVITDRVTG---LNAIKegGLPIKIVGKPLYYEPMAIAIRKGDPELRAAV 196


                  ....*.
gi 2461897830 259 NGYLAD 264
Cdd:cd13713   197 NKALAE 202
PBP2_HisJ_LAO_like cd01001
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and ...
 52-223 2.96e-08

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


Pssm-ID: 270222 [Multi-domain]  Cd Length: 228  Bit Score: 54.22  E-value: 2.96e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  52 FFFLDKGtqhgilvNQLQGFERwlnqtYLAK---EKIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFS 128
Cdd:cd01001    15 FNFLDAD-------GKLVGFDI-----DLANalcKRMKVKCEIVTQPWDGLIPALKAGKYDAIIASMSITDKRRQQIDFT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 129 DPVIAPIEEWVVSQYSLPTFNRITQLSGRRIWVRASSSYYESLRQLnwlfrelgLPPIYI---ETVPEYLQDgdllemVA 205
Cdd:cd01001    83 DPYYRTPSRFVARKDSPITDTTPAKLKGKRVGVQAGTTHEAYLRDR--------FPEADLveyDTPEEAYKD------LA 148

                         170
                  ....*....|....*...
gi 2461897830 206 AGIIQLTVTDSFKGRIWL 223
Cdd:cd01001   149 AGRLDAVFGDKVALSEWL 166
PBP2_MidA_like cd01004
Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 ...
 66-258 3.03e-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: 54.17  E-value: 3.03e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  66 NQLQGFERWLNQTyLAKeKIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIeEWVVSQYSL 145
Cdd:cd01004    22 GKLIGFDVDLAKA-IAK-RLGLKVEIVNVSFDGLIPALQSGRYDIIMSGITDTPERAKQVDFVDYMKDGL-GVLVAKGNP 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 146 PTFNRITQLSGRRIWVRASSSYYESLRQLNWLFRELGLPPIyieTVPEYLQDGDLLEMVAAGIIQLTVTDSfkgrIWLGM 225
Cdd:cd01004    99 KKIKSPEDLCGKTVAVQTGTTQEQLLQAANKKCKAAGKPAI---EIQTFPDQADALQALRSGRADAYLSDS----PTAAY 171

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2461897830 226 ISGLRAHKL----IPLRDKGRSAWALRNNSPKLLKAV 258
Cdd:cd01004   172 AVKQSPGKLelvgEVFGSPAPIGIAVKKDDPALADAV 208
PBP2_Cysteine cd13694
Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein ...
 33-273 3.44e-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: 53.89  E-value: 3.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  33 LEHILQKKELRALVvyergffFLDK---GTQ--HGilvnQLQGFErwlnqTYLAKEKIKL------KIIYIPVRQDKLLD 101
Cdd:cd13694     1 LEQIKQSGVIRIGV-------FGDKppfGYVdeNG----KFQGFD-----IDLAKQIAKDlfgsgvKVEFVLVEAANRVP 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 102 YLSEGRGDLVAANMTVTPTRREQVTFSDPVIapieeWVVSQYSLPTFNRIT---QLSGRRIWVRASSSyyeslrQLNWLF 178
Cdd:cd13694    65 YLTSGKVDLILANFTVTPERAEVVDFANPYM-----KVALGVVSPKDSNITsvaQLDGKTLLVNKGTT------AEKYFT 133

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 179 REL-GLPPIYIETVPE---YLQDGDllemvAAGIiqltVTDSFKGRIWLGMISGLRAhkLI-PLRDKGRSAWALRNNSPK 253
Cdd:cd13694   134 KNHpEIKLLKYDQNAEafqALKDGR-----ADAY----AHDNILVLAWAKSNPGFKV--GIkNLGDTDFIAPGVQKGNKE 202

                         250       260
                  ....*....|....*....|
gi 2461897830 254 LLKAVNGYLADAGKRTLYSD 273
Cdd:cd13694   203 LLEFINAEIKKLGKENFFKK 222
PBP2_GltS cd13620
Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 ...
 80-259 6.19e-08

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: 53.11  E-value: 6.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  80 LAKE-KIKLKIIyiPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQYSLPTFNRITQLSGRR 158
Cdd:cd13620    40 IAKElGVKLEIK--SMDFDNLLASLQSGKVDMAISGMTPTPERKKSVDFSDVYYEAKQSLLVKKADLDKYKSLDDLKGKK 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 159 IWVRASSSyyeslrQLNWLFRELGLPPIYIETvpeylQDGDLLEMVAAGIIQLTVTDSFKGRIWLGMISGLR-AHKLIPL 237
Cdd:cd13620   118 IGAQKGST------QETIAKDQLKNAKLKSLT-----KVGDLILELKSGKVDGVIMEEPVAKGYANNNSDLAiADVNLEN 186

                         170       180
                  ....*....|....*....|..
gi 2461897830 238 RDKGRSAWALRNNSPKLLKAVN 259
Cdd:cd13620   187 KPDDGSAVAIKKGSKDLLDAVN 208
PBP2_Ngo0372_TcyA cd13711
Substrate binding domain of ABC transporters involved in cystine import; the type 2 ...
 66-279 7.82e-08

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: 53.07  E-value: 7.82e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  66 NQLQGFErwlnqTYLAKE---KIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIapieewvVSQ 142
Cdd:cd13711    21 GKLTGFD-----VEVARAvakKLGVKVEFVETQWDSMIAGLDAGRFDVVANQVGITDERKKKYDFSTPYI-------YSR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 143 YSL---PTFNRIT---QLSGRRIWVRASSSYYESLRQLNwlfrelglppIYIETVPEYLQDgdlLEMVAAGIIQLTVTDS 216
Cdd:cd13711    89 AVLivrKDNSDIKsfaDLKGKKSAQSLTSNWGKIAKKYG----------AQVVGVDGFAQA---VELITQGRADATINDS 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2461897830 217 fkgriwLGMISGLRAHKLIPLR------DKGRSAWALRNNSPKLLKAVNGYLADagkrtLYSDMTLRGL 279
Cdd:cd13711   156 ------LAFLDYKKQHPDAPVKiaaetdDASESAFLVRKGNDELVAAINKALKE-----LKADGTLKKI 213
PBP2_Ala cd13628
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ...
 67-218 9.03e-08

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: 52.86  E-value: 9.03e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  67 QLQGFERWLNQTYLAKEKIKLKIIYIPVRQdkLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPviapieeWVVSQYSLP 146
Cdd:cd13628    22 KIVGFDIELAKTIAKKLGLKLQIQEYDFNG--LIPALASGQADLALAGITPTPERKKVVDFSEP-------YYEASDTIV 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2461897830 147 TFN--RITQ---LSGRRIWVRASSSYYESLRQLnwLFRELGLPPIYIETVPEYLQDGDLLEMVAAgIIQLTVTDSFK 218
Cdd:cd13628    93 S*KdrKIKQlqdLNGKSLGVQLGTIQEQLIKEL--SQPYPGLKTKLYNRVNELVQALKSGRVDAA-IVEDIVAETFA 166
PRK11619 PRK11619
lytic murein transglycosylase; Provisional
 321-460 1.67e-07

lytic murein transglycosylase; Provisional


Pssm-ID: 183236 [Multi-domain]  Cd Length: 644  Bit Score: 53.91  E-value: 1.67e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 321 ALAYKESGLNAGVRSERGAVGIMQLLPSTG----GEVGIRG----ARLASLEGNVEAACRYMRLILDTYFNdpgldvlNR 392
Cdd:PRK11619  499 AIARQESAWNPKARSPVGASGLMQIMPGTAthtvKMFSIPGysssSQLLDPETNINIGTSYLEYVYQQFGN-------NR 571

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2461897830 393 hLFALAAYNAGPNRVQaiRAKAEAAG-LDPnVWFgnVEQLVANEVGqgpiNYVSTIYKYYVAYRFSLPQ 460
Cdd:PRK11619  572 -ILASAAYNAGPGRVR--TWLGNSAGrIDA-VAF--VESIPFSETR----GYVKNVLAYDAYYRYFMGQ 630
LT_MltC_MltE cd16893
membrane-bound lytic murein transglycosylases MltC and MltE, and similar proteins; MltC and ...
 306-407 1.76e-07

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: 50.64  E-value: 1.76e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 306 EQQADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLPSTGGE-----VGIRGARLAS--L---EGNVEAACRYMR 375
Cdd:cd16893     4 EKYAKKYGVDPALILAIIETESSFNPYAVSHSPAYGLMQIVPSTAGRdvyrlLGGKGGLPSKsyLfdpENNIDIGTAYLH 83

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2461897830 376 LILDTYF---NDPgldvLNRHLFALAAYNAGPNRV 407
Cdd:cd16893    84 ILQNRYLkgiKNP----KSREYCAIAAYNGGAGNV 114
PBP2_GltI_DEBP cd13688
Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic ...
 86-271 6.43e-07

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: 50.33  E-value: 6.43e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  86 KLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQYSlpTFNRITQLSGRRIWVRASS 165
Cdd:cd13688    53 DLKVRYVPVTPQDRIPALTSGTIDLECGATTNTLERRKLVDFSIPIFVAGTRLLVRKDS--GLNSLEDLAGKTVGVTAGT 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 166 SYYESLRQLNwlfRELGLppiYIETVPeYLQDGDLLEMVAAGIIQLTVTDsfkgRIWLgmiSGLRAHK------LIPLRD 239
Cdd:cd13688   131 TTEDALRTVN---PLAGL---QASVVP-VKDHAEGFAALETGKADAFAGD----DILL---AGLAARSknpddlALIPRP 196

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2461897830 240 KGRSAWA--LRNNSPKLLKAVNGYLADAGKRTLY 271
Cdd:cd13688   197 LSYEPYGlmLRKDDPDFRLLVDRALAQLYQSGEI 230
PBP2_BvgS_HisK_like cd01007
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
 54-207 7.82e-07

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: 49.84  E-value: 7.82e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  54 FLDKGTQH-GILVNQLQgferwlnqtyLAKEKIKLKIIYIPVR-QDKLLDYLSEGRGDLVAAnMTVTPTRREQVTFSDP- 130
Cdd:cd01007    17 FIDEGGEPqGIAADYLK----------LIAKKLGLKFEYVPGDsWSELLEALKAGEIDLLSS-VSKTPEREKYLLFTKPy 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2461897830 131 VIAPIEewVVSQYSLPTFNRITQLSGRRIWVRASSSYYESLRQLnwlfrelgLPPIYIETVPEYLqdgDLLEMVAAG 207
Cdd:cd01007    86 LSSPLV--IVTRKDAPFINSLSDLAGKRVAVVKGYALEELLRER--------YPNINLVEVDSTE---EALEAVASG 149
PBP2_Cys_DEBP_like cd01000
Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ...
 66-175 1.11e-06

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: 49.61  E-value: 1.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  66 NQLQGFERWLNQtYLAKEKIKL--KIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIApIEEWVVSQY 143
Cdd:cd01000    28 GKIQGFDVDVAK-ALAKDLLGDpvKVKFVPVTSANRIPALQSGKVDLIIATMTITPERAKEVDFSVPYYA-DGQGLLVRK 105

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2461897830 144 SLPtFNRITQLSGRRIWVRASSSYYESLRQLN 175
Cdd:cd01000   106 DSK-IKSLEDLKGKTILVLQGSTAEAALRKAA 136
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
 87-263 6.13e-06

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: 47.19  E-value: 6.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  87 LKIIYIPVRQDKLLDYLSEGRGDLVAaNMTVTPTRREQVTFSDPVIapieewvVSQYSL------PTFNRITQLSGRRIW 160
Cdd:cd13704    41 LKVEIRLGPWSEVLQALENGEIDVLI-GMAYSEERAKLFDFSDPYL-------EVSVSIfvrkgsSIINSLEDLKGKKVA 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 161 VRASSSYYESLRQLNWLFRelglpPIYIETVPEYLQdgdlleMVAAGIIQLTVTDSFKGRIWlgmISGLRAHKLIPLRDK 240
Cdd:cd13704   113 VQRGDIMHEYLKERGLGIN-----LVLVDSPEEALR------LLASGKVDAAVVDRLVGLYL---IKELGLTNVKIVGPP 178

                         170       180
                  ....*....|....*....|....*.
gi 2461897830 241 ---GRSAWALRNNSPKLLKAVNGYLA 263
Cdd:cd13704   179 llpLKYCFAVRKGNPELLAKLNEGLA 204
PBP2_GluB cd13690
Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein ...
 88-265 8.84e-06

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: 46.88  E-value: 8.84e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  88 KIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPViapieeWVVSQYSL-PTFNRITQ----LSGRRIWVR 162
Cdd:cd13690    52 KVEFREVTSAEREALLQNGTVDLVVATYSITPERRKQVDFAGPY------YTAGQRLLvRAGSKIITspedLNGKTVCTA 125

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 163 ASSSYYESLRQLNwlfrelglPPIYIETVPEYLqdgDLLEMVAAGIIQLTVTDSFkgrIWLGMISGLRAH-KLIPLR-DK 240
Cdd:cd13690   126 AGSTSADNLKKNA--------PGATIVTRDNYS---DCLVALQQGRVDAVSTDDA---ILAGFAAQDPPGlKLVGEPfTD 191

                         170       180
                  ....*....|....*....|....*
gi 2461897830 241 GRSAWALRNNSPKLLKAVNGYLADA 265
Cdd:cd13690   192 EPYGIGLPKGDDELVAFVNGALEDM 216
PBP2_Ehub_like cd01002
Substrate binding domain of ectoine/hydroxyectoine specific ABC transport system; the type 2 ...
 99-207 1.55e-05

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


Pssm-ID: 270223 [Multi-domain]  Cd Length: 242  Bit Score: 46.12  E-value: 1.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  99 LLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQ---YSLPTFNRITQLSGRRIWVRASSSYYESLRQln 175
Cdd:cd01002    61 LIPGLQAGRFDVIAAGMFITPERCEQVAFSEPTYQVGEAFLVPKgnpKGLHSYADVAKNPDARLAVMAGAVEVDYAKA-- 138

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2461897830 176 wlfreLGLPPIYIETVPEyLQDGdlLEMVAAG 207
Cdd:cd01002   139 -----SGVPAEQIVIVPD-QQSG--LAAVRAG 162
PBP2_AA_binding_like_1 cd13625
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
 66-267 3.95e-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: 270343 [Multi-domain]  Cd Length: 230  Bit Score: 45.06  E-value: 3.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  66 NQLQGFERWLnQTYLAKeKIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPvIAPIEEWVVSQYSL 145
Cdd:cd13625    24 GKIVGFDRDL-LDEMAK-KLGVKVEQQDLPWSGILPGLLAGKFDMVATSVTITKERAKRFAFTLP-IAEATAALLKRAGD 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 146 PTFNRITQLSGRRIWVRASSSYYESLRQLNWLFRELGLP-PIYIETVPEYlqdgdllEMVAAGIIQLTVTDSFKGRIWLG 224
Cdd:cd13625   101 DSIKTIEDLAGKVVGVQAGSAQLAQLKEFNETLKKKGGNgFGEIKEYVSY-------PQAYADLANGRVDAVANSLTNLA 173

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2461897830 225 MISGLRAHKLIPLRDKGRS---AWALRNNSPKLLKAVNGYLADAGK 267
Cdd:cd13625   174 YLIKQRPGVFALVGPVGGPtyfAWVIRKGDAELRKAINDALLALKK 219
PBP2_BvgS_D2 cd13707
The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
 87-207 4.11e-05

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: 44.90  E-value: 4.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  87 LKIIYIPVRQDK-LLDYLSEGRGDLVAAnMTVTPTRREQVTFSDP-VIAPieeWV-VSQYSLPTFNRITQLSGRRIWVRA 163
Cdd:cd13707    41 LRFEVVRASSPAeMIEALRSGEADMIAA-LTPSPEREDFLLFTRPyLTSP---FVlVTRKDAAAPSSLEDLAGKRVAIPA 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2461897830 164 SSSYYESLRQLNwlfrelglPPIYIETVPEYLQdgdLLEMVAAG 207
Cdd:cd13707   117 GSALEDLLRRRY--------PQIELVEVDNTAE---ALALVASG 149
PRK11260 PRK11260
cystine ABC transporter substrate-binding protein;
67-279 1.09e-04

cystine ABC transporter substrate-binding protein;


Pssm-ID: 183061 [Multi-domain]  Cd Length: 266  Bit Score: 43.94  E-value: 1.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  67 QLQGFERWLNQTyLAKEkIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDP-VIAPIEEwVVSQYSL 145
Cdd:PRK11260   62 KLTGFEVEFAEA-LAKH-LGVKASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPyTVSGIQA-LVKKGNE 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 146 PTFNRITQLSGRRIWVRASSSYYESLRQlnwlfrelGLPPIYIETV---PEYLQDgdllemvaagiiqLTVtdsfkGRIW 222
Cdd:PRK11260  139 GTIKTAADLKGKKVGVGLGTNYEQWLRQ--------NVQGVDVRTYdddPTKYQD-------------LRV-----GRID 192

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2461897830 223 LGMISGLRAHKLI-----------PLRDKGRSAWALRNNSPKLLKAVNGYLADagkrtLYSDMTLRGL 279
Cdd:PRK11260  193 AILVDRLAALDLVkktndtlavagEAFSRQESGVALRKGNPDLLKAVNQAIAE-----MQKDGTLKAL 255
PBP2_AA_binding_like_2 cd13627
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
 79-175 1.28e-04

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: 43.54  E-value: 1.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  79 YLAK---EKIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDP-VIAPIEEWVVSQYSLPTFNRITQL 154
Cdd:cd13627    41 QIAKklaEKLDMKLVIKKIEWNGLIPALNSGDIDLIIAGMSKTPEREKTIDFSDPyYISNIVMVVKKDSAYANATNLSDF 120

                          90       100
                  ....*....|....*....|.
gi 2461897830 155 SGRRIWVRASSSYYESLRQLN 175
Cdd:cd13627   121 KGATITGQLGTMYDDVIDQIP 141
PBP2_BvgS_like_1 cd13708
Putative sensor domain similar to BvgS; the type 2 periplasmic binding protein domain; BvgS is ...
 80-207 1.39e-04

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


Pssm-ID: 270426 [Multi-domain]  Cd Length: 220  Bit Score: 43.27  E-value: 1.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  80 LAKEKIKLKIIYIPVRQ-DKLLDYLSEGRGDLVAANMTvTPTRREQVTFSDPVI-APIEewVVSQYSLPTFNRITQLSGR 157
Cdd:cd13708    34 LIAERLGIPIELVPTKSwSESLEAAKEGKCDILSLLNQ-TPEREEYLNFTKPYLsDPNV--LVTREDHPFIADLSDLGDK 110

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2461897830 158 RIWVRASSSYYESLRQLNwlfrelglPPIYIETVPEyLQDGdlLEMVAAG 207
Cdd:cd13708   111 TIGVVKGYAIEEILRQKY--------PNLNIVEVDS-EEEG--LKKVSNG 149
PBP2_Arg_3 cd13622
Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding ...
 91-216 2.05e-04

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


Pssm-ID: 270340 [Multi-domain]  Cd Length: 222  Bit Score: 42.67  E-value: 2.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  91 YIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQySLPTFNRITQLSGRRIWVRASSSYYES 170
Cdd:cd13622    45 YKPMRFDDLLAALNNGKVDVAISSISITPERSKNFIFSLPYLLSYSQFLTNK-DNNISSFLEDLKGKRIGILKGTIYKDY 123

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2461897830 171 LRQLNwlfrelglppIYIETVPEYLQDGDLLEMVAAGIIQLTVTDS 216
Cdd:cd13622   124 LLQMF----------VINPKIIEYDRLVDLLEALNNNEIDAILLDN 159
PBP2_Peb1a_like cd13691
Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 ...
 51-130 2.88e-04

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: 42.44  E-value: 2.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  51 GFFFLDKGTqhgilvNQLQGFERWLNQTyLAKEKIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDP 130
Cdd:cd13691    20 GFGYQDPET------GKYEGMEVDLARK-LAKKGDGVKVEFTPVTAKTRGPLLDNGDVDAVIATFTITPERKKSYDFSTP 92
PBP2_PheC cd01069
Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein ...
 32-132 3.42e-04

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


Pssm-ID: 270231 [Multi-domain]  Cd Length: 232  Bit Score: 41.94  E-value: 3.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  32 DLEHILQKKELRALVV--YeRGFFFLDKGTQHgilvnqlQGFERWLNQTyLAKEkIKLKIIYIPVRQDKLLDYLSEGRGD 109
Cdd:cd01069     2 RLDKILERGVLRVGTTgdY-KPFTYRDNQGQY-------EGYDIDMAEA-LAKS-LGVKVEFVPTSWPTLMDDLAADKFD 71

                          90       100
                  ....*....|....*....|...
gi 2461897830 110 LVAANMTVTPTRREQVTFSDPVI 132
Cdd:cd01069    72 IAMGGISITLERQRQAFFSAPYL 94
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 319-474 6.03e-04

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 42.03  E-value: 6.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 319 LAALAYKESGLNAGVRSERGAVGIMQLLPSTGGEVGIRGARLASLEGNVEAAcrymrlildtyfNDPGLDVLNR------ 392
Cdd:PRK10783  121 LVLLPIVESAFDPHATSGANAAGIWQIIPSTGRNYGLKQTRWYDARRDVVAS------------TTAALDMMQRlnkmfd 188

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 393 --HLFALAAYNAGPNRV-QAIRAKaEAAGLDPNVWFGNVEQLVANEVGQgpINYVSTIYKYYVAYRFSLPQL-EGKAAAI 468
Cdd:PRK10783  189 gdWLLTVAAYNSGEGRVmKAIKAN-KAKGKPTDFWSLSLPRETKIYVPK--MLALSDILKNSKRYGVRLPTTdESRALAR 265


                  ....*.
gi 2461897830 469 EAVAQP 474
Cdd:PRK10783  266 VDLGQQ 271
PBP2_mlr5654_like cd13702
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
 67-130 7.32e-04

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


Pssm-ID: 270420 [Multi-domain]  Cd Length: 223  Bit Score: 41.15  E-value: 7.32e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2461897830  67 QLQGFERWLNQTYLAKEKIKLKIiyipVRQ--DKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDP 130
Cdd:cd13702    23 KLGGFDVDIANALCAEMKAKCEI----VAQdwDGIIPALQAKKFDAIIASMSITPERKKQVDFTDP 84
PBP2_GluR0 cd00997
Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ...
 94-200 7.37e-04

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


Pssm-ID: 270218 [Multi-domain]  Cd Length: 218  Bit Score: 40.78  E-value: 7.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  94 VRQDK---LLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQysLPTFNRITQLSGRRIWVRASSSYYES 170
Cdd:cd00997    45 VRVDSvsaLLAAVAEGEADIAIAAISITAEREAEFDFSQPIFESGLQILVPN--TPLINSVNDLYGKRVATVAGSTAADY 122

                          90       100       110
                  ....*....|....*....|....*....|
gi 2461897830 171 LRQLNWLFRELGlppiYIETVPEYLQDGDL 200
Cdd:cd00997   123 LRRHDIDVVEVP----NLEAAYTALQDKDA 148
emtA PRK15470
membrane-bound lytic murein transglycosylase EmtA;
294-428 8.43e-04

membrane-bound lytic murein transglycosylase EmtA;


Pssm-ID: 185367 [Multi-domain]  Cd Length: 203  Bit Score: 40.72  E-value: 8.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 294 PLGRLATIRKVLEQQADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLPSTGGE-----VGIRG----ARLASLE 364
Cdd:PRK15470   32 PVQRAMQWMPISQKAGAAWGVDPQLITAIIAIESGGNPNAVSKSNAIGLMQLKASTSGRdvyrrMGWSGepttSELKNPE 111

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2461897830 365 GNVEAACRYMRlILDT----YFNDPglDVLNRHLFALAAYNAG-------PNRVQAIrakAEAAGLDPNVWFGNV 428
Cdd:PRK15470  112 RNISMGAAYLN-ILETgplaGIEDP--KVLQYALVVSYANGAGallrtfsSDRKKAI---SKINDLDADEFLEHV 180
PBP2_polar_AA cd13693
Substrate binding domain of polar amino-acid uptake ABC transporter; the type 2 periplasmic ...
 102-265 9.82e-04

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: 40.76  E-value: 9.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 102 YLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQYSLpTFNRITQLSGRRIWVRASSSYYESLRQlnwlfrEL 181
Cdd:cd13693    62 FLQQGKVDLLIATMGDTPERRKVVDFVEPYYYRSGGALLAAKDS-GINDWEDLKGKPVCGSQGSYYNKPLIE------KY 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 182 GLPPIYIETVPEY---LQDGDLLEMVA-AGIIQLTVTDSfkgRIWLGMISGLRAHKLIPlrdkgrSAWALRNNSPKLLKA 257
Cdd:cd13693   135 GAQLVAFKGTPEAllaLRDGRCVAFVYdDSTLQLLLQED---GEWKDYEIPLPTIEPSP------WVIAVRKGETAFQNA 205


                  ....*...
gi 2461897830 258 VNGYLADA 265
Cdd:cd13693   206 LDEIIKDW 213
PHA00368 PHA00368
internal virion protein D
 304-414 1.15e-03

internal virion protein D


Pssm-ID: 222785 [Multi-domain]  Cd Length: 1315  Bit Score: 41.69  E-value: 1.15e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  304 VLEQQADKYGLDWLMLAALAYKESGLNAGVRSERGAVGIMQLLPSTGGEVGIRGA---RLASlEGNVEAACRYMRLILDT 380
Cdd:PHA00368    14 LFQKAADAHGVSYDLLRKVGWDESRFNPTAKSPTGPKGLMQFTKATAKALGLIVDdddRLDP-ELAIDAGARYLADLVGK 92

                           90       100       110
                   ....*....|....*....|....*....|....
gi 2461897830  381 YFNDPgldvlnrhLFALAAYNAGPNRVQAIRAKA 414
Cdd:PHA00368    93 YDGDE--------LKAALAYNQGEGRLGAPQLEA 118
PBP2_AatB_like cd00996
Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong ...
 80-171 1.24e-03

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: 40.25  E-value: 1.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  80 LAKE---KIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDP------VIapieewVVSQYSlpTFNR 150
Cdd:cd00996    33 LAKEvakRLGVEVEFQPIDWDMKETELNSGNIDLIWNGLTITDERKKKVAFSKPylenrqII------VVKKDS--PINS 104

                          90       100
                  ....*....|....*....|.
gi 2461897830 151 ITQLSGRRIWVRASSSYYESL 171
Cdd:cd00996   105 KADLKGKTVGVQSGSSGEDAL 125
PBP2_GlnH cd00994
Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; ...
 80-130 1.38e-03

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


Pssm-ID: 270216 [Multi-domain]  Cd Length: 218  Bit Score: 39.95  E-value: 1.38e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2461897830  80 LAKEkIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDP 130
Cdd:cd00994    32 IAKE-AGFKYELQPMDFKGIIPALQTGRIDIAIAGITITEERKKVVDFSDP 81
PBP2_ArtJ cd00999
The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold ...
 66-130 1.57e-03

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: 40.00  E-value: 1.57e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2461897830  66 NQLQGFERWLNQTYLAKEKIKLKIIYIPVrqDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDP 130
Cdd:cd00999    24 GELVGFDIDLAEAISEKLGKKLEWRDMAF--DALIPNLLTGKIDAIAAGMSATPERAKRVAFSPP 86
PBP2_SMa0082_like cd01072
The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic ...
 66-165 1.66e-03

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: 39.94  E-value: 1.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  66 NQLQGFERWLNQtYLAKE-KIKLKIIyiPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPViAPIEEWVVSQYS 144
Cdd:cd01072    33 MQPQGYDVDVAK-LLAKDlGVKLELV--PVTGANRIPYLQTGKVDMLIASLGITPERAKVVDFSQPY-AAFYLGVYGPKD 108

                          90       100
                  ....*....|....*....|..
gi 2461897830 145 LPTFNrITQLSGRRIWV-RASS 165
Cdd:cd01072   109 AKVKS-PADLKGKTVGVtRGST 129
PBP2_Arg_Lys_His cd13624
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ...
 103-130 2.19e-03

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: 39.40  E-value: 2.19e-03
                          10        20
                  ....*....|....*....|....*...
gi 2461897830 103 LSEGRGDLVAANMTVTPTRREQVTFSDP 130
Cdd:cd13624    55 LQSGKIDIIISGMTITEERKKSVDFSDP 82
Lyz-like cd00442
lysozyme-like domains; This family contains several members, including soluble lytic ...
 318-373 2.82e-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: 2.82e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2461897830 318 MLAALAYKESGLNAGVRSERG--AVGIMQLLPSTGGEVG-IRGARLASLEGNVEAACRY 373
Cdd:cd00442     1 VLAAIIGQESGGNKPANAGSGsgAAGLFQFMPGTWKAYGkNSSSDLNDPEASIEAAAKY 59
PBP2_Dsm1740 cd13629
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ...
 88-274 4.56e-03

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: 38.71  E-value: 4.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  88 KIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQYSLPTFNRITQL--SGRRIWVRASS 165
Cdd:cd13629    40 KVEFVNTAWDGLIPALQTGKFDLIISGMTITPERNLKVNFSNPYLVSGQTLLVNKKSAAGIKSLEDLnkPGVTIAVKLGT 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830 166 SYYESLRQlnwLFRElglppiyiETVPEYLQDGDLLEMVAAGIIQLTVTDSfkgrIWLGMISGLRAHKLIPLRD---KGR 242
Cdd:cd13629   120 TGDQAARK---LFPK--------ATILVFDDEAAAVLEVVNGKADAFIYDQ----PTPARFAKKNDPTLVALLEpftYEP 184

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2461897830 243 SAWALRNNSPKLLKAVNGYLADAGKRTLYSDM 274
Cdd:cd13629   185 LGFAIRKGDPDLLNWLNNFLKQIKGDGTLDEL 216
PRK11917 PRK11917
bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
 31-130 5.80e-03

bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed


Pssm-ID: 183381 [Multi-domain]  Cd Length: 259  Bit Score: 38.37  E-value: 5.80e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  31 GDLEHILQKKELRALVVYE-RGFFFLDKGTqhgilvNQLQGFE----RWLNQTYLAKEKiKLKIIYIPVR-QDKLLDyls 104
Cdd:PRK11917   29 GKLESIKSKGQLIVGVKNDvPHYALLDQAT------GEIKGFEidvaKLLAKSILGDDK-KIKLVAVNAKtRGPLLD--- 98

                          90       100
                  ....*....|....*....|....*.
gi 2461897830 105 EGRGDLVAANMTVTPTRREQVTFSDP 130
Cdd:PRK11917   99 NGSVDAVIATFTITPERKRIYNFSEP 124
PBP2_YxeM cd13709
Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein ...
 66-175 7.62e-03

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: 38.10  E-value: 7.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2461897830  66 NQLQGFE-RWLNQtyLAKeKIKLKIIYIPVRQDKLLDYLSEGRGDLVAANMTVTPTRREQVTFSDPVIAPIEEWVVSQYS 144
Cdd:cd13709    20 GKLKGFEvDVWNA--IGK-RTGYKVEFVTADFSGLFGMLDSGKVDTIANQITITPERQEKYDFSEPYVYDGAQIVVKKDN 96

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2461897830 145 lPTFNRITQLSGRRIWVRASSSYYESLRQLN 175
Cdd:cd13709    97 -NSIKSLEDLKGKTVAVNLGSNYEKILKAVD 126
 
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