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Conserved domains on  [gi|15598061|ref|NP_251555|]
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glycosylase [Pseudomonas aeruginosa PAO1]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
 34-458 9.48e-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: 346.66  E-value: 9.48e-116
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  34 QPETRDLASIRRAGVLKVLVNQSRNSSGEVKGEPIGVEYRRLRAFEQYLNsrspsarnLTLKL-IPKPKDQLLAALQRGE 112
Cdd:COG4623   9 SSEPGDLEQIKERGVLRVLTRNSPTTYFIYRGGPMGFEYELAKAFADYLG--------VKLEIiVPDNLDELLPALNAGE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 113 GDLVAPGELLPAHDGLQVSPSAPVRaDVPLVLVARKGNRRYTRLEQLSGRTIPLPAGSAAEGAIELVNQRLAqrrmaPIR 192
Cdd:COG4623  81 GDIAAAGLTITPERKKQVRFSPPYY-SVSQVLVYRKGSPRPKSLEDLAGKTVHVRAGSSYAERLKQLNQEGP-----PLK 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 193 IEkLDASLAVEDVMEMVQAGILGFTVVEQPIAERWAKVLPKLRVDRHLVLDNRadMAWYVRRDASTLRATIDRFLADYRA 272
Cdd:COG4623 155 WE-EDEDLETEDLLEMVAAGEIDYTVADSNIAALNQRYYPNLRVAFDLSEPQP--IAWAVRKNDPSLLAALNEFFAKIKK 231

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 273 PADQDVAFQRVYRRAYKVRNPLGAADRKRLEAVRPLLQRYARQSSMDWLALAAVAYKESHLNPKARGSGGASGLMQITPA 352
Cdd:COG4623 232 GGTLARLYERYFGHVKRDTRAFLRRIEGRLPPYDPLFEKYAEEYGLDWRLLAALAYQESHWNPRARSPTGARGLMQLMPA 311

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 353 AARSVGVGNVHDKDSNVLAASRYLTKIRKQFfsSKHLDERERLAFTLAAYNMGPERVQNLRTQARRRGLDPNRWFFQVER 432
Cdd:COG4623 312 TAKELGVDDRLDPEQSIRAGAKYLRWLYDRF--PEAIDEPDRWWFALAAYNAGPGHVQDARRLAKKQGLDPDRWFDVEKS 389

                       410       420       430
                ....*....|....*....|....*....|.
gi 15598061 433 -----VAAEEIGMGVVSYVSSVNKYYLAYER 458
Cdd:COG4623 390 qpkyyDTGYARGRETVNYVPNIRAYYDIYKR 420
 
Name Accession Description Interval E-value
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
 34-458 9.48e-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: 346.66  E-value: 9.48e-116
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  34 QPETRDLASIRRAGVLKVLVNQSRNSSGEVKGEPIGVEYRRLRAFEQYLNsrspsarnLTLKL-IPKPKDQLLAALQRGE 112
Cdd:COG4623   9 SSEPGDLEQIKERGVLRVLTRNSPTTYFIYRGGPMGFEYELAKAFADYLG--------VKLEIiVPDNLDELLPALNAGE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 113 GDLVAPGELLPAHDGLQVSPSAPVRaDVPLVLVARKGNRRYTRLEQLSGRTIPLPAGSAAEGAIELVNQRLAqrrmaPIR 192
Cdd:COG4623  81 GDIAAAGLTITPERKKQVRFSPPYY-SVSQVLVYRKGSPRPKSLEDLAGKTVHVRAGSSYAERLKQLNQEGP-----PLK 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 193 IEkLDASLAVEDVMEMVQAGILGFTVVEQPIAERWAKVLPKLRVDRHLVLDNRadMAWYVRRDASTLRATIDRFLADYRA 272
Cdd:COG4623 155 WE-EDEDLETEDLLEMVAAGEIDYTVADSNIAALNQRYYPNLRVAFDLSEPQP--IAWAVRKNDPSLLAALNEFFAKIKK 231

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 273 PADQDVAFQRVYRRAYKVRNPLGAADRKRLEAVRPLLQRYARQSSMDWLALAAVAYKESHLNPKARGSGGASGLMQITPA 352
Cdd:COG4623 232 GGTLARLYERYFGHVKRDTRAFLRRIEGRLPPYDPLFEKYAEEYGLDWRLLAALAYQESHWNPRARSPTGARGLMQLMPA 311

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 353 AARSVGVGNVHDKDSNVLAASRYLTKIRKQFfsSKHLDERERLAFTLAAYNMGPERVQNLRTQARRRGLDPNRWFFQVER 432
Cdd:COG4623 312 TAKELGVDDRLDPEQSIRAGAKYLRWLYDRF--PEAIDEPDRWWFALAAYNAGPGHVQDARRLAKKQGLDPDRWFDVEKS 389

                       410       420       430
                ....*....|....*....|....*....|.
gi 15598061 433 -----VAAEEIGMGVVSYVSSVNKYYLAYER 458
Cdd:COG4623 390 qpkyyDTGYARGRETVNYVPNIRAYYDIYKR 420
MLTF-like cd13403
membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins; This subfamily ...
 310-458 8.97e-59

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: 190.82  E-value: 8.97e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 310 QRYARQSSMDWLALAAVAYKESHLNPKARGSGGASGLMQITPAAARSVGVGNVHDKDSNVLAASRYLTKIRKQFfsSKHL 389
Cdd:cd13403   2 KKYAEKYGFDWRLLAAQAYQESRFNPNARSPAGARGLMQLMPSTARELGVNDRLDPEQNIHAGAKYLRYLRDRF--PPDI 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 390 DERERLAFTLAAYNMGPERVQNLRTQARRRGLDPNRWFFQVERV-------------AAEEIGMGVVSYVSSVNKYYLAY 456
Cdd:cd13403  80 DEPDRLKFALAAYNAGPGHVRDARRLAKKYGLNPNVWFDNVEVLpllkspyydpvvkYGYARGRETVNYVRNIRKYYDAY 159


                ..
gi 15598061 457 ER 458
Cdd:cd13403 160 KQ 161
PRK10859 PRK10859
membrane-bound lytic murein transglycosylase MltF;
19-426 5.73e-49

membrane-bound lytic murein transglycosylase MltF;


Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 174.68  E-value: 5.73e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061   19 AAARITGQPdnWHREQPETrdLASIRRAGVLKVLVNQSRNSSGEVKGEPIGVEYRRLRAFEQYLNsrspsarnLTLKLIP 98
Cdd:PRK10859  19 AAALWPSIP--WFSKEENQ--LEQIQERGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADYLG--------VKLEIKV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061   99 KPK-DQLLAALQRGEGDLVAPGeLLPAHDGLQVSPSAPVRADVPLVLVARKGNRRYTRLEQLSGRTIPLPAGSAAEgaie 177
Cdd:PRK10859  87 RDNiSQLFDALDKGKADLAAAG-LTYTPERLKQFRFGPPYYSVSQQLVYRKGQPRPRSLGDLKGGTLTVAAGSSHV---- 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  178 lvnQRLAQ-RRMAPIRIEKLDASLAVEDVMEMVQAGILGFTVVEQPIAERWAKVLPKLRVDrhLVLDNRADMAWYVRRDA 256
Cdd:PRK10859 162 ---ETLQElKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPELAVA--FDLTDEQPVAWALPPSG 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  257 S-TLRATIDRFLADyrapADQDVAFQRVYRRAY---KVRNPLGA-----ADRKRLEAVRPLLQRYARQssMDWLALAAVA 327
Cdd:PRK10859 237 DdSLYAALLDFFNQ----IKEDGTLARLEEKYFghvDRFDYVDTrtflrAIDNRLPKYQPLFEKYAGE--LDWRLLAAIA 310

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  328 YKESHLNPKARGSGGASGLMQITPAAARSVGVGNVHDKDSNVLAASRYLTKIRKQFFSSkhLDERERLAFTLAAYNMGPE 407
Cdd:PRK10859 311 YQESHWNPQATSPTGVRGLMMLTRNTAQSMGVTDRLDPEQSIRGGARYLQDLMERLPES--IPEPERIWFALAAYNIGYG 388

                        410
                 ....*....|....*....
gi 15598061  408 RVQNLRTQARRRGLDPNRW 426
Cdd:PRK10859 389 HMLDARRLTKKQGGNPDSW 407
SLT pfam01464
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found ...
 310-420 8.81e-15

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: 70.41  E-value: 8.81e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061   310 QRYARQSSMDWLALAAVAYKESHLNPKARGSGGASGLMQITPAAARSVGVGNVHDKDS------NVLAASRYLTKIRKQF 383
Cdd:pfam01464   2 IKAAQKYGVDPSLLLAIAQQESGFNPKAVSKSGAVGLMQIMPSTAKRLGLRVNPGVDDlfdpekNIKAGTKYLKELYKQY 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 15598061   384 fsskhldeRERLAFTLAAYNMGPERVQNLRTQARRRG 420
Cdd:pfam01464  82 --------GGDLWLALAAYNAGPGRVRKWIKNAGAKD 110
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
 64-286 8.17e-11

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 61.58  E-value: 8.17e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061     64 KGEPIGVEYRRLRAFEQYLNsrspsarnLTLKLIPKPKDQLLAALQRGEGDLVAPGELLPAHDGLQVSPSAPVrADVPLV 143
Cdd:smart00062  19 DGELTGFDVDLAKAIAKELG--------LKVEFVEVSFDSLLTALKSGKIDVVAAGMTITPERAKQVDFSDPY-YRSGQV 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061    144 LVARKGNrRYTRLEQLSGRTIPLPAGSAAEgaielvnqRLAQRRMAPIRIEKLDASlavEDVMEMVQAGILGFTVVEQPI 223
Cdd:smart00062  90 ILVRKDS-PIKSLEDLKGKKVAVVAGTTAE--------ELLKKLYPEAKIVSYDSN---AEALAALKAGRADAAVADAPL 157

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15598061    224 AERWAKVLPKLRVD-RHLVLDNRADMAWYVRRDASTLRATIDRFLADYRApadqDVAFQRVYRR 286
Cdd:smart00062 158 LAALVKQHGLPELKiVPDPLDTPEGYAIAVRKGDPELLDKINKALKELKA----DGTLKKISEK 217
 
Name Accession Description Interval E-value
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
 34-458 9.48e-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: 346.66  E-value: 9.48e-116
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  34 QPETRDLASIRRAGVLKVLVNQSRNSSGEVKGEPIGVEYRRLRAFEQYLNsrspsarnLTLKL-IPKPKDQLLAALQRGE 112
Cdd:COG4623   9 SSEPGDLEQIKERGVLRVLTRNSPTTYFIYRGGPMGFEYELAKAFADYLG--------VKLEIiVPDNLDELLPALNAGE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 113 GDLVAPGELLPAHDGLQVSPSAPVRaDVPLVLVARKGNRRYTRLEQLSGRTIPLPAGSAAEGAIELVNQRLAqrrmaPIR 192
Cdd:COG4623  81 GDIAAAGLTITPERKKQVRFSPPYY-SVSQVLVYRKGSPRPKSLEDLAGKTVHVRAGSSYAERLKQLNQEGP-----PLK 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 193 IEkLDASLAVEDVMEMVQAGILGFTVVEQPIAERWAKVLPKLRVDRHLVLDNRadMAWYVRRDASTLRATIDRFLADYRA 272
Cdd:COG4623 155 WE-EDEDLETEDLLEMVAAGEIDYTVADSNIAALNQRYYPNLRVAFDLSEPQP--IAWAVRKNDPSLLAALNEFFAKIKK 231

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 273 PADQDVAFQRVYRRAYKVRNPLGAADRKRLEAVRPLLQRYARQSSMDWLALAAVAYKESHLNPKARGSGGASGLMQITPA 352
Cdd:COG4623 232 GGTLARLYERYFGHVKRDTRAFLRRIEGRLPPYDPLFEKYAEEYGLDWRLLAALAYQESHWNPRARSPTGARGLMQLMPA 311

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 353 AARSVGVGNVHDKDSNVLAASRYLTKIRKQFfsSKHLDERERLAFTLAAYNMGPERVQNLRTQARRRGLDPNRWFFQVER 432
Cdd:COG4623 312 TAKELGVDDRLDPEQSIRAGAKYLRWLYDRF--PEAIDEPDRWWFALAAYNAGPGHVQDARRLAKKQGLDPDRWFDVEKS 389

                       410       420       430
                ....*....|....*....|....*....|.
gi 15598061 433 -----VAAEEIGMGVVSYVSSVNKYYLAYER 458
Cdd:COG4623 390 qpkyyDTGYARGRETVNYVPNIRAYYDIYKR 420
MLTF-like cd13403
membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins; This subfamily ...
 310-458 8.97e-59

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: 190.82  E-value: 8.97e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 310 QRYARQSSMDWLALAAVAYKESHLNPKARGSGGASGLMQITPAAARSVGVGNVHDKDSNVLAASRYLTKIRKQFfsSKHL 389
Cdd:cd13403   2 KKYAEKYGFDWRLLAAQAYQESRFNPNARSPAGARGLMQLMPSTARELGVNDRLDPEQNIHAGAKYLRYLRDRF--PPDI 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 390 DERERLAFTLAAYNMGPERVQNLRTQARRRGLDPNRWFFQVERV-------------AAEEIGMGVVSYVSSVNKYYLAY 456
Cdd:cd13403  80 DEPDRLKFALAAYNAGPGHVRDARRLAKKYGLNPNVWFDNVEVLpllkspyydpvvkYGYARGRETVNYVRNIRKYYDAY 159


                ..
gi 15598061 457 ER 458
Cdd:cd13403 160 KQ 161
PRK10859 PRK10859
membrane-bound lytic murein transglycosylase MltF;
19-426 5.73e-49

membrane-bound lytic murein transglycosylase MltF;


Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 174.68  E-value: 5.73e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061   19 AAARITGQPdnWHREQPETrdLASIRRAGVLKVLVNQSRNSSGEVKGEPIGVEYRRLRAFEQYLNsrspsarnLTLKLIP 98
Cdd:PRK10859  19 AAALWPSIP--WFSKEENQ--LEQIQERGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADYLG--------VKLEIKV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061   99 KPK-DQLLAALQRGEGDLVAPGeLLPAHDGLQVSPSAPVRADVPLVLVARKGNRRYTRLEQLSGRTIPLPAGSAAEgaie 177
Cdd:PRK10859  87 RDNiSQLFDALDKGKADLAAAG-LTYTPERLKQFRFGPPYYSVSQQLVYRKGQPRPRSLGDLKGGTLTVAAGSSHV---- 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  178 lvnQRLAQ-RRMAPIRIEKLDASLAVEDVMEMVQAGILGFTVVEQPIAERWAKVLPKLRVDrhLVLDNRADMAWYVRRDA 256
Cdd:PRK10859 162 ---ETLQElKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPELAVA--FDLTDEQPVAWALPPSG 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  257 S-TLRATIDRFLADyrapADQDVAFQRVYRRAY---KVRNPLGA-----ADRKRLEAVRPLLQRYARQssMDWLALAAVA 327
Cdd:PRK10859 237 DdSLYAALLDFFNQ----IKEDGTLARLEEKYFghvDRFDYVDTrtflrAIDNRLPKYQPLFEKYAGE--LDWRLLAAIA 310

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  328 YKESHLNPKARGSGGASGLMQITPAAARSVGVGNVHDKDSNVLAASRYLTKIRKQFFSSkhLDERERLAFTLAAYNMGPE 407
Cdd:PRK10859 311 YQESHWNPQATSPTGVRGLMMLTRNTAQSMGVTDRLDPEQSIRGGARYLQDLMERLPES--IPEPERIWFALAAYNIGYG 388

                        410
                 ....*....|....*....
gi 15598061  408 RVQNLRTQARRRGLDPNRW 426
Cdd:PRK10859 389 HMLDARRLTKKQGGNPDSW 407
PBP2_YfhD_N cd01009
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ...
 47-289 1.16e-46

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: 161.22  E-value: 1.16e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  47 GVLKVLVNQSRNSSGEVKGEPIGVEYRRLRAFEQYLNsrspsarnLTLKLIPKPK-DQLLAALQRGEGDLVAPGELLPAH 125
Cdd:cd01009   1 GELRVLTRNSPTTYYIDRGGPRGFEYELAKAFADYLG--------VELEIVPADNlEELLEALEEGKGDLAAAGLTITPE 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 126 DGLQVSPSAPVRADVPlVLVARKGNRRYTRLEQLSGRTIPLPAGSAAEGAIELVNQRLAqrrmaPIRIEKLDASLaVEDV 205
Cdd:cd01009  73 RKKKVDFSFPYYYVVQ-VLVYRKGSPRPRSLEDLSGKTIAVRKGSSYAETLQKLNKGGP-----PLTWEEVDEAL-TEEL 145

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 206 MEMVQAGILGFTVVEQPIAERWAKVLPKLRVDrhLVLDNRADMAWYVRRDASTLRATIDRFLADYRapadQDVAFQRVYR 285
Cdd:cd01009 146 LEMVAAGEIDYTVADSNIAALWRRYYPELRVA--FDLSEPQPLAWAVRKNSPSLLAALNRFLAQIK----KDGTLARLYE 219


                ....
gi 15598061 286 RAYK 289
Cdd:cd01009 220 RYYG 223
MltE COG0741
Soluble lytic murein transglycosylase or regulatory protein s ( may contain LysM/invasin ...
 200-458 6.24e-20

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: 88.90  E-value: 6.24e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 200 LAVEDVMEMVQAGILGFTVVEQPIAERWAKVLPKLRVDRHLVLDNRADMAWYVRRDASTLRATIDRFLADYRAPADQDVA 279
Cdd:COG0741   2 AAAAAAAAALALAASAAAALALALLAAAAAAAALAAAAAALAAAAAAAAGAAAAAASAAAGGPALAAALAAADALAAFAA 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 280 FQRVYRRAYKvrnpLGAADRKRLEAVRPLLQRYARQSSMDWLALAAVAYKESHLNPKARGSGGASGLMQITPAAARSVGV 359
Cdd:COG0741  82 IAALAAELLA----LAALLLRRPLPYLPLIEEAAKKYGVDPALVLALIRQESAFNPNAVSPAGARGLMQLMPATARRLGL 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 360 --------GNVHDKDSNVLAASRYLTKIRKQFFSSkhldererLAFTLAAYNMGPERVQnlRTQARRRGLDPnrwffqvE 431
Cdd:COG0741 158 klglgpspDDLFDPETNIRAGAAYLRELLDRFDGD--------LVLALAAYNAGPGRVR--RWLRRNGDRDG-------E 220

                       250       260
                ....*....|....*....|....*..
gi 15598061 432 RVAAEEIgmgvVSYVSSVNKYYLAYER 458
Cdd:COG0741 221 IIPYAET----RNYVKKVLANYAIYRA 243
LT_Slt70-like cd16896
uncharacterized lytic transglycosylase subfamily with similarity to Slt70; Uncharacterized ...
 306-411 7.99e-16

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: 74.47  E-value: 7.99e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 306 RPLLQRYARQSSMDWLALAAVAYKESHLNPKARGSGGASGLMQITPAAAR---------SVGVGNVHDKDSNVLAASRYL 376
Cdd:cd16896   5 REYIEKYAKEYGVDPLLVAAVIKVESNFNPNAVSSKGAIGLMQIMPETAEwiaeklgleDFSEDDLYDPETNIRLGTWYL 84

                        90       100       110
                ....*....|....*....|....*....|....*
gi 15598061 377 TKIRKQFFSSkhlderERLAftLAAYNMGPERVQN 411
Cdd:cd16896  85 SYLLKEFDGN------LVLA--LAAYNAGPGNVDK 111
Slt70-like cd13401
70kDa soluble lytic transglycosylase (Slt70) and similar proteins; Catalytic domain of the ...
 306-437 9.74e-16

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: 74.44  E-value: 9.74e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 306 RPLLQRYARQSSMDWLALAAVAYKESHLNPKARGSGGASGLMQITPAAARSV----GVGNVHDKD-----SNVLAASRYL 376
Cdd:cd13401   7 RDLVERAAKKNGLDPALVYAIIRQESAFDPDAVSPAGALGLMQLMPATAKDVakklGLPYYSPRDlfdpeYNIRLGSAYL 86

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15598061 377 TKIRKQFFSSkhldererLAFTLAAYNMGPERVQnlRTQARRRGLDPNRWffqVERVAAEE 437
Cdd:cd13401  87 AELLDRFDGN--------PVLALAAYNAGPGRVR--RWLKRRGDLDPDLW---IETIPFSE 134
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
 64-272 1.51e-15

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: 75.79  E-value: 1.51e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  64 KGEPIGVEYRRLRAFEQYLNsrspsarnLTLKLIPKPKDQLLAALQRGEGDLVAPGELLPAHDGLQVSPSAPVrADVPLV 143
Cdd:COG0834  18 DGKLVGFDVDLARAIAKRLG--------LKVEFVPVPWDRLIPALQSGKVDLIIAGMTITPEREKQVDFSDPY-YTSGQV 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 144 LVARKGNRRYTRLEQLSGRTIPLPAGSAAEgaielvnqRLAQRRMAPIRIEKLDaslAVEDVMEMVQAGILGFTVVEQPI 223
Cdd:COG0834  89 LLVRKDNSGIKSLADLKGKTVGVQAGTTYE--------EYLKKLGPNAEIVEFD---SYAEALQALASGRVDAVVTDEPV 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*....
gi 15598061 224 AERWAKVLPKLRVDRHLVLDNRADMAWYVRRDASTLRATIDRFLADYRA 272
Cdd:COG0834 158 AAYLLAKNPGDDLKIVGEPLSGEPYGIAVRKGDPELLEAVNKALAALKA 206
SLT pfam01464
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found ...
 310-420 8.81e-15

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: 70.41  E-value: 8.81e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061   310 QRYARQSSMDWLALAAVAYKESHLNPKARGSGGASGLMQITPAAARSVGVGNVHDKDS------NVLAASRYLTKIRKQF 383
Cdd:pfam01464   2 IKAAQKYGVDPSLLLAIAQQESGFNPKAVSKSGAVGLMQIMPSTAKRLGLRVNPGVDDlfdpekNIKAGTKYLKELYKQY 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 15598061   384 fsskhldeRERLAFTLAAYNMGPERVQNLRTQARRRG 420
Cdd:pfam01464  82 --------GGDLWLALAAYNAGPGRVRKWIKNAGAKD 110
LT-like cd00254
lytic transglycosylase(LT)-like domain; Members include the soluble and insoluble ...
 323-411 1.21e-14

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: 69.93  E-value: 1.21e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 323 LAAVAYKESHLNPKARGSGGASGLMQITPAAARSVGVGNV---HDKDSNVLAASRYLTKIRKQFFsskhlderERLAFTL 399
Cdd:cd00254   4 VLAVIRVESGFNPRAVSPAGARGLMQLMPGTARDLGRRGVddlFDPEENIRAGARYLRELLDRFG--------GDLELAL 75

                        90
                ....*....|..
gi 15598061 400 AAYNMGPERVQN 411
Cdd:cd00254  76 AAYNAGPGAVDR 87
MltD-like cd16894
Membrane-bound lytic murein transglycosylase D and similar proteins; Lytic transglycosylases ...
 323-422 4.51e-11

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: 60.22  E-value: 4.51e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 323 LAAVAYKESHLNPKARGSGGASGLMQITPAAARSVGVGNVHDKD--SNVL----AASRYLTKIRKQFFSSkhldereRLA 396
Cdd:cd16894  10 LKYLALVESGFNPDAVSSAGAAGLWQFMPATAREYGLRVDSWVDerRDPEkstrAAARYLKDLYKRFGDW-------LLA 82

                        90       100
                ....*....|....*....|....*.
gi 15598061 397 ftLAAYNMGPERVQNLRTQARRRGLD 422
Cdd:cd16894  83 --LAAYNAGEGRVRRAIKRAGTDKWE 106
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
 64-286 8.17e-11

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 61.58  E-value: 8.17e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061     64 KGEPIGVEYRRLRAFEQYLNsrspsarnLTLKLIPKPKDQLLAALQRGEGDLVAPGELLPAHDGLQVSPSAPVrADVPLV 143
Cdd:smart00062  19 DGELTGFDVDLAKAIAKELG--------LKVEFVEVSFDSLLTALKSGKIDVVAAGMTITPERAKQVDFSDPY-YRSGQV 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061    144 LVARKGNrRYTRLEQLSGRTIPLPAGSAAEgaielvnqRLAQRRMAPIRIEKLDASlavEDVMEMVQAGILGFTVVEQPI 223
Cdd:smart00062  90 ILVRKDS-PIKSLEDLKGKKVAVVAGTTAE--------ELLKKLYPEAKIVSYDSN---AEALAALKAGRADAAVADAPL 157

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15598061    224 AERWAKVLPKLRVD-RHLVLDNRADMAWYVRRDASTLRATIDRFLADYRApadqDVAFQRVYRR 286
Cdd:smart00062 158 LAALVKQHGLPELKiVPDPLDTPEGYAIAVRKGDPELLDKINKALKELKA----DGTLKKISEK 217
Slt35-like cd13399
Slt35-like lytic transglycosylase; Lytic transglycosylase similar to Escherichia coli lytic ...
 318-406 1.02e-10

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


Pssm-ID: 381602 [Multi-domain]  Cd Length: 108  Bit Score: 58.47  E-value: 1.02e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 318 MDWLALAAVAYKESHLNPKARGSG-GASGLMQITPAAARSVGVGNVHD--KDSN-----VLAASRYLtkirKQFFSSKHL 389
Cdd:cd13399   3 VPPGILAAILGVESGFGPNAGGSPaGAQGIAQFMPSTWKAYGVDGNGDgkADPFnpedaIASAANYL----CRHGWDLNA 78

                        90
                ....*....|....*..
gi 15598061 390 DERERLAFTLAAYNMGP 406
Cdd:cd13399  79 FLGEDNFLALAAYNAGP 95
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
 64-272 3.74e-10

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: 59.61  E-value: 3.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061    64 KGEPIGVEYRRLRAFEQYLNsrspsarnLTLKLIPKPKDQLLAALQRGEGDLVApgellpahDGLQVSP--------SAP 135
Cdd:pfam00497  18 NGKLVGFDVDLAKAIAKRLG--------VKVEFVPVSWDGLIPALQSGKVDLII--------AGMTITPerakqvdfSDP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061   136 VrADVPLVLVARKGN--RRYTRLEQLSGRTIPLPAGSAAEgaielvnQRLAQRRMAPIRIEKLDAslaVEDVMEMVQAGI 213
Cdd:pfam00497  82 Y-YYSGQVILVRKKDssKSIKSLADLKGKTVGVQKGSTAE-------ELLKNLKLPGAEIVEYDD---DAEALQALANGR 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15598061   214 LGFTVVEQPIAERWAKVLPKLRVDRHLVLDNRADMAWYVRRDASTLRATIDRFLADYRA 272
Cdd:pfam00497 151 VDAVVADSPVAAYLIKKNPGLNLVVVGEPLSPEPYGIAVRKGDPELLAAVNKALAELKA 209
PBP2_BvgS_D2 cd13707
The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
 48-268 4.04e-10

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: 59.54  E-value: 4.04e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  48 VLKVLVNQS------RNSSGEVKGepIGVEYrrLRAFEQYLNsrspsarnltLKLIPKP---KDQLLAALQRGEGDLVAP 118
Cdd:cd13707   3 VVRVVVNPDlaplsfFDSNGQFRG--ISADL--LELISLRTG----------LRFEVVRassPAEMIEALRSGEADMIAA 68

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 119 geLLPAHD-GLQVSPSAPVrADVPLVLVARKGNRRYTRLEQLSGRTIPLPAGSAAEGAIelvnqrlaQRRMAPIRIEKLD 197
Cdd:cd13707  69 --LTPSPErEDFLLFTRPY-LTSPFVLVTRKDAAAPSSLEDLAGKRVAIPAGSALEDLL--------RRRYPQIELVEVD 137

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15598061 198 ASlavEDVMEMVQAGILGFTVVEQPIAeRWA---KVLPKLRVDRhLVLDNRADMAWYVRRDASTLRATIDRFLA 268
Cdd:cd13707 138 NT---AEALALVASGKADATVASLISA-RYLinhYFRDRLKIAG-ILGEPPAPIAFAVRRDQPELLSILDKALL 206
PRK11619 PRK11619
lytic murein transglycosylase; Provisional
 325-409 1.22e-08

lytic murein transglycosylase; Provisional


Pssm-ID: 183236 [Multi-domain]  Cd Length: 644  Bit Score: 57.38  E-value: 1.22e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  325 AVAYKESHLNPKARGSGGASGLMQITPAAAR-SVGVGNVH---------DKDSNVLAASRYLTKIRKQFfsskhldERER 394
Cdd:PRK11619 499 AIARQESAWNPKARSPVGASGLMQIMPGTAThTVKMFSIPgyssssqllDPETNINIGTSYLEYVYQQF-------GNNR 571

                         90
                 ....*....|....*
gi 15598061  395 LaFTLAAYNMGPERV 409
Cdd:PRK11619 572 I-LASAAYNAGPGRV 585
PBP2_BvgS_HisK_like cd01007
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
 58-268 1.47e-08

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: 54.85  E-value: 1.47e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  58 NSSGEVKGepIGVEYrrLRAFEQYLNsrspsarnLTLKLIPKPK-DQLLAALQRGEGDLVAPGELLPAHDGlQVSPSAPV 136
Cdd:cd01007  19 DEGGEPQG--IAADY--LKLIAKKLG--------LKFEYVPGDSwSELLEALKAGEIDLLSSVSKTPEREK-YLLFTKPY 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 137 rADVPLVLVARKGNRRYTRLEQLSGRTIPLPAGSAAEGAIelvnqrlaqRRMAP-IRIekldasLAVEDV---MEMVQAG 212
Cdd:cd01007  86 -LSSPLVIVTRKDAPFINSLSDLAGKRVAVVKGYALEELL---------RERYPnINL------VEVDSTeeaLEAVASG 149

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15598061 213 ILGFTVVEQPIAERWAKV--LPKLRVdrHLVLDNRADMAWYVRRDASTLRATIDRFLA 268
Cdd:cd01007 150 EADAYIGNLAVASYLIQKygLSNLKI--AGLTDYPQDLSFAVRKDWPELLSILNKALA 205
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
 91-272 2.47e-08

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: 54.18  E-value: 2.47e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  91 NLTLKLIPKPKDQLLAALQRGEGDLVApgellpahDGLQVSP--------SAPVrADVPLVLVARKGNRRYTRLEQLSGR 162
Cdd:cd13530  38 GVKVEFVDTDFDGLIPALQSGKIDVAI--------SGMTITPerakvvdfSDPY-YYTGQVLVVKKDSKITKTVADLKGK 108

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 163 TIPLPAGSAAEgaielvnqRLAQRRMAPIRIEKLDASlavEDVMEMVQAGILGFTVVEQPIAERWAK-VLPKLRVdrHLV 241
Cdd:cd13530 109 KVGVQAGTTGE--------DYAKKNLPNAEVVTYDNY---PEALQALKAGRIDAVITDAPVAKYYVKkNGPDLKV--VGE 175

                       170       180       190
                ....*....|....*....|....*....|.
gi 15598061 242 LDNRADMAWYVRRDASTLRATIDRFLADYRA 272
Cdd:cd13530 176 PLTPEPYGIAVRKGNPELLDAINKALAELKA 206
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
 91-286 3.92e-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: 47.96  E-value: 3.92e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  91 NLTLKLIPKPKDQLLAALQRGEGDLVAPGELLPAHDgLQVSPSAPVrADVPLVLVARKGNRRYTRLEQLSGRTIPLPAGS 170
Cdd:cd13704  40 GLKVEIRLGPWSEVLQALENGEIDVLIGMAYSEERA-KLFDFSDPY-LEVSVSIFVRKGSSIINSLEDLKGKKVAVQRGD 117

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 171 AAEgaielvnqRLAQRRMAPIRIEKLDASlavEDVMEMVQAGILGFTVVEQPIAERWAKVLPKLRVDRHLVLDNRADMAW 250
Cdd:cd13704 118 IMH--------EYLKERGLGINLVLVDSP---EEALRLLASGKVDAAVVDRLVGLYLIKELGLTNVKIVGPPLLPLKYCF 186

                       170       180       190
                ....*....|....*....|....*....|....*.
gi 15598061 251 YVRRDASTLRATIDRFLADYRApadqDVAFQRVYRR 286
Cdd:cd13704 187 AVRKGNPELLAKLNEGLAILKA----SGEYDEIYEK 218
LT_MltC_MltE cd16893
membrane-bound lytic murein transglycosylases MltC and MltE, and similar proteins; MltC and ...
 307-414 5.25e-06

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


Pssm-ID: 381614 [Multi-domain]  Cd Length: 162  Bit Score: 46.40  E-value: 5.25e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 307 PLLQRYARQSSMDWLALAAVAYKESHLNPKARGSGGASGLMQITPAAA-----RSVGVGNVH-------DKDSNVLAASR 374
Cdd:cd16893   1 PIVEKYAKKYGVDPALILAIIETESSFNPYAVSHSPAYGLMQIVPSTAgrdvyRLLGGKGGLpsksylfDPENNIDIGTA 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 15598061 375 YLTKIRKQFFSS-KHLDERERLafTLAAYNMGPERVqnLRT 414
Cdd:cd16893  81 YLHILQNRYLKGiKNPKSREYC--AIAAYNGGAGNV--LRT 117
PBP2_AA_binding_like_1 cd13625
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
 104-267 2.53e-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: 45.44  E-value: 2.53e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 104 LLAALQRGEGDLVAPGELLPAHDGLQVSPSAPVrADVPLVLVARKGNRRYTRLEQLSGRTIPLPAGSAAEGAIELVNQRL 183
Cdd:cd13625  55 ILPGLLAGKFDMVATSVTITKERAKRFAFTLPI-AEATAALLKRAGDDSIKTIEDLAGKVVGVQAGSAQLAQLKEFNETL 133

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 184 -AQRRMAPIRIEKLDAS-LAVEDVME-MVQAGILGFTVVEQPIAER---WAKVLPklrvdrhlvLDNRADMAWYVRRDAS 257
Cdd:cd13625 134 kKKGGNGFGEIKEYVSYpQAYADLANgRVDAVANSLTNLAYLIKQRpgvFALVGP---------VGGPTYFAWVIRKGDA 204

                       170
                ....*....|
gi 15598061 258 TLRATIDRFL 267
Cdd:cd13625 205 ELRKAINDAL 214
Lyz-like cd00442
lysozyme-like domains; This family contains several members, including soluble lytic ...
 323-375 4.02e-04

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: 38.54  E-value: 4.02e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15598061 323 LAAVAYKESHLNPKAR-GSG-GASGLMQITPAAARSVG---VGNVHDKDSNVLAASRY 375
Cdd:cd00442   2 LAAIIGQESGGNKPANaGSGsGAAGLFQFMPGTWKAYGknsSSDLNDPEASIEAAAKY 59
PBP2_Ala cd13628
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ...
 102-273 1.54e-03

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


Pssm-ID: 270346 [Multi-domain]  Cd Length: 219  Bit Score: 40.14  E-value: 1.54e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 102 DQLLAALQRGEGDLvapgellpAHDGLQVSPSAPVRADVPLV-------LVARKgNRRYTRLEQLSGRTIPLPAGSAAEG 174
Cdd:cd13628  50 NGLIPALASGQADL--------ALAGITPTPERKKVVDFSEPyyeasdtIVS*K-DRKIKQLQDLNGKSLGVQLGTIQEQ 120

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061 175 AIELVNQrlaqrRMAPIRIEKLDaslaveDVMEMVQA---GILGFTVVEQPIAERWAKVLPKLRVDRhLVLDNRADMAWY 251
Cdd:cd13628 121 LIKELSQ-----PYPGLKTKLYN------RVNELVQAlksGRVDAAIVEDIVAETFAQKKN*LLESR-YIPKEADGSAIA 188

                       170       180
                ....*....|....*....|..
gi 15598061 252 VRRDaSTLRATIDRFLADYRAP 273
Cdd:cd13628 189 FPKG-SPLRDDFNRWLKEMGDS 209
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 330-426 1.98e-03

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 40.49  E-value: 1.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598061  330 ESHLNPKARGSGGASGLMQITPAAARSVGvgnvhdkdsnvLAASRYLTKIRKQFFSSK-HLDERERL--------AFTLA 400
Cdd:PRK10783 128 ESAFDPHATSGANAAGIWQIIPSTGRNYG-----------LKQTRWYDARRDVVASTTaALDMMQRLnkmfdgdwLLTVA 196

                         90       100
                 ....*....|....*....|....*.
gi 15598061  401 AYNMGPERVQNLRTQARRRGLDPNRW 426
Cdd:PRK10783 197 AYNSGEGRVMKAIKANKAKGKPTDFW 222
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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