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Conserved domains on  [gi|1566441686|gb|QAZ75137|]
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Peptidoglycan hydrolase VirB1 (plasmid) [Escherichia coli]

Protein Classification

lytic transglycosylase domain-containing protein( domain architecture ID 13013948)

lytic transglycosylase domain-containing protein similar to VirB1 protein, one of twelve proteins making up type IV secretion systems (T4SS)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LT_VirB1-like cd16892
VirB1-like subfamily; This subfamily includes VirB1 protein, one of twelve proteins making up ...
 11-158 7.20e-62

VirB1-like subfamily; This subfamily includes VirB1 protein, one of twelve proteins making up type IV secretion systems (T4SS). T4SS are macromolecular assemblies generally composed of VirB1-11 and VirD4 proteins, and are used by bacteria to transport material across their membranes. VirB1 acts as a lytic transglycosylase (LT), and is important with respect to piercing the peptidoglycan layer in the periplasm. 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, the LTs in bacteriophage lambda, as well as the eukaryotic "goose-type" lysozymes (goose egg-white lysozyme; GEWL).


:

Pssm-ID: 381613 [Multi-domain]  Cd Length: 143  Bit Score: 188.52  E-value: 7.20e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  11 LISQCAPDVSPDTMNALIMTESGANPYVIANVSDGTSKYFKDEKGAIEYAEKLTAENKRFSAGLTQIYSKNFPSLNLTNK 90
Cdd:cd16892     1 LAAQCAPGVHPETLAAIVQVESGGNPYAIGVNGGKLSRQPKTKAEAIATARQLIAAGHNFDVGLGQINSRNLARLGLTVE 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  91 TVFDPCTNIKAGAAVLTDNYLR--QKEGSSNQKILRALSLYYSGNESTGFIKekkfnntSYLERVIRNAN 158
Cdd:cd16892    81 DVFDPCTNLKAGATILTECYARakKTGGDGQAALRAALSCYNTGNFTRGFSN-------GYVQKVVAAAG 143
 
Name Accession Description Interval E-value
LT_VirB1-like cd16892
VirB1-like subfamily; This subfamily includes VirB1 protein, one of twelve proteins making up ...
 11-158 7.20e-62

VirB1-like subfamily; This subfamily includes VirB1 protein, one of twelve proteins making up type IV secretion systems (T4SS). T4SS are macromolecular assemblies generally composed of VirB1-11 and VirD4 proteins, and are used by bacteria to transport material across their membranes. VirB1 acts as a lytic transglycosylase (LT), and is important with respect to piercing the peptidoglycan layer in the periplasm. 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, the LTs in bacteriophage lambda, as well as the eukaryotic "goose-type" lysozymes (goose egg-white lysozyme; GEWL).


Pssm-ID: 381613 [Multi-domain]  Cd Length: 143  Bit Score: 188.52  E-value: 7.20e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  11 LISQCAPDVSPDTMNALIMTESGANPYVIANVSDGTSKYFKDEKGAIEYAEKLTAENKRFSAGLTQIYSKNFPSLNLTNK 90
Cdd:cd16892     1 LAAQCAPGVHPETLAAIVQVESGGNPYAIGVNGGKLSRQPKTKAEAIATARQLIAAGHNFDVGLGQINSRNLARLGLTVE 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  91 TVFDPCTNIKAGAAVLTDNYLR--QKEGSSNQKILRALSLYYSGNESTGFIKekkfnntSYLERVIRNAN 158
Cdd:cd16892    81 DVFDPCTNLKAGATILTECYARakKTGGDGQAALRAALSCYNTGNFTRGFSN-------GYVQKVVAAAG 143
PRK13864 PRK13864
type IV secretion system lytic transglycosylase VirB1; Provisional
 3-193 1.70e-21

type IV secretion system lytic transglycosylase VirB1; Provisional


Pssm-ID: 237534  Cd Length: 245  Bit Score: 87.99  E-value: 1.70e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686   3 LSAAVLAALISQCAPDVSPDTMNALIMTESGANPYVIANVSDGTSKYFKDEKGAIEYAEKLTAENKRFSAGLTQIYSKNF 82
Cdd:PRK13864   25 LSFAEFNQLARECAPSVAPSTLAAIAKVESRFDPLAVHDNTTGETLHWQNHAQATQSVRHRLEARHSLDVGLMQINSKNF 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  83 PSLNLTNKTVFDPCTNIKAGAAVLTDNYLRQKEGSSNQKILR-ALSLYYSGNESTGFikekkfnNTSYLERViRNANNYI 161
Cdd:PRK13864  105 SVLGLTPDGALQPCTSLSAAANLLGSRYAGGDTADEKQLALRrAISAYNTGDFTRGF-------ANGYVRKV-ETAAQQL 176

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1566441686 162 VPSIREKTDESEIKPPNDEEktspdWDVFGDF 193
Cdd:PRK13864  177 VPPLTQRPKDDREKPKSEET-----WDVWGSY 203
SLT pfam01464
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found ...
 14-143 3.77e-05

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: 41.52  E-value: 3.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  14 QCAPDVSPDTMNALIMTESGANPYVIanvsdgtskyfkdekgaieyaekltaeNKRFSAGLTQIYSKNFPSLNLTNKT-- 91
Cdd:pfam01464   5 AQKYGVDPSLLLAIAQQESGFNPKAV---------------------------SKSGAVGLMQIMPSTAKRLGLRVNPgv 57

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1566441686  92 --VFDPCTNIKAGAAvltdnYLRQKEGSSNQKILRALSLYYSGnesTGFIKEKK 143
Cdd:pfam01464  58 ddLFDPEKNIKAGTK-----YLKELYKQYGGDLWLALAAYNAG---PGRVRKWI 103
MltE COG0741
Soluble lytic murein transglycosylase or regulatory protein s ( may contain LysM/invasin ...
 18-160 6.15e-04

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: 39.21  E-value: 6.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  18 DVSPDTMNALIMTESGANPYVianVSdgtskyfkdEKGAIeyaekltaenkrfsaGLTQI-------YSKNFpSLNLTNK 90
Cdd:COG0741   115 GVDPALVLALIRQESAFNPNA---VS---------PAGAR---------------GLMQLmpatarrLGLKL-GLGPSPD 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  91 TVFDPCTNIKAGAAvltdnYLRQKEGSSNQKILRALSLYYSG---------NESTGFIKEKKFNNTS-YLERVIRNANNY 160
Cdd:COG0741   167 DLFDPETNIRAGAA-----YLRELLDRFDGDLVLALAAYNAGpgrvrrwlrRNGDRDGEIIPYAETRnYVKKVLANYAIY 241
 
Name Accession Description Interval E-value
LT_VirB1-like cd16892
VirB1-like subfamily; This subfamily includes VirB1 protein, one of twelve proteins making up ...
 11-158 7.20e-62

VirB1-like subfamily; This subfamily includes VirB1 protein, one of twelve proteins making up type IV secretion systems (T4SS). T4SS are macromolecular assemblies generally composed of VirB1-11 and VirD4 proteins, and are used by bacteria to transport material across their membranes. VirB1 acts as a lytic transglycosylase (LT), and is important with respect to piercing the peptidoglycan layer in the periplasm. 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, the LTs in bacteriophage lambda, as well as the eukaryotic "goose-type" lysozymes (goose egg-white lysozyme; GEWL).


Pssm-ID: 381613 [Multi-domain]  Cd Length: 143  Bit Score: 188.52  E-value: 7.20e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  11 LISQCAPDVSPDTMNALIMTESGANPYVIANVSDGTSKYFKDEKGAIEYAEKLTAENKRFSAGLTQIYSKNFPSLNLTNK 90
Cdd:cd16892     1 LAAQCAPGVHPETLAAIVQVESGGNPYAIGVNGGKLSRQPKTKAEAIATARQLIAAGHNFDVGLGQINSRNLARLGLTVE 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  91 TVFDPCTNIKAGAAVLTDNYLR--QKEGSSNQKILRALSLYYSGNESTGFIKekkfnntSYLERVIRNAN 158
Cdd:cd16892    81 DVFDPCTNLKAGATILTECYARakKTGGDGQAALRAALSCYNTGNFTRGFSN-------GYVQKVVAAAG 143
PRK13864 PRK13864
type IV secretion system lytic transglycosylase VirB1; Provisional
 3-193 1.70e-21

type IV secretion system lytic transglycosylase VirB1; Provisional


Pssm-ID: 237534  Cd Length: 245  Bit Score: 87.99  E-value: 1.70e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686   3 LSAAVLAALISQCAPDVSPDTMNALIMTESGANPYVIANVSDGTSKYFKDEKGAIEYAEKLTAENKRFSAGLTQIYSKNF 82
Cdd:PRK13864   25 LSFAEFNQLARECAPSVAPSTLAAIAKVESRFDPLAVHDNTTGETLHWQNHAQATQSVRHRLEARHSLDVGLMQINSKNF 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  83 PSLNLTNKTVFDPCTNIKAGAAVLTDNYLRQKEGSSNQKILR-ALSLYYSGNESTGFikekkfnNTSYLERViRNANNYI 161
Cdd:PRK13864  105 SVLGLTPDGALQPCTSLSAAANLLGSRYAGGDTADEKQLALRrAISAYNTGDFTRGF-------ANGYVRKV-ETAAQQL 176

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1566441686 162 VPSIREKTDESEIKPPNDEEktspdWDVFGDF 193
Cdd:PRK13864  177 VPPLTQRPKDDREKPKSEET-----WDVWGSY 203
LT_IagB-like cd13400
Escherichia coli invasion protein IagB and similar proteins; Lytic transglycosylase-like ...
 18-159 5.91e-09

Escherichia coli invasion protein IagB and similar proteins; Lytic transglycosylase-like protein, similar to Escherichia coli invasion protein IagB. IagB is encoded within a pathogenicity island in Salmonella enterica and has been shown to degrade polymeric peptidoglycan. IagB-like invasion proteins are implicated in the invasion of eukaryotic host cells by bacteria. Lytic transglycosylase (LT) catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do "goose-type" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Members of this family resemble the soluble and insoluble membrane-bound LTs in bacteria and the LTs in bacteriophage lambda.


Pssm-ID: 381603 [Multi-domain]  Cd Length: 109  Bit Score: 51.76  E-value: 5.91e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  18 DVSPDTMNALIMTESGANPYVIANVSDGTSKYfkdekgaieyaekltaenkrfsaGLTQIYSKNFPSLN----LTNKTVF 93
Cdd:cd13400     2 GVPPRLLRAIAKVESGFNPNAINRNKNGSYDI-----------------------GLMQINSIWLPELArygiTREELLN 58

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1566441686  94 DPCTNIKAGAAVLTDNYlrQKEGSSnqkiLRALSLYYSGNEStgfikekkfNNTSYLERVIRNANN 159
Cdd:cd13400    59 DPCTNIYVGAWILARNI--KRYGNT----WKAVGAYNSGTPK---------KNDKYARKVYRIYRR 109
SLT pfam01464
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found ...
 14-143 3.77e-05

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: 41.52  E-value: 3.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  14 QCAPDVSPDTMNALIMTESGANPYVIanvsdgtskyfkdekgaieyaekltaeNKRFSAGLTQIYSKNFPSLNLTNKT-- 91
Cdd:pfam01464   5 AQKYGVDPSLLLAIAQQESGFNPKAV---------------------------SKSGAVGLMQIMPSTAKRLGLRVNPgv 57

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1566441686  92 --VFDPCTNIKAGAAvltdnYLRQKEGSSNQKILRALSLYYSGnesTGFIKEKK 143
Cdd:pfam01464  58 ddLFDPEKNIKAGTK-----YLKELYKQYGGDLWLALAAYNAG---PGRVRKWI 103
PRK15328 PRK15328
type III secretion system invasion protein IagB;
19-108 3.91e-05

type III secretion system invasion protein IagB;


Pssm-ID: 185228 [Multi-domain]  Cd Length: 160  Bit Score: 42.16  E-value: 3.91e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  19 VSPDTMNALIMTESGANPYVIANVSDGTSkyfkdekgaieyaekltaenkrfSAGLTQIYSKNFPSLNL----TNKTVFD 94
Cdd:PRK15328   31 IESELLYAIAQQESAMKPGAIGHNRDGST-----------------------DLGLMQINSFHMKRLKKmgisEKQLLQD 87

                          90
                  ....*....|....
gi 1566441686  95 PCTNIKAGAAVLTD 108
Cdd:PRK15328   88 PCISVIVGASILSD 101
MltE COG0741
Soluble lytic murein transglycosylase or regulatory protein s ( may contain LysM/invasin ...
 18-160 6.15e-04

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: 39.21  E-value: 6.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  18 DVSPDTMNALIMTESGANPYVianVSdgtskyfkdEKGAIeyaekltaenkrfsaGLTQI-------YSKNFpSLNLTNK 90
Cdd:COG0741   115 GVDPALVLALIRQESAFNPNA---VS---------PAGAR---------------GLMQLmpatarrLGLKL-GLGPSPD 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  91 TVFDPCTNIKAGAAvltdnYLRQKEGSSNQKILRALSLYYSG---------NESTGFIKEKKFNNTS-YLERVIRNANNY 160
Cdd:COG0741   167 DLFDPETNIRAGAA-----YLRELLDRFDGDLVLALAAYNAGpgrvrrwlrRNGDRDGEIIPYAETRnYVKKVLANYAIY 241
LT-like cd00254
lytic transglycosylase(LT)-like domain; Members include the soluble and insoluble ...
 26-132 3.81e-03

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: 35.65  E-value: 3.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566441686  26 ALIMTESGANPYVianvsdgTSKyfkdeKGAIeyaekltaenkrfsaGLTQIYSKNFPSLNLTNKTV-FDPCTNIKAGAA 104
Cdd:cd00254     6 AVIRVESGFNPRA-------VSP-----AGAR---------------GLMQLMPGTARDLGRRGVDDlFDPEENIRAGAR 58

                          90       100
                  ....*....|....*....|....*...
gi 1566441686 105 vltdnYLRQKEGSSNQKILRALSLYYSG 132
Cdd:cd00254    59 -----YLRELLDRFGGDLELALAAYNAG 81
 
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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