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Conserved domains on  [gi|1261086913|ref|WP_097678089.1|]
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outer membrane protein assembly factor BamD

Protein Classification

outer membrane protein assembly factor BamD( domain architecture ID 11467870)

outer membrane protein assembly factor BamD is part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
BamD COG4105
Outer membrane protein assembly factor BamD, BamD/ComL family [Cell wall/membrane/envelope ...
 4-196 2.44e-19

Outer membrane protein assembly factor BamD, BamD/ComL family [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 443281 [Multi-domain]  Cd Length: 254  Bit Score: 83.39  E-value: 2.44e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913   4 KHFKTFLFIAMAVIVIgTGCANKKKkkDEYNKPAIFWYQGILREILFANLETADNYYSSLQSEHINSPLVPEAMLALGQA 83
Cdd:COG4105     2 KKLLKLLLLLLLALLL-AGCSSFKK--ALKSWDAEELYEEAKEALEKGDYEKAIKLFEELEPRYPGSPYAEQAQLMLAYA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913  84 HMKKKEYVLASFYFDEYIKRFGTKDNVDYLTFLKLQSHYYAFKNHSKDQEFISNSIVSLGEFIEQYPNSRYRPYVEYM-- 161
Cdd:COG4105    79 YYKQGDYEEAIAAADRFIKLYPNSPNADYAYYLRGLSYYEQSPDSDRDQTSTRKAIEAFQELINRYPDSEYAEDAKKRid 158

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1261086913 162 QIKFILGQNELNraIANVYKKRHKPEGVKRYLERI 196
Cdd:COG4105   159 ELRDKLARKELE--VARYYLKRGAYVAAINRFQNV 191
 
Name Accession Description Interval E-value
BamD COG4105
Outer membrane protein assembly factor BamD, BamD/ComL family [Cell wall/membrane/envelope ...
 4-196 2.44e-19

Outer membrane protein assembly factor BamD, BamD/ComL family [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 443281 [Multi-domain]  Cd Length: 254  Bit Score: 83.39  E-value: 2.44e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913   4 KHFKTFLFIAMAVIVIgTGCANKKKkkDEYNKPAIFWYQGILREILFANLETADNYYSSLQSEHINSPLVPEAMLALGQA 83
Cdd:COG4105     2 KKLLKLLLLLLLALLL-AGCSSFKK--ALKSWDAEELYEEAKEALEKGDYEKAIKLFEELEPRYPGSPYAEQAQLMLAYA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913  84 HMKKKEYVLASFYFDEYIKRFGTKDNVDYLTFLKLQSHYYAFKNHSKDQEFISNSIVSLGEFIEQYPNSRYRPYVEYM-- 161
Cdd:COG4105    79 YYKQGDYEEAIAAADRFIKLYPNSPNADYAYYLRGLSYYEQSPDSDRDQTSTRKAIEAFQELINRYPDSEYAEDAKKRid 158

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1261086913 162 QIKFILGQNELNraIANVYKKRHKPEGVKRYLERI 196
Cdd:COG4105   159 ELRDKLARKELE--VARYYLKRGAYVAAINRFQNV 191
YfiO pfam13525
Outer membrane lipoprotein; This outer membrane lipoprotein carries a TPR-like region towards ...
 51-186 2.14e-14

Outer membrane lipoprotein; This outer membrane lipoprotein carries a TPR-like region towards its N-terminal. YfiO in E.coli is one of three outer membrane lipoproteins that form a multicomponent YaeT complex in the outer membrane of Gram-negative bacteria that is involved in the targeting and folding of beta-barrel outer membrane proteins. YfiO is the only essential lipoprotein component of the complex. It is required for the proper assembly and/or targeting of outer membrane proteins to the outer membrane. Through its interactions with NlpB it maintains the functional integrity of the YaeT complex.


Pssm-ID: 433282 [Multi-domain]  Cd Length: 200  Bit Score: 68.89  E-value: 2.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913  51 ANLETADNYYSSLQSEHINSPLVPEAMLALGQAHMKKKEYVLASFYFDEYIKRFGTKDNVDYLTFLKLQSHYYAFKN--- 127
Cdd:pfam13525  18 GDYGDAIKKLEALDNRYPFSPYAEQAQLDLIYAYYKDADYADALAAAERFLRLYPTHPNIDYVYYMRGLSNFAQDRDffr 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1261086913 128 HSKDQEFISNSIVSLGEFIEQYPNSRYRPYVEYM--QIKFILGQNELNraIANVYKKRHKP 186
Cdd:pfam13525  98 SDRDPESARQAFEDFATLIRKYPDSEYATDAEQRitYLRERLARHELY--IAKFYLKRGAY 156
OM_YfiO TIGR03302
outer membrane assembly lipoprotein YfiO; Members of this protein family include YfiO, a ...
 7-185 2.32e-14

outer membrane assembly lipoprotein YfiO; Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795). [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 274513 [Multi-domain]  Cd Length: 235  Bit Score: 69.50  E-value: 2.32e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913   7 KTFLFIAMAVIVIGTGCANKKKkkDEYNKPAIFWYQGILREILFA----NLETADNYYSSLQSEHINSPLVPEAMLALGQ 82
Cdd:TIGR03302   1 LLLLILLLALLLLLAGCSSKKK--KEADPVEEWPAEELYEEAKEAldsgDYTEAIKYFEALESRYPFSPYAEQAQLDLAY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913  83 AHMKKKEYVLASFYFDEYIKRFGTKDNVDYLTFLKLQSHYYAFKNHSKDQEFISNSIVSLGEFIEQYPNSRYRPYVEYM- 161
Cdd:TIGR03302  79 AYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRm 158

                         170       180
                  ....*....|....*....|....*
gi 1261086913 162 -QIKFILGQNELnrAIANVYKKRHK 185
Cdd:TIGR03302 159 dYLRNRLAGKEL--YVARFYLKRGA 181
BamD cd15830
BamD lipoprotein, a component of the beta-barrel assembly machinery; BamD, also called YfiO, ...
 52-192 1.71e-12

BamD lipoprotein, a component of the beta-barrel assembly machinery; BamD, also called YfiO, is part of the beta-barrel assembly machinery (BAM), which is essential for the folding and insertion of outer membrane proteins (OMPs) in the OM of Gram-negative bacteria. Transmembrane OMPs carry out important functions including nutrient and waste management, cell adhesion, and structural roles. The BAM complex is composed of the beta-barrel OMP BamA (also called Omp85/YaeT) and four lipoproteins BamBCDE. BamD is the only BAM lipoprotein required for viability. Both BamA and BamD are broadly distributed in Gram-negative bacteria, and may constitute the core of the BAM complex. BamD contains five Tetratricopeptide repeats (TPRs). The three TPRs at the N-terminus may participate in interaction with substrates, while the two TPRs in the C-terminus may be involved in binding with other BAM components.


Pssm-ID: 276939 [Multi-domain]  Cd Length: 213  Bit Score: 63.81  E-value: 1.71e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913  52 NLETADNYYSSLQSEHINSPLVPEAMLALGQAHMKKKEYVLASFYFDEYIKRFGTKDNVDYLTFLKLQSHYYAFKN---- 127
Cdd:cd15830    18 NYDGAIKYLEALDSRYPFGPYAEQAQLDLIYAYYKNADYELALASAERFIRLYPRHPNIDYVYYMRGLSNYKLDRSflqr 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1261086913 128 ------HSKDQEFISNSIVSLGEFIEQYPNSRYRPYVE--YMQIKFILGQNELNraIANVYKKRHKPEGV-KRY 192
Cdd:cd15830    98 ffpidrSDRDQSYAREAFQDFKDLIQRYPNSEYATDAKqrMIYLRNRLAEHELS--IARYYLKRGAYIAAiNRA 169
 
Name Accession Description Interval E-value
BamD COG4105
Outer membrane protein assembly factor BamD, BamD/ComL family [Cell wall/membrane/envelope ...
 4-196 2.44e-19

Outer membrane protein assembly factor BamD, BamD/ComL family [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 443281 [Multi-domain]  Cd Length: 254  Bit Score: 83.39  E-value: 2.44e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913   4 KHFKTFLFIAMAVIVIgTGCANKKKkkDEYNKPAIFWYQGILREILFANLETADNYYSSLQSEHINSPLVPEAMLALGQA 83
Cdd:COG4105     2 KKLLKLLLLLLLALLL-AGCSSFKK--ALKSWDAEELYEEAKEALEKGDYEKAIKLFEELEPRYPGSPYAEQAQLMLAYA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913  84 HMKKKEYVLASFYFDEYIKRFGTKDNVDYLTFLKLQSHYYAFKNHSKDQEFISNSIVSLGEFIEQYPNSRYRPYVEYM-- 161
Cdd:COG4105    79 YYKQGDYEEAIAAADRFIKLYPNSPNADYAYYLRGLSYYEQSPDSDRDQTSTRKAIEAFQELINRYPDSEYAEDAKKRid 158

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1261086913 162 QIKFILGQNELNraIANVYKKRHKPEGVKRYLERI 196
Cdd:COG4105   159 ELRDKLARKELE--VARYYLKRGAYVAAINRFQNV 191
YfiO pfam13525
Outer membrane lipoprotein; This outer membrane lipoprotein carries a TPR-like region towards ...
 51-186 2.14e-14

Outer membrane lipoprotein; This outer membrane lipoprotein carries a TPR-like region towards its N-terminal. YfiO in E.coli is one of three outer membrane lipoproteins that form a multicomponent YaeT complex in the outer membrane of Gram-negative bacteria that is involved in the targeting and folding of beta-barrel outer membrane proteins. YfiO is the only essential lipoprotein component of the complex. It is required for the proper assembly and/or targeting of outer membrane proteins to the outer membrane. Through its interactions with NlpB it maintains the functional integrity of the YaeT complex.


Pssm-ID: 433282 [Multi-domain]  Cd Length: 200  Bit Score: 68.89  E-value: 2.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913  51 ANLETADNYYSSLQSEHINSPLVPEAMLALGQAHMKKKEYVLASFYFDEYIKRFGTKDNVDYLTFLKLQSHYYAFKN--- 127
Cdd:pfam13525  18 GDYGDAIKKLEALDNRYPFSPYAEQAQLDLIYAYYKDADYADALAAAERFLRLYPTHPNIDYVYYMRGLSNFAQDRDffr 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1261086913 128 HSKDQEFISNSIVSLGEFIEQYPNSRYRPYVEYM--QIKFILGQNELNraIANVYKKRHKP 186
Cdd:pfam13525  98 SDRDPESARQAFEDFATLIRKYPDSEYATDAEQRitYLRERLARHELY--IAKFYLKRGAY 156
OM_YfiO TIGR03302
outer membrane assembly lipoprotein YfiO; Members of this protein family include YfiO, a ...
 7-185 2.32e-14

outer membrane assembly lipoprotein YfiO; Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795). [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 274513 [Multi-domain]  Cd Length: 235  Bit Score: 69.50  E-value: 2.32e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913   7 KTFLFIAMAVIVIGTGCANKKKkkDEYNKPAIFWYQGILREILFA----NLETADNYYSSLQSEHINSPLVPEAMLALGQ 82
Cdd:TIGR03302   1 LLLLILLLALLLLLAGCSSKKK--KEADPVEEWPAEELYEEAKEAldsgDYTEAIKYFEALESRYPFSPYAEQAQLDLAY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913  83 AHMKKKEYVLASFYFDEYIKRFGTKDNVDYLTFLKLQSHYYAFKNHSKDQEFISNSIVSLGEFIEQYPNSRYRPYVEYM- 161
Cdd:TIGR03302  79 AYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRm 158

                         170       180
                  ....*....|....*....|....*
gi 1261086913 162 -QIKFILGQNELnrAIANVYKKRHK 185
Cdd:TIGR03302 159 dYLRNRLAGKEL--YVARFYLKRGA 181
BamD cd15830
BamD lipoprotein, a component of the beta-barrel assembly machinery; BamD, also called YfiO, ...
 52-192 1.71e-12

BamD lipoprotein, a component of the beta-barrel assembly machinery; BamD, also called YfiO, is part of the beta-barrel assembly machinery (BAM), which is essential for the folding and insertion of outer membrane proteins (OMPs) in the OM of Gram-negative bacteria. Transmembrane OMPs carry out important functions including nutrient and waste management, cell adhesion, and structural roles. The BAM complex is composed of the beta-barrel OMP BamA (also called Omp85/YaeT) and four lipoproteins BamBCDE. BamD is the only BAM lipoprotein required for viability. Both BamA and BamD are broadly distributed in Gram-negative bacteria, and may constitute the core of the BAM complex. BamD contains five Tetratricopeptide repeats (TPRs). The three TPRs at the N-terminus may participate in interaction with substrates, while the two TPRs in the C-terminus may be involved in binding with other BAM components.


Pssm-ID: 276939 [Multi-domain]  Cd Length: 213  Bit Score: 63.81  E-value: 1.71e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913  52 NLETADNYYSSLQSEHINSPLVPEAMLALGQAHMKKKEYVLASFYFDEYIKRFGTKDNVDYLTFLKLQSHYYAFKN---- 127
Cdd:cd15830    18 NYDGAIKYLEALDSRYPFGPYAEQAQLDLIYAYYKNADYELALASAERFIRLYPRHPNIDYVYYMRGLSNYKLDRSflqr 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1261086913 128 ------HSKDQEFISNSIVSLGEFIEQYPNSRYRPYVE--YMQIKFILGQNELNraIANVYKKRHKPEGV-KRY 192
Cdd:cd15830    98 ffpidrSDRDQSYAREAFQDFKDLIQRYPNSEYATDAKqrMIYLRNRLAEHELS--IARYYLKRGAYIAAiNRA 169
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 52-154 9.62e-07

Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane constriction [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441335 [Multi-domain]  Cd Length: 113  Bit Score: 46.14  E-value: 9.62e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913  52 NLETADNYYSSLQSEHINSPLVPEAMLALGQAHMKKKEYVLASFYFDEYIKRFGTKDNV-DYLtfLKLQSHYYAFKNHSK 130
Cdd:COG1729     8 DYDEAIAAFKAFLKRYPNSPLAPDALYWLGEAYYALGDYDEAAEAFEKLLKRYPDSPKApDAL--LKLGLSYLELGDYDK 85

                          90       100
                  ....*....|....*....|....
gi 1261086913 131 dqefisnSIVSLGEFIEQYPNSRY 154
Cdd:COG1729    86 -------ARATLEELIKKYPDSEA 102
tol_pal_ybgF TIGR02795
tol-pal system protein YbgF; Members of this protein family are the product of one of seven ...
 69-152 2.16e-05

tol-pal system protein YbgF; Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.


Pssm-ID: 188247 [Multi-domain]  Cd Length: 117  Bit Score: 42.27  E-value: 2.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1261086913  69 NSPLVPEAMLALGQAHMKKKEYVLASFYFDEYIKRFGTKDNV-DYLtfLKLQSHYYAFKNHSKDQefisnsiVSLGEFIE 147
Cdd:TIGR02795  32 KSTYAPNAHYWLGEAYYAQGDYADAAKAFLAVVKKYPKSPKApDAL--LKLGMSLQELGDKEKAK-------ATLQQVIK 102


                  ....*
gi 1261086913 148 QYPNS 152
Cdd:TIGR02795 103 RYPGS 107
 
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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