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Conserved domains on  [gi|1783537879|ref|WP_156439398|]
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BMP family ABC transporter substrate-binding protein, partial [Olsenella sp. DNF00959]

Protein Classification

type 1 periplasmic-binding domain-containing protein( domain architecture ID 70)

type 1 periplasmic-binding domain-containing protein such as the ligand binding domains of the LacI family of transcriptional regulators, the ABC transporter substrate-binding proteins, the family C GPCRs, membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal LIVBP-like domains of the ionotropic glutamate receptors (iGluRs); contains the Venus flytrap-like domain which undergoes transition from an open to a closed conformational state upon ligand binding

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_type1 super family cl10011
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ...
 52-228 1.09e-34

Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins, the ligands are monosaccharides, including lactose, ribose, fructose, xylose, arabinose, galactose/glucose and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold.


The actual alignment was detected with superfamily member cd06304:

Pssm-ID: 471960  Cd Length: 262  Bit Score: 124.19  E-value: 1.09e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879  52 KVAMIMSGTITDGGWDQGHYESLKRAiESHPKWEmLEPKENTPDADAATAAQSYVDQGVDLIIGNGNQFASDWAEVVADa 131
Cdd:cd06304     1 KVALILPGPINDGGWNQAAYEGLKKA-AKELGIE-VAYSENVPPADAERVLRDYASQGYDLIIGHGFQFEDAAKEVAPE- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879 132 egNDKVHFLITNTNPTSEmadykslAKVETVLPNFKQTGALAGVVAGLMTKTNSIGFIGGMKLPSTEAKYAAYLAAAQKI 211
Cdd:cd06304    78 --FPDTKFVVISGNVTAA-------PNVASYDFKEEEGGYLAGALAALMTKTGKVGFVGGMEIPPIKRLLAGFEAGAKAV 148

                         170
                  ....*....|....*..
gi 1783537879 212 NPEIKGQYNFEAGFTDA 228
Cdd:cd06304   149 NPDAKVLVAYTGSWDDV 165
 
Name Accession Description Interval E-value
PBP1_BmpA_Med_PnrA-like cd06304
periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and ...
 52-228 1.09e-34

periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria; Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type 1 periplasmic sugar-binding protein-like fold.


Pssm-ID: 380527  Cd Length: 262  Bit Score: 124.19  E-value: 1.09e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879  52 KVAMIMSGTITDGGWDQGHYESLKRAiESHPKWEmLEPKENTPDADAATAAQSYVDQGVDLIIGNGNQFASDWAEVVADa 131
Cdd:cd06304     1 KVALILPGPINDGGWNQAAYEGLKKA-AKELGIE-VAYSENVPPADAERVLRDYASQGYDLIIGHGFQFEDAAKEVAPE- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879 132 egNDKVHFLITNTNPTSEmadykslAKVETVLPNFKQTGALAGVVAGLMTKTNSIGFIGGMKLPSTEAKYAAYLAAAQKI 211
Cdd:cd06304    78 --FPDTKFVVISGNVTAA-------PNVASYDFKEEEGGYLAGALAALMTKTGKVGFVGGMEIPPIKRLLAGFEAGAKAV 148

                         170
                  ....*....|....*..
gi 1783537879 212 NPEIKGQYNFEAGFTDA 228
Cdd:cd06304   149 NPDAKVLVAYTGSWDDV 165
Med COG1744
Lipoprotein Med, regulator of KinD/Spo0A, PBP1-ABC superfamily, includes NupN [Signal ...
 46-229 8.23e-30

Lipoprotein Med, regulator of KinD/Spo0A, PBP1-ABC superfamily, includes NupN [Signal transduction mechanisms];


Pssm-ID: 441350  Cd Length: 300  Bit Score: 112.16  E-value: 8.23e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879  46 SSEGSYKVAMIMSGTITDGGWDQGHYESLKRAiESHPKWEMLEpKENTPDADAATAAQSYVDQGVDLIIGNGNQFASDWA 125
Cdd:COG1744     1 AAAEKLKVALVYVGGIGDKSFNQAAYEGLEAA-EKELGVEVKY-VESVPEADYEPALRQLAEQGYDLIIGVGFGFADALL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879 126 EVvadAEGNDKVHFLITNTNPTSemadyksLAKVETVLPNFKQTGALAGVVAGLMTKTNSIGFIGGMKLPSTEAKYAAYL 205
Cdd:COG1744    79 KV---AKEFPDVKFAIIDGYVDG-------APNVASYFFREEEGSYLAGVLAALMTKTGKVGFVGGMPIPEVIRFINGFA 148

                         170       180
                  ....*....|....*....|....
gi 1783537879 206 AAAQKINPEIKGQYNFEAGFTDAS 229
Cdd:COG1744   149 LGAKYVNPDIKVLVVYTGSFSDPA 172
Bmp pfam02608
ABC transporter substrate-binding protein PnrA-like; Proteins containing this domain were ...
 52-228 6.78e-12

ABC transporter substrate-binding protein PnrA-like; Proteins containing this domain were originally annotated as basic membrane lipoproteins. However, several proteins containing this domain were later predicted as ABC transporter substrate-binding proteins, such as PnrA (also known as TmpC or TP0319) and RfuA (also known as Tpn38 or TP0298) from Treponema pallidum. PnrA transports purine nucleosides, while RfuA transports riboflavin. Proteins containing this domain also include Med from Bacillus subtilis. Med was annotated as a transcriptional activator protein that regulates comK. This domain can also found at the N terminus of glutamate receptor-like proteins from Dictyostelium (slime mold).


Pssm-ID: 396943  Cd Length: 302  Bit Score: 63.52  E-value: 6.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879  52 KVAMIMSGTITDGGWDQGHYESLKRAIESHPkwemLEPKENTPDADAATaaqSYV-------DQGVDLIIGNGNQFaSDW 124
Cdd:pfam02608   3 VVAVLDPGTIDDKSFNESAYEGIRRFKKEFN----IELIYKESSSLTDE---DYEsdlknlaDQGSDLIVGTGFRL-QDA 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879 125 AEVVADAegNDKVHFLITNTNPTsemADYKSLAkveTVLPNFKQTGALAGVVAGLMTKTNSIGFIGGMKLPSTEAKYAAY 204
Cdd:pfam02608  75 LILVSSD--FPKTKFLIIDAVVK---ADYQNVI---SVSFRSEEGAFLAGYAAALMSKTNKIGFVGGVESPVVKDFIYGF 146

                         170       180
                  ....*....|....*....|....
gi 1783537879 205 LAAAQKINPEIKGQYNFEAGFTDA 228
Cdd:pfam02608 147 EAGAKYVNPDIEVVVKYAGTWSDP 170
 
Name Accession Description Interval E-value
PBP1_BmpA_Med_PnrA-like cd06304
periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and ...
 52-228 1.09e-34

periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria; Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type 1 periplasmic sugar-binding protein-like fold.


Pssm-ID: 380527  Cd Length: 262  Bit Score: 124.19  E-value: 1.09e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879  52 KVAMIMSGTITDGGWDQGHYESLKRAiESHPKWEmLEPKENTPDADAATAAQSYVDQGVDLIIGNGNQFASDWAEVVADa 131
Cdd:cd06304     1 KVALILPGPINDGGWNQAAYEGLKKA-AKELGIE-VAYSENVPPADAERVLRDYASQGYDLIIGHGFQFEDAAKEVAPE- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879 132 egNDKVHFLITNTNPTSEmadykslAKVETVLPNFKQTGALAGVVAGLMTKTNSIGFIGGMKLPSTEAKYAAYLAAAQKI 211
Cdd:cd06304    78 --FPDTKFVVISGNVTAA-------PNVASYDFKEEEGGYLAGALAALMTKTGKVGFVGGMEIPPIKRLLAGFEAGAKAV 148

                         170
                  ....*....|....*..
gi 1783537879 212 NPEIKGQYNFEAGFTDA 228
Cdd:cd06304   149 NPDAKVLVAYTGSWDDV 165
Med COG1744
Lipoprotein Med, regulator of KinD/Spo0A, PBP1-ABC superfamily, includes NupN [Signal ...
 46-229 8.23e-30

Lipoprotein Med, regulator of KinD/Spo0A, PBP1-ABC superfamily, includes NupN [Signal transduction mechanisms];


Pssm-ID: 441350  Cd Length: 300  Bit Score: 112.16  E-value: 8.23e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879  46 SSEGSYKVAMIMSGTITDGGWDQGHYESLKRAiESHPKWEMLEpKENTPDADAATAAQSYVDQGVDLIIGNGNQFASDWA 125
Cdd:COG1744     1 AAAEKLKVALVYVGGIGDKSFNQAAYEGLEAA-EKELGVEVKY-VESVPEADYEPALRQLAEQGYDLIIGVGFGFADALL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879 126 EVvadAEGNDKVHFLITNTNPTSemadyksLAKVETVLPNFKQTGALAGVVAGLMTKTNSIGFIGGMKLPSTEAKYAAYL 205
Cdd:COG1744    79 KV---AKEFPDVKFAIIDGYVDG-------APNVASYFFREEEGSYLAGVLAALMTKTGKVGFVGGMPIPEVIRFINGFA 148

                         170       180
                  ....*....|....*....|....
gi 1783537879 206 AAAQKINPEIKGQYNFEAGFTDAS 229
Cdd:COG1744   149 LGAKYVNPDIKVLVVYTGSFSDPA 172
PBP1_PrnA-like cd06354
periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its ...
 52-195 8.44e-15

periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type 1 periplasmic sugar-binding protein-like fold.


Pssm-ID: 380577  Cd Length: 268  Bit Score: 71.44  E-value: 8.44e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879  52 KVAMI-MSGTITDGGWDQGHYESLKRAIESHPkwemLEPKENTPDADAATAA--QSYVDQGVDLIIGNGNQFASDwaeVV 128
Cdd:cd06354     1 KVALVtDSGGIGDKSFNQSAWEGLQRAAKELG----IKVKYLESKSDADYEPnlRALADEGYDLIITVGFAMADA---VE 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1783537879 129 ADAEGNDKVHFLITNtnptsemadykslAKVETVLPN-----FK--QTGALAGVVAGLMTKTNSIGFIGGMKLP 195
Cdd:cd06354    74 EAAKANPDTKFIIID-------------ATVDETPPNvrsivFReeEAAFLAGYLAALMTKTGKVGFIGGMDIP 134
PBP1_BMP-like cd19963
periplasmic binding component of a basic membrane lipoprotein (BMP) from Brucella abortus and ...
 52-195 1.46e-13

periplasmic binding component of a basic membrane lipoprotein (BMP) from Brucella abortus and its close homologs in other bacteria; Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type 1 periplasmic sugar-binding protein-like fold.


Pssm-ID: 380618  Cd Length: 279  Bit Score: 67.91  E-value: 1.46e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879  52 KVAMIMSGTITDGGWDQGHYESLKRAIESHPKWEMLEpKEN-TPDADAATAAQSYVDQGVDLIIGNGNQFASDWAEVvad 130
Cdd:cd19963     1 KVGFIYVGPVGDGGWTQAHDEGRLAVEKEGDKVETIY-VENvPEGADAERVIEELIAQGAKLIFGTSFGYMDPMLKV--- 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1783537879 131 AEGNDKVHFLitntnptsEMADYKSLAKVETVLPNFKQTGALAGVVAGLMTKTNSIGFIGGMKLP 195
Cdd:cd19963    77 AKKYPDVAFE--------HASGYKTAPNLGTYFGRIYEARYLAGIAAGLMTKSNKIGYVAAFPIP 133
PBP1_BMP-like cd19964
periplasmic binding component of a basic membrane lipoprotein (BMP) from Aeropyrum pernix K1 ...
 52-227 4.58e-13

periplasmic binding component of a basic membrane lipoprotein (BMP) from Aeropyrum pernix K1 and its close homologs in other bacteria; Periplasmic binding component of a family of basic membrane lipoproteins from Aeropyrum pernix K1 and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type 1 periplasmic sugar-binding protein-like fold.


Pssm-ID: 380619  Cd Length: 263  Bit Score: 66.47  E-value: 4.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879  52 KVAMIMSGTITDGGWDQGHYESLKRAIESHPkwemLEPK--ENTPDADAATAAQSYVDQGVDLIIGNGNQFAsDWAEVVA 129
Cdd:cd19964     1 KVALVTPGPLGDKSFNDSAAAGLKKLAEELG----VEIKviEAGDASKYEEQLRAAAEAGYDVIVATGDDLA-DALEKVA 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879 130 DAegNDKVHFLITNTNPTSEMADYKSLakvetvlpNFKQTGA--LAGVVAGLMTKTNSIGFIGGMKLPSTEAKYAAYLAA 207
Cdd:cd19964    76 PE--YPDQKFILLDTDIDEKLPNVASV--------SFDQNEGsyLAGVVAALMTKTGVVGFVGGMDIPVINDFLAGYEAG 145

                         170       180
                  ....*....|....*....|
gi 1783537879 208 AQKINPEIKGQYNFEAGFTD 227
Cdd:cd19964   146 AKYVNPDIKVIVSYVGSFTD 165
PBP1_Med-like cd06353
periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close ...
 52-191 3.37e-12

periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with structures of transcription regulators from the LacI family. Nevertheless, Med has significant overall sequence homology to various periplasmic substrate-binding proteins. Moreover, the structure of Med shows a striking similarity to PnrA, a periplasmic nucleoside binding protein of an ATP-binding cassette transport system. Members of this group contain the type 1 periplasmic sugar-binding protein-like fold.


Pssm-ID: 380576  Cd Length: 260  Bit Score: 63.84  E-value: 3.37e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879  52 KVAMIMSGTITDGGWDQGHYESLKrAIESHPKWEMlEPKENTPDADAATAA-QSYVDQGVDLIIGNGNQFASDWAEVvad 130
Cdd:cd06353     1 KVGLLVEGTISDQGWGSKAYKGLL-NIEEKFGVDV-EYKENIDSEEKIEEAvEELVEKGVNLIFGHGREFGEYFNEI--- 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1783537879 131 AEGNDKVHFLITNTNPTSEmadykslaKVETVLPNFKQTGALAGVVAGLMTKTNSIGFIGG 191
Cdd:cd06353    76 APDYPDVHFVSFNGEAKHD--------NVTSIHFDGYAMGYFAGMLAAHMTKTNKVGVIAA 128
Bmp pfam02608
ABC transporter substrate-binding protein PnrA-like; Proteins containing this domain were ...
 52-228 6.78e-12

ABC transporter substrate-binding protein PnrA-like; Proteins containing this domain were originally annotated as basic membrane lipoproteins. However, several proteins containing this domain were later predicted as ABC transporter substrate-binding proteins, such as PnrA (also known as TmpC or TP0319) and RfuA (also known as Tpn38 or TP0298) from Treponema pallidum. PnrA transports purine nucleosides, while RfuA transports riboflavin. Proteins containing this domain also include Med from Bacillus subtilis. Med was annotated as a transcriptional activator protein that regulates comK. This domain can also found at the N terminus of glutamate receptor-like proteins from Dictyostelium (slime mold).


Pssm-ID: 396943  Cd Length: 302  Bit Score: 63.52  E-value: 6.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879  52 KVAMIMSGTITDGGWDQGHYESLKRAIESHPkwemLEPKENTPDADAATaaqSYV-------DQGVDLIIGNGNQFaSDW 124
Cdd:pfam02608   3 VVAVLDPGTIDDKSFNESAYEGIRRFKKEFN----IELIYKESSSLTDE---DYEsdlknlaDQGSDLIVGTGFRL-QDA 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783537879 125 AEVVADAegNDKVHFLITNTNPTsemADYKSLAkveTVLPNFKQTGALAGVVAGLMTKTNSIGFIGGMKLPSTEAKYAAY 204
Cdd:pfam02608  75 LILVSSD--FPKTKFLIIDAVVK---ADYQNVI---SVSFRSEEGAFLAGYAAALMSKTNKIGFVGGVESPVVKDFIYGF 146

                         170       180
                  ....*....|....*....|....
gi 1783537879 205 LAAAQKINPEIKGQYNFEAGFTDA 228
Cdd:pfam02608 147 EAGAKYVNPDIEVVVKYAGTWSDP 170
 
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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