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Conserved domains on  [gi|2329219840|ref|WP_265451286|]
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MULTISPECIES: BMP family protein [Bacillus]

Protein Classification

BMP family lipoprotein( domain architecture ID 11448319)

BMP (basic membrane protein) family lipoprotein similar to Lactococcus cremoris ABC transporter nucleoside-binding protein BmpA and Listeria monocytogenes CD4+ T-cell-stimulating antigen; belongs to the type 1 periplasmic binding fold superfamily

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Med COG1744
Lipoprotein Med, regulator of KinD/Spo0A, PBP1-ABC superfamily, includes NupN [Signal ...
28-296 3.39e-101

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


:

Pssm-ID: 441350  Cd Length: 300  Bit Score: 299.36  E-value: 3.39e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  28 AAEKTKTIGiMLTDNGLGDQSFNDSGFQGLMKARDELGITFDYREIKDTGTYEKGLTQLVREGNDLVVGLGYSMQADLEK 107
Cdd:COG1744     1 AAAEKLKVA-LVYVGGIGDKSFNQAAYEGLEAAEKELGVEVKYVESVPEADYEPALRQLAEQGYDLIIGVGFGFADALLK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 108 VAKKYPKQRFVLIDS-VSDLDNVTSVTFKEDEGSCLAGALAAMTSKTGTIGFIGGSDADVIKRFKKGYLKGAESVKPKIR 186
Cdd:COG1744    80 VAKEFPDVKFAIIDGyVDGAPNVASYFFREEEGSYLAGVLAALMTKTGKVGFVGGMPIPEVIRFINGFALGAKYVNPDIK 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 187 VLSDISGTFDDDKLGKRIAQNMIRKKADVLFTAAGFTGVGALKEAEAQ-KVYAIGVDSDQYYTAEHAVISSLVKNVDHVI 265
Cdd:COG1744   160 VLVVYTGSFSDPAKGKEAALALIDQGADVIFQAAGGTGVGVIQAAKEAgKVYAIGVDSDQSALAPDVVLTSAVKRVDVAV 239
                         250       260       270
                  ....*....|....*....|....*....|.
gi 2329219840 266 YELAKDLKDNKeIKSGEIVYGLKENGMDLAK 296
Cdd:COG1744   240 YDAVKAVLDGT-FKGGDYVLGLKEGGVGLAP 269
 
Name Accession Description Interval E-value
Med COG1744
Lipoprotein Med, regulator of KinD/Spo0A, PBP1-ABC superfamily, includes NupN [Signal ...
28-296 3.39e-101

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


Pssm-ID: 441350  Cd Length: 300  Bit Score: 299.36  E-value: 3.39e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  28 AAEKTKTIGiMLTDNGLGDQSFNDSGFQGLMKARDELGITFDYREIKDTGTYEKGLTQLVREGNDLVVGLGYSMQADLEK 107
Cdd:COG1744     1 AAAEKLKVA-LVYVGGIGDKSFNQAAYEGLEAAEKELGVEVKYVESVPEADYEPALRQLAEQGYDLIIGVGFGFADALLK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 108 VAKKYPKQRFVLIDS-VSDLDNVTSVTFKEDEGSCLAGALAAMTSKTGTIGFIGGSDADVIKRFKKGYLKGAESVKPKIR 186
Cdd:COG1744    80 VAKEFPDVKFAIIDGyVDGAPNVASYFFREEEGSYLAGVLAALMTKTGKVGFVGGMPIPEVIRFINGFALGAKYVNPDIK 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 187 VLSDISGTFDDDKLGKRIAQNMIRKKADVLFTAAGFTGVGALKEAEAQ-KVYAIGVDSDQYYTAEHAVISSLVKNVDHVI 265
Cdd:COG1744   160 VLVVYTGSFSDPAKGKEAALALIDQGADVIFQAAGGTGVGVIQAAKEAgKVYAIGVDSDQSALAPDVVLTSAVKRVDVAV 239
                         250       260       270
                  ....*....|....*....|....*....|.
gi 2329219840 266 YELAKDLKDNKeIKSGEIVYGLKENGMDLAK 296
Cdd:COG1744   240 YDAVKAVLDGT-FKGGDYVLGLKEGGVGLAP 269
PBP1_PrnA-like cd06354
periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its ...
37-295 2.00e-98

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: 291.01  E-value: 2.00e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  37 IMLTDNG-LGDQSFNDSGFQGLMKARDELGITFDYREIKDTGTYEKGLTQLVREGNDLVVGLGYSMQADLEKVAKKYPKQ 115
Cdd:cd06354     3 ALVTDSGgIGDKSFNQSAWEGLQRAAKELGIKVKYLESKSDADYEPNLRALADEGYDLIITVGFAMADAVEEAAKANPDT 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 116 RFVLIDSVSD--LDNVTSVTFKEDEGSCLAGALAAMTSKTGTIGFIGGSDADVIKRFKKGYLKGAESVKPKIRVLSDISG 193
Cdd:cd06354    83 KFIIIDATVDetPPNVRSIVFREEEAAFLAGYLAALMTKTGKVGFIGGMDIPPVRRFEDGFAAGAKYANPDIVVDVTVIG 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 194 T----FDDDKLGKRIAQNMIRKKADVLFTAAGFTGVGALKEAEAQKVYAIGVDSDQYYTAEHAVISSLVKNVDHVIYELA 269
Cdd:cd06354   163 TyagsFNDPAKGKAIAQEMIDQGADVIFAAAGGTGLGVIEAAKEAGKYAIGVDVDQNYLAPGNVLTSVVKRVDVAVYDAI 242
                         250       260
                  ....*....|....*....|....*.
gi 2329219840 270 KDLKDNKEiKSGEIVYGLKENGMDLA 295
Cdd:cd06354   243 KDLVNGKF-GGGVIVLGLAEGGVGLA 267
Bmp pfam02608
ABC transporter substrate-binding protein PnrA-like; Proteins containing this domain were ...
33-291 1.13e-58

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: 190.64  E-value: 1.13e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  33 KTIGIMLTDNGLGDQSFNDSGFQGLMKARDELGITFDYREI--KDTGTYEKGLTQLVREGNDLVVGLGYSMQADLEKVAK 110
Cdd:pfam02608   1 KVVVAVLDPGTIDDKSFNESAYEGIRRFKKEFNIELIYKESssLTDEDYESDLKNLADQGSDLIVGTGFRLQDALILVSS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 111 KYPKQRFVLIDSV--SDLDNVTSVTFKEDEGSCLAGALAAMTSKTGTIGFIGGSDADVIKRFKKGYLKGAESVKPKIRVL 188
Cdd:pfam02608  81 DFPKTKFLIIDAVvkADYQNVISVSFRSEEGAFLAGYAAALMSKTNKIGFVGGVESPVVKDFIYGFEAGAKYVNPDIEVV 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 189 SDISGTFDDDKLGKRIAQNMIRKKADVLFTAAGFTGVGALKEAEAQKV--YAIGVDSDQYYTAEHAVISSLVKNVDHVIY 266
Cdd:pfam02608 161 VKYAGTWSDPAKGKSLASSMYKEGVDVIFPAAGGAGIGVIQAAKELGLyyYVIGVDQDQSYLAPENVITSSVKNVGDAYY 240
                         250       260
                  ....*....|....*....|....*.
gi 2329219840 267 ELA-KDLKDNKEIKSGEIVYGLKENG 291
Cdd:pfam02608 241 SITsKVAKGGVFPGGESITYGLKDGV 266
 
Name Accession Description Interval E-value
Med COG1744
Lipoprotein Med, regulator of KinD/Spo0A, PBP1-ABC superfamily, includes NupN [Signal ...
28-296 3.39e-101

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


Pssm-ID: 441350  Cd Length: 300  Bit Score: 299.36  E-value: 3.39e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  28 AAEKTKTIGiMLTDNGLGDQSFNDSGFQGLMKARDELGITFDYREIKDTGTYEKGLTQLVREGNDLVVGLGYSMQADLEK 107
Cdd:COG1744     1 AAAEKLKVA-LVYVGGIGDKSFNQAAYEGLEAAEKELGVEVKYVESVPEADYEPALRQLAEQGYDLIIGVGFGFADALLK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 108 VAKKYPKQRFVLIDS-VSDLDNVTSVTFKEDEGSCLAGALAAMTSKTGTIGFIGGSDADVIKRFKKGYLKGAESVKPKIR 186
Cdd:COG1744    80 VAKEFPDVKFAIIDGyVDGAPNVASYFFREEEGSYLAGVLAALMTKTGKVGFVGGMPIPEVIRFINGFALGAKYVNPDIK 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 187 VLSDISGTFDDDKLGKRIAQNMIRKKADVLFTAAGFTGVGALKEAEAQ-KVYAIGVDSDQYYTAEHAVISSLVKNVDHVI 265
Cdd:COG1744   160 VLVVYTGSFSDPAKGKEAALALIDQGADVIFQAAGGTGVGVIQAAKEAgKVYAIGVDSDQSALAPDVVLTSAVKRVDVAV 239
                         250       260       270
                  ....*....|....*....|....*....|.
gi 2329219840 266 YELAKDLKDNKeIKSGEIVYGLKENGMDLAK 296
Cdd:COG1744   240 YDAVKAVLDGT-FKGGDYVLGLKEGGVGLAP 269
PBP1_PrnA-like cd06354
periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its ...
37-295 2.00e-98

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: 291.01  E-value: 2.00e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  37 IMLTDNG-LGDQSFNDSGFQGLMKARDELGITFDYREIKDTGTYEKGLTQLVREGNDLVVGLGYSMQADLEKVAKKYPKQ 115
Cdd:cd06354     3 ALVTDSGgIGDKSFNQSAWEGLQRAAKELGIKVKYLESKSDADYEPNLRALADEGYDLIITVGFAMADAVEEAAKANPDT 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 116 RFVLIDSVSD--LDNVTSVTFKEDEGSCLAGALAAMTSKTGTIGFIGGSDADVIKRFKKGYLKGAESVKPKIRVLSDISG 193
Cdd:cd06354    83 KFIIIDATVDetPPNVRSIVFREEEAAFLAGYLAALMTKTGKVGFIGGMDIPPVRRFEDGFAAGAKYANPDIVVDVTVIG 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 194 T----FDDDKLGKRIAQNMIRKKADVLFTAAGFTGVGALKEAEAQKVYAIGVDSDQYYTAEHAVISSLVKNVDHVIYELA 269
Cdd:cd06354   163 TyagsFNDPAKGKAIAQEMIDQGADVIFAAAGGTGLGVIEAAKEAGKYAIGVDVDQNYLAPGNVLTSVVKRVDVAVYDAI 242
                         250       260
                  ....*....|....*....|....*.
gi 2329219840 270 KDLKDNKEiKSGEIVYGLKENGMDLA 295
Cdd:cd06354   243 KDLVNGKF-GGGVIVLGLAEGGVGLA 267
PBP1_BMP-like cd19964
periplasmic binding component of a basic membrane lipoprotein (BMP) from Aeropyrum pernix K1 ...
38-295 3.23e-84

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: 254.83  E-value: 3.23e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  38 MLTDNGLGDQSFNDSGFQGLMKARDELGITFDYREIKDTGTYEKGLTQLVREGNDLVVGLGYSMQADLEKVAKKYPKQRF 117
Cdd:cd19964     4 LVTPGPLGDKSFNDSAAAGLKKLAEELGVEIKVIEAGDASKYEEQLRAAAEAGYDVIVATGDDLADALEKVAPEYPDQKF 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 118 VLIDSV--SDLDNVTSVTFKEDEGSCLAGALAAMTSKTGTIGFIGGSDADVIKRFKKGYLKGAESVKPKIRVLSDISGTF 195
Cdd:cd19964    84 ILLDTDidEKLPNVASVSFDQNEGSYLAGVVAALMTKTGVVGFVGGMDIPVINDFLAGYEAGAKYVNPDIKVIVSYVGSF 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 196 DDDKLGKRIAQNMIRKKADVLFTAAGFTGVGALKEAEAQKVYAIGVDSDQYYTAEHAVISSLVKNVDHVIYELAKDLKDN 275
Cdd:cd19964   164 TDPAKGKELALALYNQGADVIFQVAGGSGLGVIEAAAEAGKYAIGVDSDQNDIYPGVILTSALKDVDNAVYDAVKDVLDG 243
                         250       260
                  ....*....|....*....|
gi 2329219840 276 KEiKSGEIVYGLKENGMDLA 295
Cdd:cd19964   244 TF-KGGVVSLGLKEGGVGLA 262
PBP1_BmpA_Med_PnrA-like cd06304
periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and ...
35-295 4.12e-81

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: 246.68  E-value: 4.12e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  35 IGIMLTDNGlGDQSFNDSGFQGLMKARDELGITFDYREIKDTGTYEKGLTQLVREGNDLVVGLGYSMQADLEKVAKKYPK 114
Cdd:cd06304     2 VALILPGPI-NDGGWNQAAYEGLKKAAKELGIEVAYSENVPPADAERVLRDYASQGYDLIIGHGFQFEDAAKEVAPEFPD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 115 QRFVLIDS-VSDLDNVTSVTFKEDEGSCLAGALAAMTSKTGTIGFIGGSDADVIKRFKKGYLKGAESVKPKIRVLSDISG 193
Cdd:cd06304    81 TKFVVISGnVTAAPNVASYDFKEEEGGYLAGALAALMTKTGKVGFVGGMEIPPIKRLLAGFEAGAKAVNPDAKVLVAYTG 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 194 TFDDDKLGKRIAQNMIRKKADVLFTAAGFTGVGALKEAEAQKVYAIGVDSDQYYTAEHAVISSLVKNVDHVIYELAKDLK 273
Cdd:cd06304   161 SWDDVAKAKEAALAMIAQGADVIFGAANAAGLGVIEAAKEKGVYAIGNVSDQNSLAPDTVVTSVVWDMDPAIYAAVKDVK 240
                         250       260
                  ....*....|....*....|..
gi 2329219840 274 DNKEiKSGEIVYGLKENGMDLA 295
Cdd:cd06304   241 AGTF-GGGVYEYGLKEGGVGLA 261
Bmp pfam02608
ABC transporter substrate-binding protein PnrA-like; Proteins containing this domain were ...
33-291 1.13e-58

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: 190.64  E-value: 1.13e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  33 KTIGIMLTDNGLGDQSFNDSGFQGLMKARDELGITFDYREI--KDTGTYEKGLTQLVREGNDLVVGLGYSMQADLEKVAK 110
Cdd:pfam02608   1 KVVVAVLDPGTIDDKSFNESAYEGIRRFKKEFNIELIYKESssLTDEDYESDLKNLADQGSDLIVGTGFRLQDALILVSS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 111 KYPKQRFVLIDSV--SDLDNVTSVTFKEDEGSCLAGALAAMTSKTGTIGFIGGSDADVIKRFKKGYLKGAESVKPKIRVL 188
Cdd:pfam02608  81 DFPKTKFLIIDAVvkADYQNVISVSFRSEEGAFLAGYAAALMSKTNKIGFVGGVESPVVKDFIYGFEAGAKYVNPDIEVV 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 189 SDISGTFDDDKLGKRIAQNMIRKKADVLFTAAGFTGVGALKEAEAQKV--YAIGVDSDQYYTAEHAVISSLVKNVDHVIY 266
Cdd:pfam02608 161 VKYAGTWSDPAKGKSLASSMYKEGVDVIFPAAGGAGIGVIQAAKELGLyyYVIGVDQDQSYLAPENVITSSVKNVGDAYY 240
                         250       260
                  ....*....|....*....|....*.
gi 2329219840 267 ELA-KDLKDNKEIKSGEIVYGLKENG 291
Cdd:pfam02608 241 SITsKVAKGGVFPGGESITYGLKDGV 266
PBP1_Med-like cd06353
periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close ...
35-296 2.21e-40

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: 142.03  E-value: 2.21e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  35 IGIMLTDNgLGDQSFNDSGFQGLMKARDELGITFDYREIKDTGT-YEKGLTQLVREGNDLVVGLGYSMQADLEKVAKKYP 113
Cdd:cd06353     2 VGLLVEGT-ISDQGWGSKAYKGLLNIEEKFGVDVEYKENIDSEEkIEEAVEELVEKGVNLIFGHGREFGEYFNEIAPDYP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 114 KQRFVLIDSVSDLDNVTSVTFKEDEGSCLAGALAAMTSKTGTIGFIggsDADVIKRFKKGYLKGAESVKPKIRVLSDISG 193
Cdd:cd06353    81 DVHFVSFNGEAKHDNVTSIHFDGYAMGYFAGMLAAHMTKTNKVGVI---AAFPWQPEVEGFEEGVKYVSPEAKVLVRFVN 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 194 TFDDDKLGKRIAQNMIRKKADVLFTAA-GFTgVGALKEAEAQKVYAIGVDSDQYYTAEHAVISSLVKNVDHvIYELAKDL 272
Cdd:cd06353   158 DWDDGEKAMELAQELISQGVDVVYPAGdGFN-VEVIEQAKEDGLYAIGYIDDQSYIGPNTVLTSTVQDVPQ-LYEAIANQ 235
                         250       260
                  ....*....|....*....|....
gi 2329219840 273 KDNKEIKSGEIVYGLKENGMDLAK 296
Cdd:cd06353   236 FNEGELTPGNITYDFNDGVVSLGP 259
PBP1_ABC_RfuA-like cd19962
periplasmic riboflavin-binding component (RfuA) of ABC transporter (RfuABCD) from Treponema ...
35-289 2.38e-34

periplasmic riboflavin-binding component (RfuA) of ABC transporter (RfuABCD) from Treponema pallidum and its close homologs in other bacteria; This group includes the basic membrane lipoprotein (BMP) family ABC transporter substrate-binding protein RfuA from Treponema pallidum and its close homologs in other bacteria. RfuA is the riboflavin-binding component of ABC transporter (RfuABCD) in spirochetes. The members of this group are highly similar to that of the periplasmic binding domain of basic membrane lipoprotein (BMP), PnrA. 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. PnrA-like proteins are likely to have similar nucleoside-binding functions and a similar type 1 periplasmic sugar-binding protein-like fold.


Pssm-ID: 380617  Cd Length: 305  Bit Score: 127.25  E-value: 2.38e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  35 IGIMLTDNgLGDQSFNDSGFQGLMKARDELGITFDYREIKDTGT-YEKGLTQLVREGN-DLVVGLGYSMQADLEKVAKKY 112
Cdd:cd19962     2 VAVFVPGN-VGDSPYYEMLVLGVTRAAEKYGLSLQVIEAGNNPAkWAPTLDDLAATGGyDLIVSSNPQLPELVEQAARQF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 113 PKQRFVLIDSVSDL--DNVTSVTFKEDEGSCLAGALAAMTSKTGT--------IGFIGGSD-ADVIKRFKKGYLKGAESV 181
Cdd:cd19962    81 PEQKFLLLDAYYDGgcENVYSITYRQTEQAYLAGYLAGLVTKSAGeranadkrIGLLAGQDyPVMTQEIRPGYLAGARAV 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 182 KPKIRVLSDISGTFDDDKLGKRIAQNMIRKKADVLFTAAGFTGVGALKEAEAQKVYAIGVDSDQYYTAEHAVISSLVKNV 261
Cdd:cd19962   161 DPQIEVDFRVVGSWYDPAKGKDLAAGMFDQGVDIILTIAGGTNQGVIEAAAAGNAYVIGNDSNGYDRAPGLIVGSTLETQ 240
                         250       260
                  ....*....|....*....|....*....
gi 2329219840 262 DHVIYELA-KDLKDNKEIKSGEIVyGLKE 289
Cdd:cd19962   241 ETAAYEETlRLISGELLVGSTRSL-GVKE 268
PBP1_BMP-like cd19963
periplasmic binding component of a basic membrane lipoprotein (BMP) from Brucella abortus and ...
45-297 3.46e-29

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: 112.98  E-value: 3.46e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  45 GDQSFNDSGFQGLMKARDE-LGITFDYRE-IKDTGTYEKGLTQLVREGNDLVVGLGYSMQADLEKVAKKYPKQRFVLIDS 122
Cdd:cd19963    11 GDGGWTQAHDEGRLAVEKEgDKVETIYVEnVPEGADAERVIEELIAQGAKLIFGTSFGYMDPMLKVAKKYPDVAFEHASG 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 123 VSDLDNVTSVTFKEDEGSCLAGALAAMTSKTGTIGFIGG-SDADVIkRFKKGYLKGAESVKPKIRVLSDISGTFDDDKLG 201
Cdd:cd19963    91 YKTAPNLGTYFGRIYEARYLAGIAAGLMTKSNKIGYVAAfPIPEVI-RGINAFALGARSVNPDATVKVVWTNSWFDPAKE 169
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 202 KRIAQNMIRKKADVLFTAAGFTGVgaLKEAEAQKVYAIGVDSDQYYTAEHAVISSLVKNVDHVIYELAKDLKDNKEiKSG 281
Cdd:cd19963   170 REAANALIDQGADVITQHQDSPAV--VQVAEERGVYSIGYNSDMSKFAPKAYLTSVVWNWGPYYTDIVKAVLDGTW-KPG 246
                         250
                  ....*....|....*.
gi 2329219840 282 EIVYGLKENGMDLAKI 297
Cdd:cd19963   247 DYWGGLKEGAVDLAPL 262
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
2-245 1.06e-10

ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH domain [Carbohydrate transport and metabolism];


Pssm-ID: 441483 [Multi-domain]  Cd Length: 307  Bit Score: 61.48  E-value: 1.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840   2 RKMAIFAAVLLIALSTAGCAGRSEETAAEKTKTIGIMLTDNGLGDqSFNDSGFQGLMKARDELGITFDYREIK-DTGTYE 80
Cdd:COG1879     1 KRLALLAAVLALALALAACGSAAAEAAAAAAKGKTIGFVVKTLGN-PFFVAVRKGAEAAAKELGVELIVVDAEgDAAKQI 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  81 KGLTQLVREGNDLVVGLGYSMQAdLEKVAKKYpKQR---FVLIDS-VSDLDNVTSVTFKEDEGSCLAG-ALAAMTSKTGT 155
Cdd:COG1879    80 SQIEDLIAQGVDAIIVSPVDPDA-LAPALKKA-KAAgipVVTVDSdVDGSDRVAYVGSDNYAAGRLAAeYLAKALGGKGK 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 156 IGFIGGS-DADVIKRFKKGYLKGAESvKPKIRVLSDISGTFDDDKlGKRIAQNMIRK--KADVLFTAAGFTGVGALKEAE 232
Cdd:COG1879   158 VAILTGSpGAPAANERTDGFKEALKE-YPGIKVVAEQYADWDREK-ALEVMEDLLQAhpDIDGIFAANDGMALGAAQALK 235
                         250
                  ....*....|....*..
gi 2329219840 233 A----QKVYAIGVDSDQ 245
Cdd:COG1879   236 AagrkGDVKVVGFDGSP 252
Periplasmic_Binding_Protein_type1 cd01391
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ...
35-278 2.41e-10

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.


Pssm-ID: 380477 [Multi-domain]  Cd Length: 280  Bit Score: 60.36  E-value: 2.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840  35 IGIMLTDNGLGDQSFNDSGFQGLMKARDELGITFDYREI-KDTGTYEKGLTQLVREGNDLVVGLGYSMQADLEKVAKKYP 113
Cdd:cd01391     2 IGVVTSSLHQIREQFGIQRVEAIFHTADKLGASVEIRDScWHGSVALEQSIEFIRDNIAGVIGPGSSSVAIVIQNLAQLF 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 114 KQRFVLIDSVSDLDN-------VTSVTFKEDEGSCLAGALAAMTSKTgTIGFIGGSDADVIKRFKKGYLKGAESVKPKIr 186
Cdd:cd01391    82 DIPQLALDATSQDLSdktlykyFLSVVFSDTLGARLGLDIVKRKNWT-YVAAIHGEGLNSGELRMAGFKELAKQEGICI- 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2329219840 187 VLSDISGTFDDDKlGKRIAQNMIRK--KADVLFTAAGFTGVGALKEAE----AQKVYAIGVDSDQ-----YYTAEHAVIS 255
Cdd:cd01391   160 VASDKADWNAGEK-GFDRALRKLREglKARVIVCANDMTARGVLSAMRrlglVGDVSVIGSDGWAdrdevGYEVEANGLT 238
                         250       260
                  ....*....|....*....|....*..
gi 2329219840 256 SLVKNVD----HVIYELAKDLKDNKEI 278
Cdd:cd01391   239 TIKQQKMgfgiTAIKAMADGSQNMHEE 265
 
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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