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Conserved domains on  [gi|2181016855|ref|WP_235062693|]
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ABC transporter permease [Mycobacterium avium]

Protein Classification

ABC transporter permease( domain architecture ID 11427312)

ABC transporter permease similar to ABC oligopeptide transporter permease proteins (OppB, AppB, and AmiC), the transmembrane subunits (TM) found in periplasmic binding protein (PBP)-dependent ATP-binding cassette (ABC) transporters which generally bind type 2 PBPs

Gene Ontology:  GO:0055085
PubMed:  18535149|17723295
TCDB:  3.A.1

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DppB super family cl33970
ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Amino acid ...
 1-153 5.89e-39

ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Amino acid transport and metabolism, Inorganic ion transport and metabolism];


The actual alignment was detected with superfamily member COG0601:

Pssm-ID: 440366 [Multi-domain]  Cd Length: 314  Bit Score: 134.42  E-value: 5.89e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855   1 MLQVFSVQLGLislFPDGSVTSLLVAALVLAV-----------PVSAPIAQVLGKNIDATLALPHVNTARAKGGTPGWVI 69
Cdd:COG0601   151 LILLFAVKLGW---LPVSGRVSPWEDFLDALRhlilpaltlalGSLAGIARLTRSSMLEVLGQDYVRTARAKGLSERRVL 227

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  70 RKHVVKNAAGPALTVTATTVGALLGGSVVTETVFSRSGVGAVLLQAVSSQDISLIQGLVLLTAVAIVTANLAVDLIHPLL 149
Cdd:COG0601   228 LRHALRNALIPVVTVLGLQLGGLLGGAVVVETVFSWPGLGRLLVDAILNRDYPVVQGIVLLIAVLVVLVNLLVDLLYALL 307


                  ....
gi 2181016855 150 DPRV 153
Cdd:COG0601   308 DPRI 311
 
Name Accession Description Interval E-value
DppB COG0601
ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Amino acid ...
 1-153 5.89e-39

ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Amino acid transport and metabolism, Inorganic ion transport and metabolism];


Pssm-ID: 440366 [Multi-domain]  Cd Length: 314  Bit Score: 134.42  E-value: 5.89e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855   1 MLQVFSVQLGLislFPDGSVTSLLVAALVLAV-----------PVSAPIAQVLGKNIDATLALPHVNTARAKGGTPGWVI 69
Cdd:COG0601   151 LILLFAVKLGW---LPVSGRVSPWEDFLDALRhlilpaltlalGSLAGIARLTRSSMLEVLGQDYVRTARAKGLSERRVL 227

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  70 RKHVVKNAAGPALTVTATTVGALLGGSVVTETVFSRSGVGAVLLQAVSSQDISLIQGLVLLTAVAIVTANLAVDLIHPLL 149
Cdd:COG0601   228 LRHALRNALIPVVTVLGLQLGGLLGGAVVVETVFSWPGLGRLLVDAILNRDYPVVQGIVLLIAVLVVLVNLLVDLLYALL 307


                  ....
gi 2181016855 150 DPRV 153
Cdd:COG0601   308 DPRI 311
PRK15081 PRK15081
glutathione ABC transporter permease GsiC; Provisional
 1-151 1.85e-21

glutathione ABC transporter permease GsiC; Provisional


Pssm-ID: 185039 [Multi-domain]  Cd Length: 306  Bit Score: 88.23  E-value: 1.85e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855   1 MLQVFSVQLGLISLFPDGSVTSLLVAALVLAVPVSAPIAQVLGKNIDATLALPHVNTARAKGGTPGWVIRKHVVKNAAGP 80
Cdd:PRK15081  151 LMQVFSVELGWLPTVGADSWQHYILPSLTLGAAVAAVMARFTRASFVEVLSEDYMRTARAKGVSETWVVLKHGLRNAMIP 230

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2181016855  81 ALTVTATTVGALLGGSVVTETVFSRSGVGAVLLQAVSSQDISLIQGLVLLTAVAIVTANLAVDLIHPLLDP 151
Cdd:PRK15081  231 VVTMMGLQFGFLLGGSIVVEKVFNWPGLGRLLVDSVEMRDYPVIQAEVLLFSLEFILINLVVDVLYAAINP 301
BPD_transp_1 pfam00528
Binding-protein-dependent transport system inner membrane component; The alignments cover the ...
 35-155 3.26e-16

Binding-protein-dependent transport system inner membrane component; The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have a variable number of transmembrane helices.


Pssm-ID: 334128 [Multi-domain]  Cd Length: 183  Bit Score: 71.95  E-value: 3.26e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  35 SAPIAQVLGKNIDATLALPHVNTARAKGGTPGWVIRKHVVKNAAGPALTVTATTVGALLGGSVVTETVFSRSGVGAVLLQ 114
Cdd:pfam00528  63 WAGYARLIRRAALRSLPSDLVEAARALGASRWQIFRKIILPNALPPILTGLALAFGGALGGAVLLEFLGSWPGLGLLLIE 142

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2181016855 115 AVSSQDISLIQGLVLLTAVAIVTANLAVDLIHPLLDPRVTR 155
Cdd:pfam00528 143 AILGYDYPEIQGPVLAAALILLLLNLLVDILQRLLDPRVRK 183
TM_PBP2 cd06261
Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding ...
 54-144 1.64e-03

Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. For these transporters the ABCs and TMs are on independent polypeptide chains. These systems transport a diverse range of substrates. Most are specific for a single substrate or a group of related substrates; however some transporters are more promiscuous, transporting structurally diverse substrates such as the histidine/lysine and arginine transporter in Enterobacteriaceae. In the latter case, this is achieved through binding different PBPs with different specificities to the TMs. For other promiscuous transporters such as the multiple-sugar transporter Msm of Streptococcus mutans, the PBP has a wide substrate specificity. These transporters include the maltose-maltodextrin, phosphate and sulfate transporters, among others.


Pssm-ID: 119394 [Multi-domain]  Cd Length: 190  Bit Score: 37.26  E-value: 1.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  54 HVNTARAKGGTPGWVIRKHVVKNAAGPALTVTATTVGALLGGSVVTETVFSRSGVGAVLLqavSSQDISLIQGLVLLTAV 133
Cdd:cd06261   103 LVEAARALGASPWQIFRRIILPLALPPILTGLVLAFARALGEFALVSFLGGGEAPGPGTG---LLLIFAILFPGDLGVAA 179

                          90
                  ....*....|.
gi 2181016855 134 AIVTANLAVDL 144
Cdd:cd06261   180 AVALILLLLSL 190
 
Name Accession Description Interval E-value
DppB COG0601
ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Amino acid ...
 1-153 5.89e-39

ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Amino acid transport and metabolism, Inorganic ion transport and metabolism];


Pssm-ID: 440366 [Multi-domain]  Cd Length: 314  Bit Score: 134.42  E-value: 5.89e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855   1 MLQVFSVQLGLislFPDGSVTSLLVAALVLAV-----------PVSAPIAQVLGKNIDATLALPHVNTARAKGGTPGWVI 69
Cdd:COG0601   151 LILLFAVKLGW---LPVSGRVSPWEDFLDALRhlilpaltlalGSLAGIARLTRSSMLEVLGQDYVRTARAKGLSERRVL 227

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  70 RKHVVKNAAGPALTVTATTVGALLGGSVVTETVFSRSGVGAVLLQAVSSQDISLIQGLVLLTAVAIVTANLAVDLIHPLL 149
Cdd:COG0601   228 LRHALRNALIPVVTVLGLQLGGLLGGAVVVETVFSWPGLGRLLVDAILNRDYPVVQGIVLLIAVLVVLVNLLVDLLYALL 307


                  ....
gi 2181016855 150 DPRV 153
Cdd:COG0601   308 DPRI 311
PRK15081 PRK15081
glutathione ABC transporter permease GsiC; Provisional
 1-151 1.85e-21

glutathione ABC transporter permease GsiC; Provisional


Pssm-ID: 185039 [Multi-domain]  Cd Length: 306  Bit Score: 88.23  E-value: 1.85e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855   1 MLQVFSVQLGLISLFPDGSVTSLLVAALVLAVPVSAPIAQVLGKNIDATLALPHVNTARAKGGTPGWVIRKHVVKNAAGP 80
Cdd:PRK15081  151 LMQVFSVELGWLPTVGADSWQHYILPSLTLGAAVAAVMARFTRASFVEVLSEDYMRTARAKGVSETWVVLKHGLRNAMIP 230

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2181016855  81 ALTVTATTVGALLGGSVVTETVFSRSGVGAVLLQAVSSQDISLIQGLVLLTAVAIVTANLAVDLIHPLLDP 151
Cdd:PRK15081  231 VVTMMGLQFGFLLGGSIVVEKVFNWPGLGRLLVDSVEMRDYPVIQAEVLLFSLEFILINLVVDVLYAAINP 301
PRK10352 PRK10352
nickel transporter permease NikB; Provisional
 54-155 5.01e-18

nickel transporter permease NikB; Provisional


Pssm-ID: 182400 [Multi-domain]  Cd Length: 314  Bit Score: 78.97  E-value: 5.01e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  54 HVNTARAKGGTPGWVIRKHVVKNAAGPALTVTATTVGALLGGSVVTETVFSRSGVGAVLLQAVSSQDISLIQGLVLLTAV 133
Cdd:PRK10352  207 HVTWARLRGLSERQVERRHILRNASLPMITAVGMHIGELIGGTMIIENIFAWPGVGRYAVSAIFNRDYPVIQCFTLMMVV 286

                          90       100
                  ....*....|....*....|..
gi 2181016855 134 AIVTANLAVDLIHPLLDPRVTR 155
Cdd:PRK10352  287 VFVVCNLIVDLLNAALDPRIRR 308
PRK10914 PRK10914
dipeptide ABC transporter permease DppB;
54-153 6.33e-18

dipeptide ABC transporter permease DppB;


Pssm-ID: 182834 [Multi-domain]  Cd Length: 339  Bit Score: 79.09  E-value: 6.33e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  54 HVNTARAKGGTPGWVIRKHVVKNAAGPALTVTATTVGALLGGSVVTETVFSRSGVGAVLLQAVSSQDISLIQGLVLLTAV 133
Cdd:PRK10914  236 YIRTARAKGLTRMRVIIVHALRNAMLPVVTVIGLQVGTLLAGAILTETIFSWPGLGRWLIDALQRRDYPVVQGGVLLVAT 315

                          90       100
                  ....*....|....*....|
gi 2181016855 134 AIVTANLAVDLIHPLLDPRV 153
Cdd:PRK10914  316 MIILVNLLVDLLYGVVNPRI 335
BPD_transp_1 pfam00528
Binding-protein-dependent transport system inner membrane component; The alignments cover the ...
 35-155 3.26e-16

Binding-protein-dependent transport system inner membrane component; The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have a variable number of transmembrane helices.


Pssm-ID: 334128 [Multi-domain]  Cd Length: 183  Bit Score: 71.95  E-value: 3.26e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  35 SAPIAQVLGKNIDATLALPHVNTARAKGGTPGWVIRKHVVKNAAGPALTVTATTVGALLGGSVVTETVFSRSGVGAVLLQ 114
Cdd:pfam00528  63 WAGYARLIRRAALRSLPSDLVEAARALGASRWQIFRKIILPNALPPILTGLALAFGGALGGAVLLEFLGSWPGLGLLLIE 142

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2181016855 115 AVSSQDISLIQGLVLLTAVAIVTANLAVDLIHPLLDPRVTR 155
Cdd:pfam00528 143 AILGYDYPEIQGPVLAAALILLLLNLLVDILQRLLDPRVRK 183
oppB PRK09471
oligopeptide ABC transporter permease OppB;
36-153 8.70e-10

oligopeptide ABC transporter permease OppB;


Pssm-ID: 181886 [Multi-domain]  Cd Length: 306  Bit Score: 55.84  E-value: 8.70e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  36 APIAQVLGKNIDATLALPHVNTARAKGGTPGWVIRKHVVKNAAGPALTVTATTVGALLGGSVVTETVFSRSGVGAVLLQA 115
Cdd:PRK09471  187 ASIARITRGSMIEVLHSNFIRTARAKGLPMRRIILRHALKPALLPVLSYMGPAFVGIITGSMVIETIFGLPGIGQLFVNG 266

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2181016855 116 VSSQDISLIQGLVLLTAVAIVTANLAVDLIHPLLDPRV 153
Cdd:PRK09471  267 ALNRDYSLVLSLTILVGALTILFNAIVDVLYAVIDPKI 304
PRK15133 PRK15133
microcin C ABC transporter permease YejB; Provisional
 54-153 7.62e-06

microcin C ABC transporter permease YejB; Provisional


Pssm-ID: 185087 [Multi-domain]  Cd Length: 364  Bit Score: 44.74  E-value: 7.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  54 HVNTARAKGGTPGWVIRKHVVKNA-----AGpaltVTATTVGALLGGSVVTETVFSRSGVGAVLLQAVSSQDISLIQG-L 127
Cdd:PRK15133  259 YVVTARAKGVSEKNILWKHVFRNAmllviAG----FPATFISMFFTGSLLIEVMFSLNGLGLLGYEATVSRDYPVMFGtL 334

                          90       100
                  ....*....|....*....|....*.
gi 2181016855 128 VLLTAVAIVTaNLAVDLIHPLLDPRV 153
Cdd:PRK15133  335 YIFTLIGLLL-NIVSDISYTLVDPRI 359
PRK15110 PRK15110
peptide ABC transporter permease SapB;
68-151 3.63e-05

peptide ABC transporter permease SapB;


Pssm-ID: 185065 [Multi-domain]  Cd Length: 321  Bit Score: 42.75  E-value: 3.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  68 VIRKHVVKNAAGPALTVTATTVGALLGGSVVTETVFSRSGVGAVLLQAVSSQDISLIQGLVLLTAVAIVTANLAVDLIHP 147
Cdd:PRK15110  228 ILRRHVLHNALPPVIPRLGLQFSTMLTLAMITEMVFSWPGLGRWLINAIRQQDYAAISAGVMVVGSLVIIVNVLSDILGA 307


                  ....
gi 2181016855 148 LLDP 151
Cdd:PRK15110  308 MANP 311
TM_PBP2 cd06261
Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding ...
 54-144 1.64e-03

Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. For these transporters the ABCs and TMs are on independent polypeptide chains. These systems transport a diverse range of substrates. Most are specific for a single substrate or a group of related substrates; however some transporters are more promiscuous, transporting structurally diverse substrates such as the histidine/lysine and arginine transporter in Enterobacteriaceae. In the latter case, this is achieved through binding different PBPs with different specificities to the TMs. For other promiscuous transporters such as the multiple-sugar transporter Msm of Streptococcus mutans, the PBP has a wide substrate specificity. These transporters include the maltose-maltodextrin, phosphate and sulfate transporters, among others.


Pssm-ID: 119394 [Multi-domain]  Cd Length: 190  Bit Score: 37.26  E-value: 1.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181016855  54 HVNTARAKGGTPGWVIRKHVVKNAAGPALTVTATTVGALLGGSVVTETVFSRSGVGAVLLqavSSQDISLIQGLVLLTAV 133
Cdd:cd06261   103 LVEAARALGASPWQIFRRIILPLALPPILTGLVLAFARALGEFALVSFLGGGEAPGPGTG---LLLIFAILFPGDLGVAA 179

                          90
                  ....*....|.
gi 2181016855 134 AIVTANLAVDL 144
Cdd:cd06261   180 AVALILLLLSL 190
 
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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