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Table 1 Demonstration that most ABC uptake membrane proteins are homologous 1,2,3

From: Evolutionary relationships of ATP-Binding Cassette (ABC) uptake porters

  1.1 MalG 2.1 RbsC 2.4 XylH 3.2 GlnP 3.8 AapM 4.1 LivM 12.3 OPBD 12.8 OpuBB 14.3 FhuB 14.16 FeuC 20.1 BitE 23.2 CbiQ 25.1 BioN 26.1 CbiQ 28.1 QrtT 29.1 MtsU
1.6 CymF            12      
2.5 GguB           13SD       
2.10 PnrE     16SD             
3.2 GlnP        15SD          
3.19 GtsC 16                
4.4 UrtB    14SD              
5.2 DppC        13.5SD          
6.3 CysW            14      
6.5 WtpB     8             
7.1 PstA        12SD          
8.1 ModB 10                
9.2 PhnE         12         
10.3 FbpB            21      
11.4 ChtK 8                
13.1 BtuC          30        
15.4 YfeC          18SD        
16.3 CmpB        10          
17.2 SsuC        9          
18.1 CbiQ             15SD     
19.1 ThiP            17SD      
22.1 CbiQ               13SD   
24.1 MetI        9          
25.1 BioY homologue gi145224049     11SD 11SD            
26.7 EcfT              8    
27.2 Tgd1 homologue gi54023080       11SD           
28.1 QrtT               13   
29.1 MtsU             6     
30.1 YkoC               7 17SD  
31.1 HtsTUV               14SD   
32.1 CbrT                 18.9SD
33.1 MtaT                6 13
34.1 TrpY   12               
  1. 1 Since completion of the work reported here, a new ABC family (3.A.1.35; CPC) has been introduced into TCDB. 35.1; EtcT gave e-12 with 26.5 and e-9 with 30.1 and 33.1, thus indicating homology between families 26, 30, 33 and 35.
  2. 2 Usually, superfamilies in TCDB, half of which have been introduced during the last 2.5 years, contain multiple TC families (and are hence, by definition, more divergent in sequence than the APC family 2.A.3). However, in 2.A.3, all recognized members of this family were initially included under 2.A.3. This is a historical fact that cannot be readily corrected because the IUBMB and UniProt require a stable system of classification. Subsequently, we could show that other families previously existing in TCDB were members of this superfamily. The same was true for the MFS. Thus, we call what would normally be called “subfamilies” the families for both the MFS (2.A.1) and the APC (2.A.3). The same is true for the ABC functional superfamily, except that the membrane proteins actually comprise three superfamilies, ABC1, ABC2 and ABC3 as discussed above [16].
  3. 3 The numbers in bold indicate comparison scores expressed in S.D [16]. Non-bolded numbers are the exponential numbers (e-values) obtained with TC-BLAST. For instance, the number “12” in the first row of column 12 indicates that the comparison score between 1.6 CymF and 20.1 BitE was e-12. The TC# provided is the family/protein number (e.g. 1.1 for MalF and MalG, the two membrane constituents of the E. coli maltose transporter). The first three digits in the TC# (3.A.1.) refer to the ABC functional superfamily and are not shown. They are the same for all entries. The protein TC# is followed by the protein abbreviation. All members of a single family are demonstrably homologous, giving high comparison scores (greater than 15 S.D.). Any two families for which a number is provided in the table below are demonstrably homologous based on the criteria stated in the Methods section. All proteins are within the ABC superfamily (3.A.1), but only the family and protein TC#s are provided below, e.g. 1.6 means 3.A.1.1.6, i.e., ABC family 1, member 6.