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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.