Table 3.
Conserved Tandem Clusters with Known Functions
| Category | Function | Average cluster size | Organisms (Number of clusters) | Typical arrangement of membrane proteins |
| Membrane transport | ABC transporter (sugar, phosphate, sulfate, spermidine/putrescine, sn-glycerol-3-phospate) | 2.2 | Mj, Mt, Af (2), Ph (4), Ec (7), Hi (2), Bs (8), Mg (2), Mp (2), Mtu (7), Bb (2), Tp (2), Aa, Ss (4) | Ec: b1124[6]–b1125[6] |
| ABC transporter (di-, oligo-peptide) | 2.1 | Af, Ph (4), Ec (7), Hi (3), Hp (2), Bs (3), Mg, Mp, Mtu (2), Bb (2) | Ec: b1485[6]–b1486[6] | |
| ABC transporter (ribose) | 2.7 | Ph, Bs, Mg, Mp, Bb (2), Tp (3) | Mp: A65_orf517[9]– A65_orf311[7] | |
| ABC transporter (branched-chain amino acid, sugar) | 2.1 | Mj, Af (4), Ec (2), Ss | Ec: b3456[8]–b3457[7] | |
| ABC transporter (polar amino acid) | 2.1 | Ec (4), Hi, Hp, Bs (2) | Bs: glnP[4]–glnM[6] | |
| ABC transporter (ferrichrome, iron) | 3.4 | Ec (2), Bs (5), Ss | Bs: fhuG[9]–fhuB[10] | |
| ABC transporter (iron (III) dicitrate) | 2.0 | Hi, Bs, Tp | Bs: ytgD[9]–ytgC[7] | |
| ABC transporter | 2.8 | Ph, Ec (2), Hi (2), Bs (3), Mg, Mp, Mtu (3) | Ec: b0886[4]–b0887[6] | |
| ABC transporter? | 2.5 | Mtu (4) | Mtu: Rv0587[6]–Rv0588[6] | |
| PTS system IID, IIC component | 2.7 | Ec (2), Bs | Ec: b1818[7]–b1819[4] | |
| Cobalt transport permease and cobalamin biosynthesis protein | 3.3 | Mj (2), Mt (2), Af (2), Ss | Mj: MJ1089[5]–MJ1090[2]– MJ1091[6] | |
| Branched-chain amino acid transporter | 3.0 | Hi, Hp, Bs | Bs: azlD[4]–azlC[6] | |
| Glucose, hexose transporter | 3.0 | Sc (3) | Sc: YDR342[9]–YDR343C[9] | |
| Protein export membrane protein | 2.9 | Ph, Ec, Hi, Hp, Mtu, Bb, Tp, Ss | Hp: HP1549[5]–HP1550[5] | |
| Biopolymer transport protein | 3.3 | Ec (2), Hi (2), Hp (2), Ss (3) | Ec: b3005[1]–b3006[2] | |
| Multidrug resistance protein Major facilitator family transporter | 2.5 | Ec (3), hi, Aa, Bs | Ec: b2685[1]–b2686[10] | |
| ATP synthesis (A, B, C chain) | 4.8 | Ec, Hi, Bs, Mtu, Ss | Bs: atpF[1]–atpE[1]–atpB[5] | |
| K+ transporting ATPase (A, B, C chain) | 3.5 | Ec, Mtu, Ss | Ss: slr1728[9]–slr1729[7]– slr1730[1] | |
| Transporting ATPase (Na+, Ca2+, H+) | 3.0 | Sc (2) | Sc: YDR038C[10]– YDR039C[10]– YDR040C[10] | |
| Electron transport system | NADH (monoxide) dehydrogenase quinone oxidoreductase formate hydrogenase, hydrogenase-4 | 5.5 | Af, Ph, Ec (3), Hp, Bs, Mtu (2), Aa (2), Ss (3) | Ec: b2276[11]–b2277[12]– b2278[13]–b2279[1]– b2280[3]–b2281[1]– b2282[7] |
| Cytochrome c oxidase cytochrome o ubiquinol oxidase | 5.6 | Aa (2), Bs (2), Ec, Ss (3), Mtu | Bs: ctaA[7]–ctaB[7]–ctaC[3]– ctaD[14]–ctaE[4] | |
| Cytochrome d ubiquinol oxidase cytochrome bd II oxidase | 4.0 | Ec (2), Hi, Bs, Mtu, Aa, Ss | Ec: b0733[6]–b0734[7] | |
| Cytochrome c-type biogenesis protein | 5.0 | Ec, Hi | Ec: b2196[13]–b2197[1]– b2198[1]–b2199[6]– b2200[7] | |
| Cell motility | Flagellar motor protein chemotaxis motB,A protein | 2.3 | Ec, Hp, Bs (2), Bb, Tp, Aa | Ec: b1889[1]–b1890[4] |
| Flagellar biosynthesis protein | 5 | Ec (2), Bs, Tp, Aa | Bs: fliP[4]–fliQ[2]–fliR[6]– flhB[4]–flhA[7] | |
| Metyl-accepting chemotaxis protein | 2.9 | Ec, Bs, Bb (2), Tp, Ss (2) | Bb: BB0596[2]–BB0597[2] | |
| Spore germination protein | 2.0 | Bs (3) | Bs: yndD[5]–yndE[10] | |
| Others | Two-component system (sensor kinase, response regulator) | 2.2 | Ec (2), Bs, Ss | Ec: b2218[1]–b229[1] |
| Formate dehydrogenase | 2.0 | Ec (2), Hi, Aa | Ec: b1475[1]–b1476[4] | |
| NAD(P) transhydrogenase | 3.3 | E, Hi, Mtu | Ec: b1602[7]–b1603[5] | |
| Rod shape-determinant protein and penicillin binding protein 2 | 2.5 | Ec, Hi, Bb, Tp | Ec: b0634[8]–b0635[1] | |
| HflK, HflC γCII stability-governing protein | 2.7 | Ec, Hi, Tp | Ec: b4174[1]–b4175[1] | |
| Tetrahydromethanopterin S-methyltransferase | 4 | Mj, Mt | Mj: MJ0847[5]–MJ0848[6]– MJ0849[8]–MJ0850[1] |
