Table 1. Conserved amino acid motifs in the five pectinase families and the sequences of the degenerate primers designed accordingly to retrieve pectinase gene fragments from ruminal microbial genomes.
| Pectinasefamily | Conserved motif(5′ → 3′) | Primer (5′ → 3′)a | |
| PF00295 | GDDC(H)I(V)AI(V)K | GGCGAYGAYTGYRTNGCAITNAA | |
| GL(I)RIKS | CGGWCTTGATYCTNAKNCC | ||
| PF00544 | GTHV(I)WI(V)DH | GGTACGCACRTNTGGRTNGAYCA | |
| HV(A)Y(V)NNYYE | CTCGTAGTARTTRTTRTAIRCRTG | ||
| PF03211 | W(F)EDV(I)G(C)ED | GTGGGAGGACRTNKGNGARGA | |
| GKLY(L)RSCG | GCCACAGGAGCGNWANAGYTTICC | ||
| PF06917 | GLLYWGGH | GGNCTNCTNTAYTGGGGNGGNCA | |
| DGYYGKKG | CCCTTCTTGCCRTARTANCCRTC | ||
| PF09492 | AQYPNGGW(F) | GCTCAGTACCCNAAYGGNGGNT | |
| WA(G)QQH(Y)DE | CTCGTCGTRYTGYTGNSCCCA | ||
a
Y = C/T, K = T/G, R = A/G, N = A/T/G/C.