TABLE 2.
Conserved regions 3, 7, and 8 (the others are not shown) in proteins similar to AlpP used to clone the gene coding for marinocine by degenerate PCR
| Organism | Accession no. (size [amino acids]) | Sequences ofa:
|
||
|---|---|---|---|---|
| Conserved region 3 | Conserved region 7 | Conserved region 8 | ||
| P. tunicata | AAP73876 (727) | 82IVWTVHLANKKAAWY98 | 488RMAOPWQADFFQCT503 | 595YYSYWWPPQSPWDVL610 |
| C. violaceum | AAQ60932 (606) | 82IRWTAHLANKKPSWY98 | 476YMAIPWQADFNECS491 | 496RRLWWWPAQRPEFVY512 |
| Magnetococcus sp. strain MC-1 | ZP_00289207 (608) | 90IEWTVHLANKKSIWY106 | 486FMAIPWQADFNLCS501 | 506RTLWWWPAQRPLNVY522 |
| C. crescentus | NP_419374 (687) | 116IVWTVHLANKKANSY132 | 556FMAVPWHTDYNACA571 | 582ALYWSWPAQRPVQVH598 |
| M. degradans 2-40 | ZP_00318138 (767) | 119IEWSVYLANKKSSWF135 | 649FSALPWQADFNECS664 | 692SETLWWPAYRPMQVY708 |
| R. palustris | NP_947813 (684) | 111VTWSVHVANTKAAWY127 | 523WMGVPWQGDAFSCQ538 | 545PTPVWWPALLPVDVL561 |
| R. baltica | NP_866009 (527) | 79IQWRVSLANRKAAGD95 | 449GNALPWQADFLKCA464 | 461CAGSWWPAQRPDEVF477 |
| Degenerate deoxyoligonucleotidesb | 5′ GTNYAYYTNGCNAAYAARAA 3′ | 5′ RAARTCNGCYTGCCANGG 3′ | 5′ GGNNNYTGNGSNGGCCACC 3′ | |
| M. mediterraneac | AY968053 (726) | 82IEWTVHLANKKAAWY98 | 503RMACPWQADFFNCT518 | 576YSYWWPPQSPWDVL591 |
a
Boldface letters indicate the specific amino acids actually used in the design of the three degenerate deoxyoligonucleotides (one forward, MARDIR1; two reverse, MAREV1 and MAREV2).
b
Conserved region 3, MARDIR1; conserved region 7, MAREV1; conserved region 8, MAREV2.
c
Marinocine sequence.