Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate Dsui_2880 Dsui_2880 adenosylmethionine-8-amino-7-oxononanoate transaminase
Query= uniprot:A0A806JQF3 (400 letters) >FitnessBrowser__PS:Dsui_2880 Length = 447 Score = 156 bits (395), Expect = 1e-42 Identities = 133/421 (31%), Positives = 196/421 (46%), Gaps = 55/421 (13%) Query: 24 GTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGHTSNL- 82 G P I + SG G +TD DGR Y+D + VN+ GHR+P + A+ Q+ TL H Sbjct: 30 GLPLIPVQSGAGVWLTDFDGRRYLDGVSSWWVNLFGHRNPRINAALRDQLETLEHVILAG 89 Query: 83 YATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLS----RLTG---RTKLVAA 135 + EP + L+E L AL G F+ + GA A E A K+S R TG +T + Sbjct: 90 FTHEPVVQLSERLSALTGG-ALGHAFYASDGASATEIALKMSHHYWRNTGQPEKTDFLCL 148 Query: 136 HDAFHGRTMGSLALTGQPAKQTPFAPL--------------------PGDVTHVGYGDVD 175 ++HG T+G+LA+T + +APL DV ++ Sbjct: 149 EGSYHGETVGALAVTDVALFKDAYAPLIRPAAVLPSPDARLARDGETAADVARRAAAALE 208 Query: 176 ALAAAVDDHTAAVFLEP-IMGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTG 234 A A H AA+ +EP I +G+ + YL+ AR R G L+ DE+ G GR+G Sbjct: 209 AHLQAHHGHIAALIVEPLIQCATGMAMHDPLYLSLARQACDRYGVHLICDEIAVGFGRSG 268 Query: 235 AFFAHQH---DG--ITPDVVTLAKGLGGG-LPIGACLAVGPAAE-----LLTPG-LHGST 282 FFAH+ DG + PD + L+KG+ GG LP+ L E +T G LH + Sbjct: 269 TFFAHEQAAVDGKTVRPDFLCLSKGITGGYLPLSVVLTTDTVYEAFLDDAVTRGFLHSHS 328 Query: 283 FGGNPVCAAAALAVLRVLASDGLVRRAEVLGKSLRHGIEAL-GHPLIDHVRGRGLLLGIA 341 + GN + AALA L + D ++ L + L +E L HP + H R RG++L Sbjct: 329 YTGNALACRAALATLDIFEQDDVIAANRQLSERLHQLLEPLRQHPRVRHYRRRGMILAFD 388 Query: 342 LTAPHAKDAEATAR--DAGY---LVNAAAPDVIRLAPPLIIAEAQ----LDGFVAALPAI 392 + DA + R AG L+ + + L PP +++E + G +A L A Sbjct: 389 V---EGADASFSRRFYKAGLERELMLRPIGNTVYLMPPYVLSEDEARHLCQGTLATLEAT 445 Query: 393 L 393 L Sbjct: 446 L 446 Lambda K H 0.320 0.136 0.399 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 449 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 400 Length of database: 447 Length adjustment: 32 Effective length of query: 368 Effective length of database: 415 Effective search space: 152720 Effective search space used: 152720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory