Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_005454569.1 SACCYDRAFT_RS06165 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= uniprot:A0A806JQF3 (400 letters) >NCBI__GCF_000244975.1:WP_005454569.1 Length = 430 Score = 137 bits (346), Expect = 5e-37 Identities = 125/402 (31%), Positives = 178/402 (44%), Gaps = 44/402 (10%) Query: 26 PPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGHTSNLYAT 85 PP+ + G + DGR +D + + G+RHP + A+ Q + H T Sbjct: 30 PPLLVEEASGVRLRLADGRELVDGMSSWWAAIHGYRHPVLDAALAEQAGRMSHVMFGGLT 89 Query: 86 -EPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLSRL-------TGRTKLVAAHD 137 EP I LA LV L D VF C+SG+ + E A K+ G+T+++ Sbjct: 90 HEPAIRLATTLVDLT-PDGLEHVFLCDSGSVSVEVALKMCLQYWRSVGRAGKTRMLTWRG 148 Query: 138 AFHGRTMGSLALTGQ------------PAKQTPFAPLPGDVTHVGYGDVDALAAAVDDHT 185 +HG T +++ P + AP PG V VD L V++H Sbjct: 149 GYHGDTFHPMSVCDPEGGMHALWRGVLPEQLFVPAPPPGFEAPVDESYVDTLVRTVEEHA 208 Query: 186 ---AAVFLEPIM-GESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQH 241 AAV +EP++ G G+ YL R++T LLV DE+ TG GRTGA FA +H Sbjct: 209 GELAAVVVEPVVQGAGGMRFHNPAYLRVLREVTRAHDVLLVFDEIATGFGRTGALFAAEH 268 Query: 242 DGITPDVVTLAKGLGGG-LPIGACLAVGPAAELLTPG-----LHGSTFGGNPVCAAAALA 295 G TPDV+ + K L GG L + A L A+ ++ G HG TF GNP+ +A A A Sbjct: 269 AGATPDVLCVGKALTGGYLTMAATLCTTRVADGISRGEVPVLAHGPTFMGNPLASAVANA 328 Query: 296 VLRVLASDGLVRRAEVLGKSLRHGI-EALGHPLIDHVRGRGLLLGIALTAPHAKD----A 350 + +LA + + LR G+ A P + VR G + + L HA D Sbjct: 329 SIGLLADGAWRHEVRRVERRLRDGLAPAADVPGVVDVRVLGAIGVVQL--DHAVDMAVAT 386 Query: 351 EATARDAGYLVNAAAPDVIRLAPPLIIAEAQL----DGFVAA 388 EA +L D+I PP I ++ L D VAA Sbjct: 387 EALTSRGVWL--RPFRDLIYTMPPYITSDEDLALVTDAMVAA 426 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: 504 Number of extensions: 33 Number of successful extensions: 4 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: 430 Length adjustment: 31 Effective length of query: 369 Effective length of database: 399 Effective search space: 147231 Effective search space used: 147231 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