Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_041530883.1 PERMA_RS04485 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000021565.1:WP_041530883.1 Length = 454 Score = 219 bits (557), Expect = 2e-61 Identities = 149/416 (35%), Positives = 221/416 (53%), Gaps = 54/416 (12%) Query: 25 GEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL-YYNEPQAEA 83 GEG V+D GN Y+D V+ + NV GH HP + +A+ +QV R+ H + L N P Sbjct: 36 GEGVYVYDIHGNRYLDGVSSLWCNVHGHNHPKLNQALIDQVNRIAHFTTLGASNVPAVVF 95 Query: 84 ARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGC------TKFIAFEGGFHGRTMG 137 A+ L + AP L KVF+ G E++E AIK+A + KF+ +HG T+G Sbjct: 96 AKNLIDIAPPKLRKVFYSEDGAEAMEIAIKIAYHYWHNKGEFQRNKFVTLSEAYHGDTIG 155 Query: 138 ALSATWKPEFREPFEPLVPEFEHVPYGDVNAV-----EKAIDDDTAAVIVEPV------- 185 ++S F E + PL+ + +P + AV EKA++ DT +++E V Sbjct: 156 SVSVGGINIFHEKYRPLLFDVYKMPSPYLEAVKKAGREKALEYDTTKLLIEEVEEFIFKN 215 Query: 186 -------------QGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFE 232 QG AG+ P+G+L+E+R +CDE+ +L+IVDEV +G GR+G FA E Sbjct: 216 HQEIAGFVLEGGVQGAAGILPFPKGYLKEIRRICDEYNILMIVDEVATGFGRSGYMFACE 275 Query: 233 HEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAF--EPGD-----HGSTFGGNPLACAA 284 E + PDI+ L KG+ GG +P+ AT+ +E+ F E G+ HG T+ GNPLAC+ Sbjct: 276 KEGIEPDIMALGKGITGGYLPLAATLVTDEIFNEFLGEFGEAKHFYHGHTYTGNPLACSV 335 Query: 285 VCAAVSTVLEENLPEAAERKGKLAMRILSEAEDV--VEEVRGRGLMMGVEVGDDERAKD- 341 A + EE + + K KL L E D+ V +VR G M G+E+ D ++ + Sbjct: 336 AIANLEVFEEEQTLKKLQPKIKLLEERLKEFWDLKHVGDVRQYGFMAGIELVRDRKSMEP 395 Query: 342 ----------VAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADALRA 387 VA EML RG V GDV+ ++PPLVI ED+L L L ++++A Sbjct: 396 FPYGERTGFKVAGEMLKRGIWVR-PLGDVMVIMPPLVITEDQLNYFLDSLKESIKA 450 Lambda K H 0.318 0.137 0.405 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: 435 Number of extensions: 23 Number of successful extensions: 8 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: 389 Length of database: 454 Length adjustment: 32 Effective length of query: 357 Effective length of database: 422 Effective search space: 150654 Effective search space used: 150654 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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