Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_028309837.1 H566_RS0100150 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000482785.1:WP_028309837.1 Length = 452 Score = 186 bits (473), Expect = 9e-52 Identities = 138/411 (33%), Positives = 206/411 (50%), Gaps = 46/411 (11%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL-YYN 77 P+ +V GEGA + +G Y+D V+ VN+ GH HPA+ EA+ EQ L H + Sbjct: 27 PLAIVRGEGAWLHAADGRRYLDAVSSWWVNLHGHAHPAIAEAIAEQARTLPHTMFAGITH 86 Query: 78 EPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF-----TGCTKFIAFEGGFH 132 EP A A L AP L+ VFF ++G+ ++E A+K+A ++ +F+AFEGG+H Sbjct: 87 EPAARLAAELVARAPAPLSHVFFSDNGSTAIEVALKIACQYWINQGQKRHRFLAFEGGYH 146 Query: 133 GRTMGALSATWKPEFREPFEPLVPEFEHVPYGDVNAVEKAIDDDTAAVIV---------- 182 G T GA++A F PFE + + +P+ + +DD+ AAV+ Sbjct: 147 GDTFGAMAAGRSSGFYAPFEDWLFSVDFMPWPQTWIDKPGLDDEEAAVLARLDAWLDRHG 206 Query: 183 --------EP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEH 233 EP VQG +G+R+ FLR + E G+ +I DEV +G GRTG+ FA EH Sbjct: 207 HELAAFVFEPLVQGASGMRMARAPFLRTVCEKVRACGVPVIFDEVMTGFGRTGRMFAAEH 266 Query: 234 EDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPGD-------HGSTFGGNPLACAAV 285 PD++CL KGL GG +P+ T+A + +AF GD HG TF NPL CAA Sbjct: 267 IGFTPDLLCLCKGLTGGFLPMAVTLATPAIHDAF-LGDGVDRALLHGHTFTANPLGCAAA 325 Query: 286 CAAVSTV-LEENLPEAAERKGKLAMRILSEA-EDVVEEVRGRGLMMGVEV--------GD 335 A++ E+ + A + A R+ + A +V R G + ++ G Sbjct: 326 LASLRLFDSEDTMQRIASLEAMQAQRLAALASHPLVSRSRQWGTIAAFDLVPAGAASAGY 385 Query: 336 DERAKDVARE-MLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADAL 385 + RE M+ RG L+ GD I ++PP I +L+ A +L + L Sbjct: 386 GSASGRALREAMIARGVLMR-PMGDAIYVLPPYCISVADLDFAYGQLREVL 435 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: 413 Number of extensions: 20 Number of successful extensions: 7 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: 452 Length adjustment: 32 Effective length of query: 357 Effective length of database: 420 Effective search space: 149940 Effective search space used: 149940 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