Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011952099.1 SWIT_RS06380 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q7MAE6 (393 letters) >NCBI__GCF_000016765.1:WP_011952099.1 Length = 417 Score = 99.4 bits (246), Expect = 2e-25 Identities = 103/399 (25%), Positives = 174/399 (43%), Gaps = 34/399 (8%) Query: 9 YVLHSYGRNYVQFTQGKNATLWDSEGKDYIDFASGIAVCSVGHGNERLAGAICDQAKKLI 68 + H G + + + A L ++G+ Y+D S V + GH N R+ AI Q +KL Sbjct: 9 FTQHGLGEDIPLIERAEGAGLHAADGRRYVDAISSWWVTTHGHCNPRIMAAIRAQTEKLD 68 Query: 69 HTSNLYYIE-PQARLAEKLVKLS--GYDMRVFFANSGAEANEGAIKIARKFGESHEGEVK 125 + P LA LV ++ G D VFF++SG+ + E A+K+A G Sbjct: 69 QLIFAGWTHGPAETLARALVDITPAGLD-HVFFSDSGSTSVEVALKMA--LGTWLNWGEP 125 Query: 126 RYKIITLESSFHGRTITALKATGQEKMHHYFGP---------YP--DGFVYAKNLDHVFK 174 R++I+ +E S+HG TI A+ + + + P +P DG L+ + Sbjct: 126 RHRIVVMEHSYHGDTIGAMSVGERGVYNRAYQPLLFDVDTLPFPVGDGDRTIAALEAICA 185 Query: 175 LVDEKTCAVLLELVQGEGGIEPQDREGIKKLERFLKERGVLLMVDEVQTGIYRSGELFAS 234 ++ L+ G GG+ +K L GVL + DEV TG R+G LFA Sbjct: 186 QGTPPAALIVEPLILGAGGMLIYPPHVLKALRDICAREGVLFIADEVMTGWGRTGMLFAC 245 Query: 235 QAYGIVPDVITVAKGLAGG-VPIGAVMTT--LKDIFAPGD------HGSTFGGNFLSTRA 285 Q G+ PD++ ++KGL GG +P+ A + T + D D H S++ N ++ A Sbjct: 246 QQAGVKPDLMCLSKGLTGGAIPLAATLATREIFDAHLSQDRARMFFHSSSYTANPIACAA 305 Query: 286 GLEVLSILESLYQEGTLQKSIDRFSAELRALCVEFPSLFECEVGLGLMRGIR-----AKS 340 ++I + +E L + + R L L + LG + + Sbjct: 306 ANANIAIWQ---EEPVLDRIGALVHRQARRLDRLDHPLIVGKRQLGTITAMEFVDPYGDY 362 Query: 341 AEIQKSVIDEAFKKRVLVLRSGRNTVRFLPPLTLSEREM 379 ++ F+ L+LR NTV +PP + ++++ Sbjct: 363 LSAMAPMLGRFFRDNGLLLRPMGNTVYVMPPYCIDDKDL 401 Lambda K H 0.319 0.138 0.394 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: 366 Number of extensions: 24 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 393 Length of database: 417 Length adjustment: 31 Effective length of query: 362 Effective length of database: 386 Effective search space: 139732 Effective search space used: 139732 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 (21.7 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