Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_010529905.1 ON01_RS04970 ornithine--oxo-acid transaminase
Query= curated2:Q58131 (398 letters) >NCBI__GCF_000224785.1:WP_010529905.1 Length = 398 Score = 301 bits (771), Expect = 2e-86 Identities = 161/389 (41%), Positives = 240/389 (61%), Gaps = 5/389 (1%) Query: 7 IDLEKKYHLQIYGRLPVVLVEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKK 66 ID ++Y + Y LPVV+ + +G+ V D +G +Y+D L+ N GH HPK+++A+KK Sbjct: 9 IDQTQEYGAKNYHPLPVVINKAEGVWVEDPEGNRYMDMLSSYSALNQGHRHPKIIDALKK 68 Query: 67 QAETLIHTSNIYYTIPQIKLAKKLVELSGLDRAFFCNSGAEANEGAIKFARKYVSKVLG- 125 QA+ + TS ++ +K+ +L+ + N+GAEA E A+K AR++ V G Sbjct: 69 QADAVTLTSRAFHNDQLGPWYEKICKLTNKEMTLPMNTGAEAVETAVKAARRWAYDVKGV 128 Query: 126 -REGGEIISMYNAFHGRTLTTLAATPKPKYQDGFYPLPPGFKYVPFNDIEALKEAITDKT 184 EII FHGRT+T ++ + + +YQ GF PL PG K +P+ D++ALKEAI + T Sbjct: 129 AENKAEIIVAEGNFHGRTMTAVSLSSESEYQRGFGPLLPGIKIIPYGDVDALKEAINENT 188 Query: 185 AAIMIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAFEHYGVE 244 AA + EP+QGE GI++ + +LK D+C + N++ + DE+Q G+ RTG+MFA + GV Sbjct: 189 AAFLFEPIQGEAGINIPPEGFLKEAYDVCAENNVLYMADEIQSGLARTGKMFACDWEGVT 248 Query: 245 PDILTLAKALGGGV-PIGAVVLKEEIAKALSYGDHGTTFGGNPLACSAALASVEVIEELI 303 PD+L L KALGGGV PI AVV ++I + G HG+TFGGNPLAC+ + S+EV+EE Sbjct: 249 PDVLILGKALGGGVFPISAVVANKDILGVFNPGSHGSTFGGNPLACAVSTVSLEVLEEEK 308 Query: 304 KDDKVIEKGKYFIRKLENLIEKYNFIKEVRGLGLMIGAELEFNGADIVKKMLEKGFLINC 363 D+ E G Y + +L+ + K IKEVRG GL IG EL + + EKG L Sbjct: 309 LADRSNELGNYMMGELKKI--KNPKIKEVRGKGLFIGVELTEAARPYCEALKEKGLLCKE 366 Query: 364 TSDTVLRFLPPLIVEKEHIDALINALDEV 392 T + V+RF PPL+++K ++ + + EV Sbjct: 367 THENVIRFAPPLVIDKPDLEWAVGHIKEV 395 Lambda K H 0.320 0.141 0.409 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: 411 Number of extensions: 17 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: 398 Length of database: 398 Length adjustment: 31 Effective length of query: 367 Effective length of database: 367 Effective search space: 134689 Effective search space used: 134689 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 Jul 26 2024. The underlying query database was built on Jul 25 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