Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_041304058.1 BTUS_RS09720 ornithine--oxo-acid transaminase
Query= curated2:Q58131 (398 letters) >NCBI__GCF_000092905.1:WP_041304058.1 Length = 394 Score = 300 bits (768), Expect = 5e-86 Identities = 160/390 (41%), Positives = 236/390 (60%), Gaps = 5/390 (1%) Query: 7 IDLEKKYHLQIYGRLPVVLVEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKK 66 I+ E +Y + Y LPVVL +G+G+ V D++G++YLD L+ N GH HP++++A+K Sbjct: 2 IEREDRYGARNYDPLPVVLTKGEGVWVEDVEGRRYLDMLSAYSALNQGHRHPRIIQALKA 61 Query: 67 QAETLIHTSNIYYTIPQIKLAKKLVELSGLDRAFFCNSGAEANEGAIKFARKYVSKVLG- 125 QA+ + TS +Y ++L +L+ D N+G EA E AIK R++ +V G Sbjct: 62 QADRITLTSRAFYNDKLGFFYERLAQLTHKDTILPMNTGTEAVETAIKAMRRWAYRVRGV 121 Query: 126 -REGGEIISMYNAFHGRTLTTLAATPKPKYQDGFYPLPPGFKYVPFNDIEALKEAITDKT 184 + EII FHGRT T ++ + +P+Y++GF PL PGF+ VP+ DIEAL+ A T Sbjct: 122 PEDQAEIIVATGNFHGRTTTVISFSSEPEYREGFGPLTPGFRVVPYGDIEALRRAAGPHT 181 Query: 185 AAIMIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAFEHYGVE 244 A +++EP+QGE GI + YL+ VR +C + IV DE+Q G+GRTG+ FA + V Sbjct: 182 AGVLLEPIQGEAGIVLPPDGYLREVRRICTENGIVFAADEIQTGLGRTGQWFACDWENVT 241 Query: 245 PDILTLAKALGGGV-PIGAVVLKEEIAKALSYGDHGTTFGGNPLACSAALASVEVIEELI 303 PD+ L KALGGGV P+ AV +I G HG+TFGGNPLA + A+ +++VIE+ Sbjct: 242 PDLYILGKALGGGVYPVSAVAANRDILGVFEPGSHGSTFGGNPLAAAVAVTALQVIEDEK 301 Query: 304 KDDKVIEKGKYFIRKLENLIEKYNFIKEVRGLGLMIGAELEFNGADIVKKMLEKGFLINC 363 D+ E G YF+ +L L ++ I+EVRG GL IG EL +K+ +G L Sbjct: 302 LVDRSRELGAYFLVRLRTL--RHPAIREVRGRGLFIGLELTSPARPYCEKLKNRGLLCKE 359 Query: 364 TSDTVLRFLPPLIVEKEHIDALINALDEVF 393 T +T +RF PPL+++KE +D + EVF Sbjct: 360 THETTIRFAPPLVIQKEELDWAFEQIAEVF 389 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: 381 Number of extensions: 21 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: 394 Length adjustment: 31 Effective length of query: 367 Effective length of database: 363 Effective search space: 133221 Effective search space used: 133221 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 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