Align Acetylornithine aminotransferase, chloroplastic/mitochondrial; ACOAT; Acetylornithine transaminase; AOTA; Protein HOPW1-1-INTERACTING 1; EC 2.6.1.11 (characterized)
to candidate WP_013684628.1 ARCVE_RS09865 acetylornithine transaminase
Query= SwissProt::Q9M8M7 (457 letters) >NCBI__GCF_000194625.1:WP_013684628.1 Length = 380 Score = 321 bits (823), Expect = 2e-92 Identities = 177/391 (45%), Positives = 245/391 (62%), Gaps = 22/391 (5%) Query: 63 EEEAKVIVGTYARAPVVLSSGKGCKLFDPEGKEYLDCASGIAVNALGHGDPDWLRAVTEQ 122 E E V + Y R PVV G+GC L+D EGK+YLD +GIA LGH P ++ V+EQ Sbjct: 6 ERERAVHIQFYRRQPVVFVKGEGCYLYDVEGKKYLDMVAGIAAATLGHCHPKFIARVSEQ 65 Query: 123 AGVLAHVSNVYYTIPQIELAKRLVASSFADRVFFCNSGTEANEAAIKFSRKFQRFTHPED 182 L HVSN+YYT PQIELA++L + DR FFCNSG EA EA++K +RK Sbjct: 66 LKKLVHVSNLYYTTPQIELAEKLREITGMDRFFFCNSGAEAVEASLKIARK--------- 116 Query: 183 KEVATG---FIAFTNSFHGRTLGALALTSKEQYRTPFEPIMPGVTFLEYGNIQAATDLIR 239 ATG F+AF+ SFHGRT+GAL++T KE++R PFEP++ V F E+ +++ + Sbjct: 117 ---ATGRKKFVAFSGSFHGRTMGALSVTWKEKFRRPFEPLVQPVEFAEFNSVEDLEKKVD 173 Query: 240 SGKIAAVFVEPIQGEGGIYSATKEFLQSLRSACDAAGSLLVFDEVQCGLGRTGLMWAYEA 299 + AAV +EP+QGE G+Y ATKEF+ L D L++FDEVQ G GRTG +A E Sbjct: 174 E-ETAAVILEPVQGEAGVYPATKEFINELFRLRDEYNFLVIFDEVQTGFGRTGRWFAKEH 232 Query: 300 FGVTPDIMTVAKPLAGGLPIGAVLVTEKVAETINYGDHGSTFAGSPLVCSAAIAVMDKVS 359 +GV PDIM +AK + G PIG V V+E+VAE + G+H STF G+PL C A++A ++ + Sbjct: 233 YGVKPDIMAMAKAMGSGFPIGGVGVSEEVAEKLEAGEHASTFGGNPLACVASLATIEIIE 292 Query: 360 KPSFLSSVSNKGRYFRDLLVKKLGGNSHVKEVRGEGLIIGVELDVPASSLVDACRDSGLL 419 + + + G+Y R K+L +KEVRG GL+IG +++ A +V + GLL Sbjct: 293 EEKLVENSEKTGKYLR----KRLEELDGIKEVRGMGLMIGAKVE-NAPGMVSRSLEKGLL 347 Query: 420 ILTAGKGNVVRIVPPLVISEEEIERAVEIMS 450 + A N +R VPPL+ EEI+ AV+I+S Sbjct: 348 V-NATSENALRFVPPLIAGREEIDFAVDILS 377 Lambda K H 0.318 0.135 0.385 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: 17 Number of successful extensions: 5 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: 457 Length of database: 380 Length adjustment: 31 Effective length of query: 426 Effective length of database: 349 Effective search space: 148674 Effective search space used: 148674 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