Align Acetylornithine aminotransferase, chloroplastic/mitochondrial; ACOAT; Acetylornithine transaminase; AOTA; Protein HOPW1-1-INTERACTING 1; EC 2.6.1.11 (characterized)
to candidate WP_012964905.1 FERP_RS01920 aspartate aminotransferase family protein
Query= SwissProt::Q9M8M7 (457 letters) >NCBI__GCF_000025505.1:WP_012964905.1 Length = 378 Score = 314 bits (804), Expect = 4e-90 Identities = 177/393 (45%), Positives = 250/393 (63%), Gaps = 24/393 (6%) Query: 60 KVIEEEAKVIVGTYARAPVVLSSGKGCKLFDPEGKEYLDCASGIAVNALGHGDPDWLRAV 119 ++ E E ++++ + R VV G+GC L+D GK+YLD +GIA ++GH + ++ V Sbjct: 3 EIFELEKELLIPFFKRQRVVFVKGEGCWLYDERGKKYLDLVAGIACVSIGHSNKYFIERV 62 Query: 120 TEQAGVLAHVSNVYYTIPQIELAKRLVASSFADRVFFCNSGTEANEAAIKFSRKFQRFTH 179 EQ L HVSN+YYT+PQIELAK+L S D+ FFCNSGTEA EAAIK +RK Sbjct: 63 KEQLEKLVHVSNLYYTLPQIELAKKLREVSGMDKFFFCNSGTEAVEAAIKLARK------ 116 Query: 180 PEDKEVATG---FIAFTNSFHGRTLGALALTSKEQYRTPFEPIMPGVTFLEYGNIQAATD 236 ATG ++FT +FHGRT+GAL+LT KE++R PFEP++ V F E+ N++ Sbjct: 117 ------ATGRKRLVSFTGNFHGRTMGALSLTWKEKFRKPFEPLIGEVVFAEFNNVEDLKK 170 Query: 237 LIRSGKIAAVFVEPIQGEGGIYSATKEFLQSLRSACDAAGSLLVFDEVQCGLGRTGLMWA 296 + S ++AAVFVE IQGE G+Y A +EF+Q + + G L+VFDEVQ G GRTG +A Sbjct: 171 KL-SEEVAAVFVEAIQGEAGVYPAKEEFIQEIFELKEKYGFLVVFDEVQTGFGRTGEWFA 229 Query: 297 YEAFGVTPDIMTVAKPLAGGLPIGAVLVTEKVAETINYGDHGSTFAGSPLVCSAAIAVMD 356 + + V PDI+ +AK +A G P+GAV V + VAE + GDHGSTF G+PL C+AA+A ++ Sbjct: 230 KDIYNVEPDIIAMAKGIANGFPMGAVGVKDYVAEKVEAGDHGSTFGGNPLACTAALATIE 289 Query: 357 KVSKPSFLSSVSNKGRYFRDLLVKKLGGNSHVKEVRGEGLIIGVELDVPASSLVDACRDS 416 + K + + G +F++ L +LG E G GL+IG + + A V + + Sbjct: 290 YIEKNKLVENSRRMGEFFKEKL-SELG-----FEADGFGLMIGFDKE-KAFDFVSSMLEK 342 Query: 417 GLLILTAGKGNVVRIVPPLVISEEEIERAVEIM 449 G+L+ A N +RIVPPL+IS EE+E AVE M Sbjct: 343 GVLV-NATSENRIRIVPPLIISREEVEFAVERM 374 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: 409 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: 457 Length of database: 378 Length adjustment: 31 Effective length of query: 426 Effective length of database: 347 Effective search space: 147822 Effective search space used: 147822 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