Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_013452021.1 CALNI_RS09630 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000183405.1:WP_013452021.1 Length = 467 Score = 117 bits (292), Expect = 9e-31 Identities = 88/262 (33%), Positives = 126/262 (48%), Gaps = 20/262 (7%) Query: 18 FPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYN 77 +P+ EGA D +GN YID+ G V GH V +A+KE++ER Sbjct: 65 YPIISHSSEGAYFTDIDGNRYIDIAMGYGVCFHGHKPKFVYDAIKERLERGFELGP--QT 122 Query: 78 EPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCTKFIAFEGGFHGRTMG 137 EAA L+ D +V FC +G+E+V A+++AR FT K + F FHG G Sbjct: 123 VESGEAAYLIHHLTGVD--RVTFCGTGSEAVMFALRIARGFTRKKKIVIFANSFHGTFDG 180 Query: 138 ALSATWK----PEFREPFEPLVPEFEHVPYGDVNAVE--KAIDDDTAAVIVEPVQGEAGV 191 L + P E +V + + YG A++ + D AAV+ EPVQ Sbjct: 181 VLGKMAEDITIPVSPGTTEGMVEDLVVLEYGSDAALDYIRKNADGLAAVMAEPVQ-TRNP 239 Query: 192 RIPPEGFLRELRELCDEHGLLLIVDEVQSGM----GRTGQFFAFEHEDVLPDIVCLAKGL 247 + P FL+E+R+L DE G LLI DE +G G + F D+ DIV K L Sbjct: 240 SLRPVEFLKEIRKLADEKGFLLIFDETVTGFRVHYGGIQKLF-----DIKADIVIYGKAL 294 Query: 248 GGGVPVGATIAREEVAEAFEPG 269 GGG+P+ A R++V + + G Sbjct: 295 GGGMPIAAVCGRDDVMKIVDGG 316 Lambda K H 0.318 0.137 0.405 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: 393 Number of extensions: 22 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: 389 Length of database: 467 Length adjustment: 32 Effective length of query: 357 Effective length of database: 435 Effective search space: 155295 Effective search space used: 155295 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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