Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_028486300.1 B076_RS0104740 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:P30900 (393 letters) >NCBI__GCF_000483485.1:WP_028486300.1 Length = 426 Score = 148 bits (374), Expect = 3e-40 Identities = 103/323 (31%), Positives = 157/323 (48%), Gaps = 30/323 (9%) Query: 13 PLAFVRGEGSWLWTADGSRYLDLGAGIAVNALGHAAPDLVATLTEQA--GKLWHVSNLYR 70 P+ F +G++L D Y+D LGHA P+++ T+ E+A G + Sbjct: 33 PVFFKAAKGAYLVDEDDKTYIDYVGSWGPAILGHAHPEVIKTVQEKAEFGLSFGAPTKIE 92 Query: 71 IPEQERLADMLVAKTFADTVFFTNSGTEACELAVKMVRKHFYDKGQPERTEILTFSGAFH 130 + + D++ + D V +SGTEA A+++ R G R +I+ F G +H Sbjct: 93 TTMADLVCDLIPSM---DMVRMVSSGTEATMTAIRLAR------GYTGRDKIVKFEGCYH 143 Query: 131 GRSSAAIAAAGTEKMVKGFGPLLPGF--------VHLPWGDLDAVK---AAVTETTAAIL 179 G S + + AG+ + G P PG + L D D V+ A + + A I+ Sbjct: 144 GHSDSLLVKAGSGALTLGV-PSSPGVPAALAEETLTLTHNDSDEVRKVFAEIGDQIACII 202 Query: 180 IEPIQGEGGIRPAPEGFLRALREICDETGTLLVFDEVQCGVARTGKLFAHEWAGVTPDVM 239 +EP+ G P EGFL LR++CDE+G +L+FDEV CG R G A VTPD+ Sbjct: 203 VEPVAGNMNCIPPEEGFLETLRQVCDESGAVLIFDEVMCGF-RVGLQGAQGRYNVTPDLT 261 Query: 240 MVAKGIGGGFPLGAVLATEDAASGMI---AGTHGSTYGGNPLGCAIGAKMIEIVTAPGFL 296 K IGGG P+GA ++ + T GNP+ A G K +E+++APGF Sbjct: 262 TFGKVIGGGMPVGAFGGKQEVMQHIAPLGPVYQAGTLSGNPIAMAAGLKTLELISAPGFF 321 Query: 297 DEVSRKAGFLRQWLEGLVAAHPD 319 +E+ +K L ++GL AA D Sbjct: 322 EELEKKTTRL---VKGLQAAADD 341 Lambda K H 0.320 0.136 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: 446 Number of extensions: 27 Number of successful extensions: 6 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: 393 Length of database: 426 Length adjustment: 31 Effective length of query: 362 Effective length of database: 395 Effective search space: 142990 Effective search space used: 142990 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 (21.8 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