Align Acetylornithine aminotransferase 1; ACOAT 1; EC 2.6.1.11 (uncharacterized)
to candidate WP_044410780.1 NA59_RS08095 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:Q89VE9 (405 letters) >NCBI__GCF_000934765.1:WP_044410780.1 Length = 426 Score = 151 bits (382), Expect = 3e-41 Identities = 106/321 (33%), Positives = 157/321 (48%), Gaps = 31/321 (9%) Query: 23 FERGEGCWLIATNGDRYLDFTSGVAVNALGHAHPALVKALQEQATKLWHMSNLFQSPDGE 82 F+ G +L + +Y+D+ LGHAHP +++A+Q QA F +P Sbjct: 36 FKSAHGAYLTDEDDKKYIDYVGSWGPAILGHAHPEVIQAVQRQAEH----GLSFGAPTVM 91 Query: 83 K--LATRLCN--ESFADFVFFCNSGAEALEGVIKLVRHHHFSKGHPERYRIITFEGAFHG 138 + +A +C SF D V +SG EA I+L R G+ R +I+ FEG +HG Sbjct: 92 ETTMADLVCELIPSF-DMVRMVSSGTEATMTAIRLAR------GYTGRDKIVKFEGCYHG 144 Query: 139 RTLATLAATGSAKYLEGFGPPMDGFDQ--------VPHGDIEAVKKA---IGPQTAGILI 187 + + L GS G P G + H D + V++ IG Q A I++ Sbjct: 145 HSDSLLVKAGSGALTLGV-PSSPGVPAALASETLTLTHNDADEVRQVFSEIGDQIACIIV 203 Query: 188 EPIQGEGGVRSATPAFLKALRQLCDEKGLLLAFDEVQTGMGRTGDLFAHRRTGVTPDVMS 247 EP+ G P FL+ALR++CD+ G +L FDEV G R G A R GVTPD+ + Sbjct: 204 EPVAGNMNCIPPEPGFLEALREVCDQHGAVLIFDEVMCGF-RVGLQGAQGRYGVTPDITT 262 Query: 248 LAKALGGGFPIGAILATADA---AAGMGPGSHGSTFGGNPLAIAAANAVLDVMLKPGFFD 304 K +GGG P+GA + A +GP T GNP+A+AA L+++ P FF+ Sbjct: 263 FGKVIGGGMPVGAFGGKKEIMSHIAPLGPVYQAGTLSGNPIAMAAGLMTLNLLKSPAFFE 322 Query: 305 HVQKMSLLLKQKLASVIDRHG 325 H+++ + L L +V D G Sbjct: 323 HLEQKTKRLVDGLQAVADEAG 343 Lambda K H 0.320 0.137 0.404 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: 444 Number of extensions: 28 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: 405 Length of database: 426 Length adjustment: 31 Effective length of query: 374 Effective length of database: 395 Effective search space: 147730 Effective search space used: 147730 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