Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_025274532.1 HALAL_RS0113645 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q58131 (398 letters) >NCBI__GCF_000527155.1:WP_025274532.1 Length = 442 Score = 181 bits (460), Expect = 3e-50 Identities = 136/415 (32%), Positives = 220/415 (53%), Gaps = 50/415 (12%) Query: 22 PVVLVEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKKQAETLIHTSNIYYTI 81 P V+ E G + D+DG+++LD ++ + VGHCHP + AI+KQ TL H++ + T Sbjct: 30 PTVVSEASGAWITDVDGRRFLDGVSSLWTTTVGHCHPDINAAIEKQLRTLDHSTFLGSTH 89 Query: 82 -PQIKLAKKLVELSG------LDRAFFCNSGAEANEGAIKFARKYVSKVLGREGGEIISM 134 P I+L++ LV + L + F+ G+ A E A+K A +Y ++ GR + I + Sbjct: 90 KPGIELSEMLVNRAPTGDGPELSKVFYAGDGSSAVEIALKMAYQYSTQT-GRPRDKFIRL 148 Query: 135 YNAFHGRTLTTLA--------ATPKPKYQDGFYPLPPGFKYVPFNDIE----ALKEAIT- 181 A+HG TL +A AT KP + PG + + + + AL+E + Sbjct: 149 NYAYHGDTLGAVAVGGHDLFHATYKPLLLETIGVPSPGDRSLGDDRVARAIVALEETMAE 208 Query: 182 --DKTAAIMIEPV-QGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAF 238 D T AI++EP+ QG G+ D YL+AVR L D ++IFDEV G+GRTG M+A Sbjct: 209 HGDNTCAIIVEPLMQGAAGMLDYDASYLRAVRRLADKYGALVIFDEVATGIGRTGTMWAA 268 Query: 239 EHYGVEPDILTLAKALGGG-VPIGAVVLKEEIAKA-LSYGD--------HGTTFGGNPLA 288 E V PD+LT K + G +P+ AV++ + + A LS D HG T+ NP+ Sbjct: 269 EQAEVVPDLLTCGKGITAGYLPLSAVLVAQHVYDAFLSQPDDDGPRTFFHGHTYTANPIC 328 Query: 289 CSAALASVEVIEELIKDDKVIEKGKYFIRKLENL---IEKYNFIKEVRGLGLMIGAEL-- 343 C+AA+A++EV++ D V+ + ++L++L + + + E+R LG M+G E+ Sbjct: 329 CAAAIANLEVMDR----DNVLGQAGRLAQRLDHLFKPLADHPEVTEIRQLGTMVGVEVTS 384 Query: 344 --EFNGADIVKKMLEKGFLINCTSDTVLRFLPPLIVEKEH----IDALINALDEV 392 E G + + E G + DTV+ +PPL +++ +D L A+D+V Sbjct: 385 LGERTGFQVCQAAREHGVWLRPLGDTVI-VMPPLTLDESDTRLLVDGLGKAIDDV 438 Lambda K H 0.320 0.141 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: 380 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: 398 Length of database: 442 Length adjustment: 32 Effective length of query: 366 Effective length of database: 410 Effective search space: 150060 Effective search space used: 150060 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