Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_089301254.1 CHB84_RS09600 ornithine--oxo-acid transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_900188115.1:WP_089301254.1 Length = 409 Score = 271 bits (694), Expect = 2e-77 Identities = 164/392 (41%), Positives = 213/392 (54%), Gaps = 13/392 (3%) Query: 5 ELIDKYHMNTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQ 64 EL +++ + Y PV L G G V D +GN+Y+D +AG + GH HP +V A Q Sbjct: 18 ELDERWSTHNYHPLPVVLAEGRGCWVTDVDGNDYLDFLAGYSALNFGHRHPDLVAAASAQ 77 Query: 65 VERLIHCSNLYYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFT----- 119 +ERL S ++++ R LAE ++ V NSG E+VE A+K+ARK+ Sbjct: 78 LERLTLTSRAFHHDQFGAFCRELAELTGTEM--VLPMNSGAEAVESAVKVARKWAYRIKG 135 Query: 120 ---GCTKFIAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPYGDVNAVEKAIDDD 176 G + + FHGRT +S + + R + P P F VPYGD +AV AI + Sbjct: 136 VPDGTAEIVTMSSNFHGRTTTIVSFSEDTDARTDYGPYTPGFVTVPYGDPSAVADAITER 195 Query: 177 TAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDV 236 TAAV++EPVQGEAGV PP GFL E+R LCDE G+LLI DE+QSG+ RTG A +H V Sbjct: 196 TAAVLLEPVQGEAGVVTPPPGFLAEVRRLCDERGVLLIADEIQSGLARTGTVLALDHAGV 255 Query: 237 LPDIVCLAKGLGGGV-PVGATIAREEVAEAFEPGDHGSTFGGNPLACAAVCAAVSTV-LE 294 D+ L K LGGG+ PV A + V PG HGSTFGGNPLACA A V + Sbjct: 256 RADLYTLGKALGGGILPVSAVVGNAAVLGLLRPGQHGSTFGGNPLACAVGRAVVRLLGSG 315 Query: 295 ENLPEAAERKGKLAMRILSEAEDVVEEVRGRGLMMGVEVGDDERAKDVAREML-DRGALV 353 E A E L R+ V+ VRG GL GV++ D A EML +G L Sbjct: 316 EYQRRATELGAHLHGRLGELVGRGVDAVRGIGLWAGVDIAPDGPTGRQASEMLAAKGVLC 375 Query: 354 NVTSGDVIRLVPPLVIGEDELEKALAELADAL 385 T G +R+ PPLVI E ELE + +A L Sbjct: 376 KETHGSTLRIAPPLVIDESELESGIDAIAGVL 407 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: 382 Number of extensions: 25 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: 389 Length of database: 409 Length adjustment: 31 Effective length of query: 358 Effective length of database: 378 Effective search space: 135324 Effective search space used: 135324 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: 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