Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_281171280.1 G496_RS0112560 ornithine--oxo-acid transaminase
Query= curated2:Q58131 (398 letters) >NCBI__GCF_000429985.1:WP_281171280.1 Length = 395 Score = 291 bits (745), Expect = 2e-83 Identities = 168/402 (41%), Positives = 240/402 (59%), Gaps = 23/402 (5%) Query: 9 LEKKYHLQIYGRLPVVLVEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKKQA 68 L+KK Y L V+L G+G+ VYDID K+Y+D L+ N GHCHP +++A+++QA Sbjct: 3 LKKKLGADNYKPLDVILSRGQGVWVYDIDQKRYMDCLSAYSAVNQGHCHPAILKAMQEQA 62 Query: 69 ETLIHTSNIYYTIPQIKLAKKLVELSGLDRAFFCNSGAEANEGAIKFARKYVSKVLG--R 126 + L TS + + + EL+G + NSGAEA E A+K RK+ +V G Sbjct: 63 QKLTLTSRAFRNDQLALFYQDICELTGSHKVLPMNSGAEAVETAVKAVRKWGYEVKGIPE 122 Query: 127 EGGEIISMYNAFHGRTLTTLAATPKPKYQDGFYPLPPGFKYVPFNDIEALKEAITDKTAA 186 EII + FHGRT+T + + P + GF P PGFK VPF D +AL++AIT T A Sbjct: 123 NRAEIIVCADNFHGRTITIVGFSTDPVSRSGFGPFTPGFKIVPFGDAKALEKAITPNTVA 182 Query: 187 IMIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAFEHYGVEPD 246 + EP+QGE G+ + YLK VR++C NI+LI DE+Q G+GRTG++ A EH +E D Sbjct: 183 FLAEPIQGEAGVIIPPDGYLKEVREICSSANIMLILDEIQTGLGRTGKLLAEEHENIEAD 242 Query: 247 ILTLAKALGGG-VPIGAVVLKEEIAKALSYGDHGTTFGGNPLACSAALASVEVI--EELI 303 + + KAL GG P+ AV+ E+ L G+HG+TFGGNPLAC+ A A+++VI E L+ Sbjct: 243 LTLVGKALSGGFYPVSAVLSNNEVLGVLKPGEHGSTFGGNPLACAVARAALKVIKDENLV 302 Query: 304 KDDKVIEKGKYF---IRKLENLIEKYNFIKEVRGLGLMIGAELEFNGADIVKK----MLE 356 K+ E GKYF ++K EN N IKE+RG GL++ E + GA +K + + Sbjct: 303 KN--AAEMGKYFLDGLKKAEN-----NQIKEIRGKGLLMAVEFK-PGAGGARKYCRNLQD 354 Query: 357 KGFLINCTSDTVLRFLPPLIVEKEHIDALINALDEVFTEIKK 398 +G L T D ++RF PPL++ +E +D ALD + I K Sbjct: 355 QGILCKETHDNIIRFAPPLVITREEVDW---ALDRIIPVISK 393 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: 396 Number of extensions: 18 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: 398 Length of database: 395 Length adjustment: 31 Effective length of query: 367 Effective length of database: 364 Effective search space: 133588 Effective search space used: 133588 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 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