Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_041100608.1 SUTH_RS15840 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000828635.1:WP_041100608.1 Length = 426 Score = 160 bits (405), Expect = 6e-44 Identities = 130/398 (32%), Positives = 191/398 (47%), Gaps = 34/398 (8%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL-YYN 77 P+ +V +G R+ +G E ID ++ G+ HP + A++ Q+ L H + Sbjct: 25 PLPVVATQGVRIRLADGRELIDGISSWWTACHGYNHPHIRAAIERQLASLPHVMFAGLVH 84 Query: 78 EPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF------TGCTKFIAFEGGF 131 EP A A+ LA P DL +VFF SG+ +VE A+K+A ++ + + F G+ Sbjct: 85 EPAARLAQRLAALLPGDLERVFFTESGSVAVEVALKMAIQYWRNKGQAEKQRIVYFRHGY 144 Query: 132 HGRTMGALSATWKPE--FREPFEPLVPEFEHVPYGDVNAVEKAID-------DDTAAVIV 182 HG T + A PE F +P+ + +A + + AAVI+ Sbjct: 145 HGDTFATM-ALCDPEEGMHSLFAGAMPDQIMAELPSDETMRRAFELLLETHGERLAAVII 203 Query: 183 EP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHED----VL 237 EP VQG G+++ L + C H LLLI DE+ +G GRTG+ FA E D + Sbjct: 204 EPLVQGAGGMQMHDAATLAFIAAACARHKLLLIADEIMTGFGRTGRMFACEEADELTSTI 263 Query: 238 PDIVCLAKGL-GGGVPVGATIAREEVAEAFEPGD------HGSTFGGNPLACAAVCAAVS 290 PDIVCL+K L GG +P+ AT+AR V EAF D HG T+ N LACAA A++ Sbjct: 264 PDIVCLSKALTGGTLPLAATVARRHVFEAFLADDPAAALMHGPTYMANALACAAANASLD 323 Query: 291 TV-LEENLPEAAERKGKLAMRILSEAEDV--VEEVRGRGLMMGVEVGDDERAKDVAREML 347 E L + A + +LA L D+ V EVR +G + VE+ + R Sbjct: 324 LFESEPRLAQVAAIEAQLAAE-LGPCRDLAGVAEVRVKGAIGAVELAGRIELDALRRRFA 382 Query: 348 DRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADAL 385 + G V G V+ L+PP VI ++L A + L Sbjct: 383 ELGVWVR-PFGKVVYLMPPFVIAAEDLTTLTAAVRQVL 419 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: 404 Number of extensions: 28 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: 426 Length adjustment: 31 Effective length of query: 358 Effective length of database: 395 Effective search space: 141410 Effective search space used: 141410 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 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