Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_039652759.1 PN53_RS08440 acetylornithine/succinylornithine family transaminase
Query= curated2:Q9X2A5 (385 letters) >NCBI__GCF_000816635.1:WP_039652759.1 Length = 404 Score = 340 bits (873), Expect = 3e-98 Identities = 178/386 (46%), Positives = 240/386 (62%), Gaps = 9/386 (2%) Query: 2 YLMNTYSRFPATFVYGKGSWIYDEKGNAYLDFTSGIAVNVLGHSHPRLVEAIKDQAEKLI 61 Y++ TY R+ KG ++YD+KG YLDF GIAVN G+ + +++ +K+Q + ++ Sbjct: 20 YMIETYERYDFVCERAKGMYLYDDKGEGYLDFYGGIAVNSAGNCNDKVIATVKEQIDDVM 79 Query: 62 HCSNLFWNRPQMELAELLSKNTFGGKVFFANTGTEANEAAIKIARKYGKKK-SEKKYRIL 120 H N + PQ LAE + K K+F+ NTGTEANEA IK+ARKYG +K KY I+ Sbjct: 80 HTFNYPYTIPQALLAEKVCKTIGMDKIFYQNTGTEANEAMIKMARKYGVEKYGPNKYNIV 139 Query: 121 SAHNSFHGRTLGSLTATGQPKY--QKPFEPLVPGFEYFEFNNVEDLRRKMSEDVCAVFLE 178 +A FHGRT GSLTATGQP Q +P++PGF Y +FN++E + ++E+ A+ LE Sbjct: 140 TAKQGFHGRTYGSLTATGQPDNACQIGLKPMLPGFSYADFNDLESFKSLVTENTIAIMLE 199 Query: 179 PIQGESGIVPATKEFLEEARKLCDEYDALLVFDEVQCGMGRTGKLFAYQKYGVVPDVLTT 238 PIQGE G+VPAT+EF++ RKLCD+ LL+ DEVQ G RTGK+ AY YG+ PD+++ Sbjct: 200 PIQGEGGVVPATQEFMKGIRKLCDDKGMLLLIDEVQTGWCRTGKVMAYMHYGIKPDIVSM 259 Query: 239 AKGLGGGVPIGAVIVNER-ANVLEPGDHGTTFGGNPLACRAGVTVIKELTKEGFLEEVEE 297 AK +GGG+PIGA+ E + G HGTTFGGNPL C + I EL EE Sbjct: 260 AKAMGGGMPIGAICATEEVSKAFTMGSHGTTFGGNPLCCAGSLAEINELLDNNLAGNAEE 319 Query: 298 KGNYLMKKLQEMKEEYDVVADVRGMGLMIGIQFREEVSNREVATKCFENKLLVVPAGNNT 357 GNY MKKL+ + V DVRG GLMIGI+F + +++ CF+ KLLV G + Sbjct: 320 VGNYFMKKLKTIPH----VKDVRGKGLMIGIEF-DSPLGKDIKHGCFDRKLLVTLIGTSV 374 Query: 358 IRFLPPLTVEYGEIDLAVETLKKVLQ 383 IR LPPL + D A E LK + Sbjct: 375 IRVLPPLIATREDCDKAYEILKSAAE 400 Lambda K H 0.318 0.138 0.402 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: 480 Number of extensions: 23 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: 385 Length of database: 404 Length adjustment: 31 Effective length of query: 354 Effective length of database: 373 Effective search space: 132042 Effective search space used: 132042 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