Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_051305361.1 G494_RS0103960 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= curated2:Q9X2A5 (385 letters) >NCBI__GCF_000429965.1:WP_051305361.1 Length = 466 Score = 186 bits (472), Expect = 1e-51 Identities = 130/425 (30%), Positives = 210/425 (49%), Gaps = 60/425 (14%) Query: 15 VYGKGSWIYDEKGNAYLDFTSGIAVNVL-GHSHPRLVEAIKDQAEKLIHCSNLFWNRPQM 73 V G+G + D +GN YLD TSG +V+ G+ + EA+ Q +K+ + + +F N P + Sbjct: 42 VEGQGLMVKDIRGNEYLDATSGGVWSVMVGYGRDSIAEAVCAQLKKMPYFAGVFGNVPSI 101 Query: 74 ELAE-LLSKNTFGGKVFFANTGTEANEAAIKIARKYGKKKSEKK--YRILSAHNSFHGRT 130 + A+ LL K KV+F+N+G+EANE A KI R+ + E+K Y+I+ +HG T Sbjct: 102 KFAQKLLEKLPRMDKVYFSNSGSEANEKAFKIVRQASRISPERKGKYKIMYRDRDYHGTT 161 Query: 131 LGSLTATGQPKYQKPFEPLVPGF---------------EYFEFN-----NVEDLRRKMSE 170 +G+++ATGQ + ++ F P V GF Y E N VED+ K Sbjct: 162 IGAMSATGQAQRKQDFGPFVEGFVEFPHCACYRCPHDKTYGECNIECARKVEDIILKEGA 221 Query: 171 D-VCAVFLEPIQGESGIVPATKEFLEEARKLCDEYDALLVFDEVQCGMGRTGKLFAYQKY 229 D + A+ +EPI GI+ E+ +++C +YD ++ DEV CG GRTGK + ++ + Sbjct: 222 DTIGAMIVEPITAGGGILKPVPEYYPILQEICKKYDIWMIMDEVVCGFGRTGKFWGHEHF 281 Query: 230 GVVPDVLTTAKGLGGGV-PIGAVIVNERANVLEPGDHG------------TTFGGNPLAC 276 V PD++T AKGL + A +V + + D +T+GG A Sbjct: 282 DVDPDIVTMAKGLASSYEALSATVVKQHVYDVFLNDPANEDDRLNYFRDISTYGGCTSAM 341 Query: 277 RAGVTVIKELTKEGFLEEVEEKGNYLMKKLQEMKEEYDVVADVRGMGLMIGIQFREEVSN 336 A + + + E +E E G Y++ KL+E+K ++D V D+RG GL GI+F V+N Sbjct: 342 TAALESTRIIEDENLVENSREIGAYMISKLEELK-KFDCVGDIRGEGLFGGIEF---VTN 397 Query: 337 REVATKCFENKLLVVPAG------------------NNTIRFLPPLTVEYGEIDLAVETL 378 RE E ++ + NN + F P L + ++D V + Sbjct: 398 RETKEPITEGQMAALMGNVMAQGVIVGRTNSSFHGLNNIMNFAPCLIITKEQVDTVVGAV 457 Query: 379 KKVLQ 383 ++ Sbjct: 458 AAAIE 462 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: 464 Number of extensions: 24 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: 466 Length adjustment: 32 Effective length of query: 353 Effective length of database: 434 Effective search space: 153202 Effective search space used: 153202 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: 51 (24.3 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