Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_014148277.1 MEALZ_RS08805 acetylornithine transaminase
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000968535.2:WP_014148277.1 Length = 397 Score = 340 bits (872), Expect = 5e-98 Identities = 180/396 (45%), Positives = 249/396 (62%), Gaps = 18/396 (4%) Query: 34 YVMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVRAVSDQIQKLH 93 ++M TYGR I++ RG+G+ LWD +G YLD ++GIA C LGHAHP++ +A+ +Q KL Sbjct: 4 HIMPTYGRLSISLDRGEGAWLWDQQGNCYLDALSGIAVCNLGHAHPSIHKAICEQSAKLV 63 Query: 94 HVSNLYYIPEQGELAKWIVEHSCADRVFFCNSGAEANEAAIKLVRKYAHTVLDFLEQPVI 153 H SNLY I Q +LA + S D FFCNSGAEANEAAIK+ R+Y H +E P I Sbjct: 64 HTSNLYRIDLQEQLADRLTALSGMDNAFFCNSGAEANEAAIKIARRYGHQ--KDIENPAI 121 Query: 154 LTAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYNDIRSLENKVADLDEGNSRVA 213 + + SFHGRTLAT++ATG K QQ F PLV GF VPYNDI +++N + + +S V Sbjct: 122 IVMEKSFHGRTLATLSATGNTKIQQGFAPLVEGFIRVPYNDITAIKNAL----QQHSNVV 177 Query: 214 AIFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQVGVGRTGKLWGYEHLGVEP 273 AI +EP+QGEGGV Y +R +CD++D+L++ DE+Q G+GRTGK Y+H + P Sbjct: 178 AILIEPIQGEGGVNIPAPDYLNNIRTLCDRHDLLMMLDEIQTGIGRTGKFLAYQHNDILP 237 Query: 274 DIFTSAKGLAGGVPIGAMMCK-KFCDVFEPGNHASTFGGNPLACAAGLAVLKTIEGDRLL 332 D+ T AK LA GVPIGA + + K + PG H STFGGNPLAC+A LAVL + L+ Sbjct: 238 DVCTLAKALANGVPIGACLARGKAEQILTPGTHGSTFGGNPLACSAALAVLNELNDGHLI 297 Query: 333 DNVQARGEQLRSGLAEI---KNQYPTLFTEVRGWGLINGLEISAESSLTSVEIVKAAMEQ 389 + + +G + S L E+ N+ E+R GL+ G+E+S E+V A+ + Sbjct: 298 EQAEIKGRMIASKLDELLVGNNK----IVEIRHKGLMIGVELSVPCG----ELVSNALSK 349 Query: 390 GLLLAPAGPKVLRFVPPLVVTEAEIAQAVEILRQAI 425 GLL+ K +R +PPL++ +I + VE L I Sbjct: 350 GLLINVTNEKTIRLLPPLIIDAQQIERLVETLTAVI 385 Lambda K H 0.320 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: 431 Number of extensions: 20 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: 429 Length of database: 397 Length adjustment: 31 Effective length of query: 398 Effective length of database: 366 Effective search space: 145668 Effective search space used: 145668 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 (21.8 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