Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_010959390.1 MCA_RS00085 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000008325.1:WP_010959390.1 Length = 451 Score = 189 bits (480), Expect = 1e-52 Identities = 136/411 (33%), Positives = 215/411 (52%), Gaps = 59/411 (14%) Query: 25 GEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL-YYNEPQAEA 83 GEG + D +G Y+D ++ VN+ GHCHPA+ A+ +Q+ RL H + +EP Sbjct: 37 GEGVWLEDFDGRRYLDAISSWWVNLFGHCHPAINAALADQLGRLEHVIFAGFSHEPGIRL 96 Query: 84 ARLLAEAAPKDLNKVFFCNSGTESVECAIKLA------RKFTGCTKFIAFEGGFHGRTMG 137 A L + P L + F+ ++G+ +VE A+K++ R G T+F+ E +HG T+G Sbjct: 97 AERLVDITPPGLERCFYADNGSAAVEVALKMSFHYWRNRGRPGKTRFVTLENSYHGETLG 156 Query: 138 ALSATWKPEFREPFEPLVPEFEHVP----YG----------------DVNAVEKAIDDDT 177 AL+ P ++E + PL+ E P YG D+ A+ + D+ Sbjct: 157 ALAVGDVPLYKETYRPLLMEAVAAPSPDAYGREPGETEAGYAERRFRDMLAILERGADEI 216 Query: 178 AAVIVEP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDV 236 AVIVEP VQ G+R+ +LR LR CD G+ LI DE+ G GRTG FA E + Sbjct: 217 CAVIVEPLVQCAGGMRMYDPLYLRLLRAACDRLGIHLIADEIAVGFGRTGTLFACEQAGI 276 Query: 237 LPDIVCLAKGLGGG-VPVGATIAREEVAEAF-------EPGDHGSTFGGNPLACAAVCAA 288 PD +CL+KGL GG +P+ A + R E+ AF + H ++ GNPLAC AA Sbjct: 277 SPDFLCLSKGLTGGYLPLAAVLTRPEIYAAFYDDYGTLKAFLHSHSYTGNPLACR---AA 333 Query: 289 VSTVLEENLPEAAERKGKLAMRILSEAED------VVEEVRGRGLMMGVEVGDDERAKD- 341 ++T+ + + R +LA R +++A + V EVR RG+++ +E+ D+ ++ Sbjct: 334 LATLELFDATDVLGRNRELA-RCMADATERFQEHPHVAEVRQRGMILAIEMVKDKTTREP 392 Query: 342 ----------VAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELA 382 V R L+RG L+ G+VI +PP +I +++ + +AE+A Sbjct: 393 YPWQERRGLRVYRRALERGVLLR-PLGNVIYFMPPYLITPEQI-RLMAEVA 441 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: 433 Number of extensions: 22 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: 451 Length adjustment: 32 Effective length of query: 357 Effective length of database: 419 Effective search space: 149583 Effective search space used: 149583 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