Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_052666231.1 NITAL_RS10730 aspartate aminotransferase family protein
Query= curated2:Q7MAE6 (393 letters) >NCBI__GCF_000969705.1:WP_052666231.1 Length = 449 Score = 134 bits (336), Expect = 7e-36 Identities = 100/320 (31%), Positives = 149/320 (46%), Gaps = 30/320 (9%) Query: 24 GKNATLWDSEGKDYIDFASGIAVCSVGHGNERLAGAICDQAKKLIHTSNLYYI-EPQARL 82 G+ +WD+ GK Y+D S + VG+G + + A Q KL ++N Y +P L Sbjct: 34 GEGCYVWDTTGKRYLDGLSALFCLQVGYGRQEMVEAAATQMAKLPFSTNWSYANQPSIDL 93 Query: 83 AEKLVKLSGYDM-RVFFANSGAEANEGAIKIARKFGESHEGEVKRYKIITLESSFHGRTI 141 A L + D+ R FF NSG+EA EGA+K+A+++ + GE R K+I+ ++HG T+ Sbjct: 94 AGALAQRFPGDLNRFFFVNSGSEAVEGAVKLAQQYHRLN-GEPTRVKVISRNYAYHGTTL 152 Query: 142 TALKATGQEKMHHYFGPYPDGFVYAKNL---------------DHVFKLVDEKTCAVLLE 186 AL TG + F P +YA N D + + E V+ E Sbjct: 153 GALGVTGLAGLREPFEPLRPVHLYAPNTNAYRPQHDDPAQAIEDLILEAGPENVSLVIAE 212 Query: 187 LVQGEGGIEPQDREGIKKLERFLKERGVLLMVDEVQTGIYRSGELFASQAYGIVPDVITV 246 VQ GG + +L GVLL DEV T R G ++ YG+VPD++T Sbjct: 213 PVQNAGGCFTPPADYWPRLREICDRHGVLLACDEVITAFGRLGTWTGAERYGVVPDILTF 272 Query: 247 AKGLAGG-VPIGAVMTTLKDIFAPG---------DHGSTFGGNFLSTRAGLEVLSILESL 296 AKG+ P+G V +D A HG+T+GG+ +S L L + E+ Sbjct: 273 AKGVTSAYAPLGGV--AFRDHIAAALQSEKHTMFVHGATWGGHPVSCAVALANLEVFETE 330 Query: 297 YQEGTLQKSIDRFSAELRAL 316 +Q + D F +LR L Sbjct: 331 DVLANVQANEDWFGDQLREL 350 Lambda K H 0.319 0.138 0.394 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: 415 Number of extensions: 22 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: 393 Length of database: 449 Length adjustment: 32 Effective length of query: 361 Effective length of database: 417 Effective search space: 150537 Effective search space used: 150537 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 (21.7 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