Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012853702.1 TCUR_RS16645 aspartate aminotransferase family protein
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000024385.1:WP_012853702.1 Length = 431 Score = 230 bits (586), Expect = 7e-65 Identities = 159/413 (38%), Positives = 221/413 (53%), Gaps = 40/413 (9%) Query: 12 MNTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVER-LIH 70 M Y P+ +V G+G RV D EGN Y+D AGI N+LG+ V +AV+ Q+ ++H Sbjct: 16 MALYYERPIEIVSGKGVRVTDAEGNTYLDFFAGIITNILGYDVEEVRQAVERQLATGVVH 75 Query: 71 CSNLYYNEPQAEAA-RLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCTKFIAFEG 129 S Y Q E A +++A + KD KVFF NSGTE+ E A+ LA + +A Sbjct: 76 TSTAYLLRGQVELAEKIVALSGIKDA-KVFFVNSGTEANETALLLATYARKSNQVLAMRQ 134 Query: 130 GFHGRTMGALSAT----WKPEFREPF--------EPLVPEFEHVPYGDV---------NA 168 +HGR+ GA+ T WK P + +P+F H+ D + Sbjct: 135 SYHGRSFGAIGVTANRSWKNNAYTPLTVHFLHGGDRHLPQFAHLSDADFIKVCTEDLRHV 194 Query: 169 VEKAIDDDTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQ- 227 + A D AA+I EP+QG G +PP+G +E+ DE+G L I DEVQ+G GRTGQ Sbjct: 195 LATATGGDVAALIAEPIQGVGGFTMPPDGLYAAYKEVLDEYGALFISDEVQTGWGRTGQS 254 Query: 228 FFAFEHEDVLPDIVCLAKGLGGGVPVGATIAREEVAEAFEPGDHG-STFGGNPLACAAVC 286 FF + V PDI+ AKGLG G VG +AR ++ +A P G STFGGNP+A AA Sbjct: 255 FFGIHNHGVTPDIMTFAKGLGNGFAVGGVVARGDLMDA--PHATGLSTFGGNPIAMAAAN 312 Query: 287 AAVSTVLEENLPEAAERKGKLAMRILSEAE---DVVEEVRGRGLMMGVEV---GDDERAK 340 A + +L+ +L A R+G L + L EA VV VRG+GLM VE+ G E + Sbjct: 313 ATLDYILDHDLQSNAARQGALLLDGLKEAAPRLPVVGAVRGKGLMFAVELVEPGTGEPSP 372 Query: 341 DVAREMLD----RGALVNVTS--GDVIRLVPPLVIGEDELEKALAELADALRA 387 +A +++ RG LV G+VIR+ PPL I E++ + L L D+L A Sbjct: 373 PLAAAVMEETRKRGLLVGKGGLYGNVIRMAPPLTITEEDAREGLGILIDSLEA 425 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: 417 Number of extensions: 25 Number of successful extensions: 8 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: 431 Length adjustment: 31 Effective length of query: 358 Effective length of database: 400 Effective search space: 143200 Effective search space used: 143200 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 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