Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_051335635.1 METAC_RS0116365 aspartate aminotransferase family protein
Query= curated2:Q81M98 (386 letters) >NCBI__GCF_000427445.1:WP_051335635.1 Length = 476 Score = 231 bits (590), Expect = 2e-65 Identities = 139/339 (41%), Positives = 197/339 (58%), Gaps = 17/339 (5%) Query: 1 MISHLFQTYGRRTVEFVKGNGTKVIDNNGKQYLDFTSGIGVCNLGHCHPTVMKAVQEQLN 60 M+ + QT G V F G G + D G++YLD SG GV +G HP + +A+ L Sbjct: 41 MMVRVLQTIGF-DVGFRCGRGQYLFDREGERYLDLLSGFGVFGIGRNHPALRQALGAVLE 99 Query: 61 DIWHISNLFTNSLQEEVASLLTENIA-----LDYVFFCNSGAEANEAALKLARKHTGKSL 115 + NL + +A LL E + LD VFF NSG EA EAALK AR TG+ Sbjct: 100 S--DLPNLVQMDVSV-LAGLLAERLLRYAPYLDKVFFTNSGTEAVEAALKFARSATGRPG 156 Query: 116 VVTCEQSFHGRTFGTMSATGQNKVKEGFGPLLPSFLHTPFNDIKALKEVMNE-EVAAVMV 174 VV C+ +FHG T+G +S G ++GFGPL+P + PF+D+ AL +++ +VAA +V Sbjct: 157 VVHCDHAFHGLTYGALSLNGDEIFRDGFGPLIPGCVQIPFDDLAALDRALSKRDVAAFIV 216 Query: 175 EVVQGEGGVIPADLSFLKEIETLCKKFGSLFIIDEVQTGIGRTGTLFAYEQMGIDPHIVT 234 E +QG+G IP DL +L+ + LC+K+G+LFI DEVQTG+GRTG A E G++P +V Sbjct: 217 EPIQGKGVNIPNDL-YLRGAQALCRKYGTLFIADEVQTGLGRTGKFLAIEHWGVEPDMVL 275 Query: 235 TAKALGNG-IPVGAMIGRKEL-----GTSFTAGSHGSTFGGNYVAMAAAKEVLQVSKRLS 288 AKAL G PVGA++ RK + A HGSTF N +AMAA L V + Sbjct: 276 LAKALSGGHAPVGAVLARKAIFEKVFNRMDRAVVHGSTFAKNDLAMAAGLATLDVIESEG 335 Query: 289 FLKEVQEKGEYVLQKLQEELQHVECIQNIRGKGLMVGIE 327 ++ ++KG +L + + E ++ +RGKGLM+G+E Sbjct: 336 LVRNAEQKGARLLAAFEAMAERHELVKTVRGKGLMIGVE 374 Lambda K H 0.319 0.136 0.388 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: 345 Number of extensions: 13 Number of successful extensions: 4 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: 386 Length of database: 476 Length adjustment: 32 Effective length of query: 354 Effective length of database: 444 Effective search space: 157176 Effective search space used: 157176 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: 51 (24.3 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