Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_049768184.1 MSIL_RS14670 aspartate aminotransferase family protein
Query= curated2:Q81M98 (386 letters) >NCBI__GCF_000021745.1:WP_049768184.1 Length = 475 Score = 228 bits (582), Expect = 2e-64 Identities = 135/339 (39%), Positives = 197/339 (58%), Gaps = 17/339 (5%) Query: 1 MISHLFQTYGRRTVEFVKGNGTKVIDNNGKQYLDFTSGIGVCNLGHCHPTVMKAVQEQLN 60 M+ +FQT G V F +G G + D G +YLD SG GV +G HP + +A++ L Sbjct: 40 MMVRVFQTIGT-DVGFQRGEGQYLYDRRGARYLDLLSGWGVFGVGRNHPLIREALESVLA 98 Query: 61 DIWHISNLFTNSLQEEVASLLTENIA-----LDYVFFCNSGAEANEAALKLARKHTGKSL 115 + NL + +A LL E + LD VFF NSG EA EAALK AR+ TG++ Sbjct: 99 A--ELPNLVQMDVSV-LAGLLAERLLGFVPYLDKVFFANSGTEAVEAALKFARRATGRTE 155 Query: 116 VVTCEQSFHGRTFGTMSATGQNKVKEGFGPLLPSFLHTPFNDIKALKEVMNE-EVAAVMV 174 ++ C +FHG ++G +S G K+GFGPLLP + PFND+ AL++ ++ + AA +V Sbjct: 156 IIHCGHAFHGLSYGALSLNGDAIFKDGFGPLLPDCVEVPFNDLAALEKALSSGKAAAFIV 215 Query: 175 EVVQGEGGVIPADLSFLKEIETLCKKFGSLFIIDEVQTGIGRTGTLFAYEQMGIDPHIVT 234 E +QG+G +P D +L++ LC+K+G+LFI DE+QTG+GRTG A E G++P +V Sbjct: 216 EPIQGKGVNMPDDW-YLRDAAALCRKYGALFIADEIQTGLGRTGRFLAVEHWGVEPDMVL 274 Query: 235 TAKALGNG-IPVGAMIGRKEL-----GTSFTAGSHGSTFGGNYVAMAAAKEVLQVSKRLS 288 AK L G +PVGA++ RK + A HGSTF N +AMAA L+V + Sbjct: 275 IAKGLSGGHVPVGAVLTRKHVFEKVFNRMDRAVIHGSTFAKNDMAMAAGLATLEVIESER 334 Query: 289 FLKEVQEKGEYVLQKLQEELQHVECIQNIRGKGLMVGIE 327 + + G +L+ Q E ++ +RGKGLM+G+E Sbjct: 335 LIANAERLGARLLKSFAAMEQRYELVKAVRGKGLMIGVE 373 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: 348 Number of extensions: 11 Number of successful extensions: 3 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: 475 Length adjustment: 32 Effective length of query: 354 Effective length of database: 443 Effective search space: 156822 Effective search space used: 156822 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 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