Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_089302251.1 CHB84_RS15040 glutamate-1-semialdehyde 2,1-aminomutase
Query= uniprot:A0A806JQF3 (400 letters) >NCBI__GCF_900188115.1:WP_089302251.1 Length = 433 Score = 138 bits (347), Expect = 4e-37 Identities = 100/292 (34%), Positives = 137/292 (46%), Gaps = 19/292 (6%) Query: 21 NNYGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGHTS 80 ++ G P + SG+GA ++D DG Y+DL+ +LGH HPAV+EAV R + G + Sbjct: 31 SSVGGTPRFMVSGEGAYLSDEDGNRYVDLVSSWGPMILGHSHPAVVEAV-RSAAASGLSF 89 Query: 81 NLYATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLSR-LTGRTKLVAAHDAF 139 + LA E++ + ++ R+ NSG EA A +L+R TGR K+V + Sbjct: 90 GT-PVRGEVDLAAEIIRRVDPVEQVRL--VNSGTEATMTAIRLARAFTGRDKIVKFAGCY 146 Query: 140 HGRTMGSLALTGQPAKQTPFAPLPG-------DVTHVGYGDVDALAAAVDDHT---AAVF 189 HG L G PG D + Y D++A+ A +H AAV Sbjct: 147 HGHVDALLVQAGSGVATLGLPTSPGVSDAQAADTIVLPYNDIEAVRACFAEHAGRIAAVI 206 Query: 190 LEPIMGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQHDGITPDVV 249 E G G V P G+ A R +TA GALL++DEV TG R A + D + D+ Sbjct: 207 TEAAAGNMGAVAPVPGFNAELRRLTAEDGALLIMDEVMTGF-RVSAAGWYGLDWVAGDLY 265 Query: 250 TLAKGLGGGLPIGACLAVGPAAELLTPG---LHGSTFGGNPVCAAAALAVLR 298 T K + GGLP A +L P T GNPV AAA LA LR Sbjct: 266 TFGKVMSGGLPAAAFGGRADVLAMLAPSGSVYQAGTLAGNPVAAAAGLATLR 317 Lambda K H 0.320 0.136 0.399 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: 429 Number of extensions: 24 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: 400 Length of database: 433 Length adjustment: 31 Effective length of query: 369 Effective length of database: 402 Effective search space: 148338 Effective search space used: 148338 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 (21.8 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