Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_013430453.1 CALKRO_RS07580 glutamate-1-semialdehyde 2,1-aminomutase
Query= curated2:O30156 (375 letters) >NCBI__GCF_000166775.1:WP_013430453.1 Length = 426 Score = 165 bits (418), Expect = 2e-45 Identities = 104/307 (33%), Positives = 161/307 (52%), Gaps = 14/307 (4%) Query: 21 VIERGEGCYVYDVNGKRYLDLVAGIATVSIGHCNSHLVERLKEQLEKLIHISNLYYTTPQ 80 +I +G+GC+++DV+G Y+D V + +GHC+ +V R+KE +E+ I T + Sbjct: 37 IISKGKGCHIFDVDGNEYIDFVLSWGAMILGHCDPDVVNRIKEVVEEQIAFG--APTEIE 94 Query: 81 VELAEKLSEIAGMDRFFFCNSGAEAVEAALKFARRATGRKKFVSFTGDFHGR----TMGA 136 E+A+ + E A +D F NSG EA A++ A+ TG+KK V F G +HG A Sbjct: 95 YEMAKLVCETAQIDMVRFVNSGTEATMTAVRLAKGYTGKKKIVKFAGCYHGHHDIFLKEA 154 Query: 137 LSVTHKEKFRKPFEPLVSPVEFAEFNNPESLEKVVDE---ETAAVIVELVQGEAGVYPAD 193 S + + + E +V E+NN +S+EK E E AAVI+E V G G + Sbjct: 155 GSAVAELRLKGIDEDIVQNTIVVEYNNLDSVEKAFKENKDEIAAVIIEPVAGNMGTVASK 214 Query: 194 REFVKAIEELREKYGFLLIVDEVQTGFGRTGRWFAKDHYGIEPDMITMAKAMGSGVPIGC 253 +EF++ + E+ YG +LI DEV TGF R A+ Y +EPD+IT+ K +G G+P G Sbjct: 215 KEFLQTLREICNFYGSVLIFDEVITGF-RLSLKGARALYNVEPDLITLGKIIGGGLPCGA 273 Query: 254 CALKEEVAEKIQVGDH---GSTFGGNPLACTAALATIEVI-EREGLVENSARMGEYFVKR 309 K+E+ + + + T GNP+ + ATI+ + E N + F K Sbjct: 274 VGGKKEIMQCLAPQGNVFQAGTMSGNPIVMSVGYATIKKLKENPHFYSNLEMLAGKFEKE 333 Query: 310 LKESFEN 316 L + F N Sbjct: 334 LTQVFSN 340 Lambda K H 0.320 0.138 0.398 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: 405 Number of extensions: 25 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: 375 Length of database: 426 Length adjustment: 31 Effective length of query: 344 Effective length of database: 395 Effective search space: 135880 Effective search space used: 135880 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 Jul 26 2024. The underlying query database was built on Jul 25 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