Align Acetylornithine aminotransferase 1; ACOAT 1; EC 2.6.1.11 (uncharacterized)
to candidate Dsui_0664 Dsui_0664 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:Q89VE9 (405 letters) >FitnessBrowser__PS:Dsui_0664 Length = 427 Score = 147 bits (371), Expect = 6e-40 Identities = 106/321 (33%), Positives = 151/321 (47%), Gaps = 31/321 (9%) Query: 23 FERGEGCWLIATNGDRYLDFTSGVAVNALGHAHPALVKALQEQATKLWHMSNLFQSPDGE 82 F RGEG + G YLD+ LGHAH VKA+QE A + F +P Sbjct: 37 FTRGEGPRVWDAEGKSYLDYVGSWGPLILGHAHAPTVKAVQEAAA----LGLSFGAPTEA 92 Query: 83 KL--ATRLCNE-SFADFVFFCNSGAEALEGVIKLVRHHHFSKGHPERYRIITFEGAFHGR 139 ++ A LC+ D V +SG EA I+L R GH R ++ FEG +HG Sbjct: 93 EIEIADLLCDILPSLDMVRLVSSGTEATMSAIRLAR------GHTGRDLLVKFEGCYHGH 146 Query: 140 TLATLAATGSAKYLEGFGPPMDG---FDQVPH------GDIEAVKKAI---GPQTAGILI 187 + + L GS L FG P G D H + E + +A G + A +++ Sbjct: 147 SDSLLVKAGSG--LLTFGNPSSGGVPADVAKHTLVLEYNNAEQLAEAFAKQGSEIAAVIV 204 Query: 188 EPIQGEGGVRSATPAFLKALRQLCDEKGLLLAFDEVQTGMGRTGDLFAHRRTGVTPDVMS 247 EP+ G + + P F++A+R+LC + G +L FDEV TG R G A G+TPD+ + Sbjct: 205 EPVAGNMNLIAPKPEFMQAMRELCSKHGAVLIFDEVMTGF-RVGPQCAQGLFGITPDLTT 263 Query: 248 LAKALGGGFPIGAI---LATADAAAGMGPGSHGSTFGGNPLAIAAANAVLDVMLKPGFFD 304 L K +GGG P+ A + A +GP T GNP+A+AA L PGF+D Sbjct: 264 LGKVIGGGMPVAAFGGKREIMEKIAPLGPVYQAGTLSGNPVAVAAGLVTLKATRAPGFYD 323 Query: 305 HVQKMSLLLKQKLASVIDRHG 325 + + L L + +HG Sbjct: 324 SLAARTKQLTDGLTAAAKKHG 344 Lambda K H 0.320 0.137 0.404 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: 468 Number of extensions: 28 Number of successful extensions: 6 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: 405 Length of database: 427 Length adjustment: 31 Effective length of query: 374 Effective length of database: 396 Effective search space: 148104 Effective search space used: 148104 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