Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_022950200.1 H035_RS0117255 diaminobutyrate--2-oxoglutarate transaminase
Query= curated2:O66442 (376 letters) >NCBI__GCF_000421465.1:WP_022950200.1 Length = 425 Score = 200 bits (508), Expect = 7e-56 Identities = 127/396 (32%), Positives = 221/396 (55%), Gaps = 40/396 (10%) Query: 12 PVKFVRGKGVYLYDEEGKEYLDFVSGIGVNSLGHAYPKLTEALKEQVEK-----LLHVSN 66 P F +G +LYDEEGK+Y+DF +G GV + GH PK+++AL E +++ L + Sbjct: 19 PAVFDTAQGAHLYDEEGKKYIDFFAGAGVLNYGHNNPKISQALIEYLQRDGIVHALDKAT 78 Query: 67 LYENPWQEELAHKLVKHFWTEGKVFFAN-SGTESVEAAIKLARKYWRDKGKNKWKFISFE 125 + + + E+ ++ K+ F +GT + EAA+KLAR + + I+F Sbjct: 79 VAKRNFMEKFRDTILAPRNMHYKIQFTGPTGTNATEAALKLARMT-----QKRSNIIAFT 133 Query: 126 NSFHGRTYGSLSATGQP---------KFHKGFEPLVPGFSYAKLNDIDSVYKLLDEETAG 176 N++HG T G+++ TG +++ F P F +N ID + + L ++++G Sbjct: 134 NAYHGLTMGAMAVTGNAYYRDESYGVRYNSDFMPYDNYFG-PDVNTIDYLRRFLSDQSSG 192 Query: 177 ------IIIEVIQGEGGVNEASEDFLSKLQEICKEKDVLLIIDEVQTGIGRTGEFYAYQH 230 II E +QGEGG++ AS ++L +L+++C+E ++LLI+D++Q G GRTG F++++ Sbjct: 193 VDLPAAIITETVQGEGGIHVASIEWLQQLEQVCREFEILLIVDDIQVGNGRTGTFFSFER 252 Query: 231 FNLKPDVIALAKGLGGGVPIGAILAREEVAQSFTPGSHGSTFGGNPLACRAGTVVVD--E 288 +KPD++AL+K +GGG+P+ +L + E+ Q + PG H TF GN LA A T ++ + Sbjct: 253 AGIKPDMVALSKAIGGGLPMSLLLMKPELDQ-WQPGEHTGTFRGNNLAFVAATKALEYWD 311 Query: 289 VEKLLPHVREVGNYFKEKLKELGK------GKVKGRGLMLGLELERE--CKDYVLKALEK 340 ++L V+ G + +LK + + V+G G++ GLE D +A +K Sbjct: 312 DDELAKAVKHKGAIMEAELKRIAEKYGDIITDVRGLGMVWGLESLNSGLPTDISERAFKK 371 Query: 341 GLLINCTAG--KVLRFLPPLIIQKEHIDRAISVLRE 374 GL+I VL+FLP L I + + ++++ E Sbjct: 372 GLVIELAGADDHVLKFLPALTIDEATLREGLAIIDE 407 Lambda K H 0.318 0.139 0.409 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: 388 Number of extensions: 23 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: 376 Length of database: 425 Length adjustment: 31 Effective length of query: 345 Effective length of database: 394 Effective search space: 135930 Effective search space used: 135930 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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