Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_013459726.1 SULKU_RS04380 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:O66442 (376 letters) >NCBI__GCF_000183725.1:WP_013459726.1 Length = 431 Score = 154 bits (388), Expect = 6e-42 Identities = 124/410 (30%), Positives = 203/410 (49%), Gaps = 40/410 (9%) Query: 5 MNNYARLP-VKFVRGKGVYLYDEEGKEYLDFVSGIGVNSLGHAYPKLTEALKEQVEKLLH 63 M ++ +P V +G GVYL D EG +D +S VN GH P + +KEQ+E L H Sbjct: 21 MKDHETIPLVPIAKGDGVYLEDFEGNRIIDAISSWWVNLFGHCNPYINRKIKEQLESLEH 80 Query: 64 VSNL-YENPWQEELAHKLVKHFWTEG--KVFFANSGTESVEAAIKLARKYWRDKGKNKWK 120 V + + L+ +LV EG + F+A++G+ ++E A+K++ +++G+ + Sbjct: 81 VILAGFTHEGIVRLSERLVA-LSPEGLTRCFYADNGSSAIEVALKMSYHSHKNRGEERGL 139 Query: 121 FISFENSFHGRTYGSLSATGQPKFHKGFEPLV----------PGFSYAKLNDIDSVYKLL 170 F+S +S+HG T G+LS + + +EPL+ A L S LL Sbjct: 140 FVSLTDSYHGETLGALSVGDVALYKETYEPLLIRSIQTLSPRDQSIEAALEAAKSFEILL 199 Query: 171 DE---ETAGIIIE-VIQGEGGVNEASEDFLSKLQEICKEKDVLLIIDEVQTGIGRTGEFY 226 E E A +I+E ++QG GG+ FLS+ + +C+E + I DE+ G GRTG + Sbjct: 200 QERGKEIAALIVEPLVQGAGGMKMYHPAFLSETKRLCEEYGIHFIADEILVGFGRTGSMF 259 Query: 227 AYQHFNLKPDVIALAKGLGGG-VPIGAILAREEVAQSF-------TPGSHGSTFGGNPLA 278 A + + PD + L+KGL GG +P+ +L E V SF H ++ GN LA Sbjct: 260 ACEQAQITPDFLVLSKGLTGGYLPLSVVLTTESVYGSFYCDYNPVRSFLHSHSYTGNALA 319 Query: 279 CRAGTVVVD--EVEKLLPHVREVGNYFKEKL---KELGKGK-VKGRGLMLGLELER-ECK 331 C A +D E E ++ + R+ E+L K L K K V+ G++ +E+E E Sbjct: 320 CAAANATLDIFESENVIENNRKTIAAMAEELKRFKSLPKVKEVRQCGMIAAIEVEEFEPH 379 Query: 332 DYV-LK----ALEKGLLINCTAGKVLRFLPPLIIQKEHIDRAISVLREIL 376 + + LK +E+G+LI G V+ + P +I + + + L Sbjct: 380 ERIGLKIHRLCMEQGVLIR-PLGSVIYVMTPYVITPDELKSVFDAIESAL 428 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: 356 Number of extensions: 19 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: 376 Length of database: 431 Length adjustment: 31 Effective length of query: 345 Effective length of database: 400 Effective search space: 138000 Effective search space used: 138000 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 10 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