Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate Ga0059261_3674 Ga0059261_3674 adenosylmethionine-8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__Korea:Ga0059261_3674 Length = 415 Score = 178 bits (452), Expect = 2e-49 Identities = 130/402 (32%), Positives = 205/402 (50%), Gaps = 37/402 (9%) Query: 19 PVTLVP-GEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL-YY 76 PV LV EGA + +G ID ++ V GH +P +V A+++Q E+L + Sbjct: 18 PVPLVTHAEGAVLHTADGRRVIDAISSWWVTTHGHGNPRIVAAIRDQAEKLDQLIFAGWT 77 Query: 77 NEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLA-----RKFTGCTKFIAFEGGF 131 +EP AR L P+ L+ VFF +SG+ SVE AIK+A + + I +G + Sbjct: 78 HEPAETVARDLVAMMPRPLDHVFFSDSGSTSVEVAIKMALGHFANRGEPRHRIIVMQGSY 137 Query: 132 HGRTMGALSATWKPEFREPFEPLVPEFEHVPYGDVNAVEKAID---------DDTAAVIV 182 HG T+G +S + F + PL+ + + +P+ + +A+D AA+IV Sbjct: 138 HGDTIGGMSVGARGVFNRSYAPLLFDVDTIPFPEGANEYRALDALEQLCAQSPLPAAMIV 197 Query: 183 EP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIV 241 EP V G G+++ P G LR +RE+C HG+L I DEV +G GRTG A E V+PD++ Sbjct: 198 EPLVLGAGGMKMYPPGVLRAMREICAAHGVLFIADEVMTGWGRTGTLLACEQAAVVPDLL 257 Query: 242 CLAKGL-GGGVPVGATIAREEVAEAFEPGD------HGSTFGGNPLACAAVCAAVSTVLE 294 CL+KGL GG +P+ T+A E+ E+ D H S++ NP+ACAA A ++ E Sbjct: 258 CLSKGLTGGSLPLAVTMATPEIFESHRSKDRSKMFFHSSSYTANPIACAAAAANLAIWRE 317 Query: 295 ENLPEAAERKGKLAMRILSEAEDV---VEEVRGRGLMMGVEVGDDERA------KDVARE 345 E ER LA R S + + V +R G ++ +EV + A + Sbjct: 318 E---PVLERVAHLAHRQRSYSRALAGKVNNLRQLGTIVAMEVQAPQGAYLSVLGPRLMSF 374 Query: 346 MLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADALRA 387 +R L+ G+ + ++PP I +++L + + +AL A Sbjct: 375 FRERNVLLR-PLGNTVYVMPPYCISDEDLARVYTVIGEALEA 415 Lambda K H 0.318 0.137 0.405 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: 413 Number of extensions: 22 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: 389 Length of database: 415 Length adjustment: 31 Effective length of query: 358 Effective length of database: 384 Effective search space: 137472 Effective search space used: 137472 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