Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_026607826.1 METAC_RS0116010 ornithine--oxo-acid transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000427445.1:WP_026607826.1 Length = 410 Score = 288 bits (737), Expect = 2e-82 Identities = 165/388 (42%), Positives = 224/388 (57%), Gaps = 13/388 (3%) Query: 9 KYHMNTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERL 68 ++ Y+ FPV L G A ++D EG YID+++ + GH HP +V A+ Q+ R+ Sbjct: 12 RFSAKNYAPFPVVLSHGRDAYLFDVEGKRYIDMMSAYSAASFGHSHPRLVAALTRQLGRV 71 Query: 69 IHCSNLYYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF--------TG 120 S Y+++ LA+ + L+ N+G E+VE AIK AR++ Sbjct: 72 DLVSRAYHSDNLGAFCEALAKLS--GLDACLPMNTGAEAVETAIKAARRYGYDRLSIPQD 129 Query: 121 CTKFIAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPYGDVNAVEKAIDDDTAAV 180 + I G FHGRT + + +P R F P P F PYGD A+E I +TAAV Sbjct: 130 KAEIIVAAGNFHGRTTTIVGFSTEPSCRRGFGPFGPGFLAAPYGDAAALEALIGPNTAAV 189 Query: 181 IVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDI 240 ++EPVQGEAGV +PPEG+L LR +CD HG+LLI DEVQSG GRTG+ F FEHE+ PD Sbjct: 190 LIEPVQGEAGVIVPPEGYLAALRRICDRHGILLIFDEVQSGFGRTGRNFCFEHENARPDG 249 Query: 241 VCLAKGLGGG-VPVGATIAREEVAEAFEPGDHGSTFGGNPLACAAVCAAVSTVLEENLPE 299 + + K LGGG +PV A +AR V + F+PG HGSTFGGNPLA A A+ + +ENL Sbjct: 250 LIVGKALGGGLLPVSAFVARRAVMDVFDPGSHGSTFGGNPLAAAVALEAMRLLQDENLAR 309 Query: 300 AAERKGKLAMRILSEAE-DVVEEVRGRGLMMGVEVGDDE-RAKDVAREMLDRGALVNVTS 357 + GK L+ + + EVRG+GL +GVE+ + +AKDV M+ RG L T Sbjct: 310 RSLLLGKTLRETLARVDHPAIVEVRGKGLWVGVELDPAKVKAKDVCLAMMRRGVLTKETH 369 Query: 358 GDVIRLVPPLVIGEDELEKALAELADAL 385 VIR PPLVI E +L +A+ DAL Sbjct: 370 ATVIRFAPPLVIEEADLLQAIEIFQDAL 397 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: 396 Number of extensions: 21 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: 389 Length of database: 410 Length adjustment: 31 Effective length of query: 358 Effective length of database: 379 Effective search space: 135682 Effective search space used: 135682 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