Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_208597676.1 G494_RS0112760 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= curated2:O27392 (390 letters) >NCBI__GCF_000429965.1:WP_208597676.1 Length = 472 Score = 179 bits (454), Expect = 1e-49 Identities = 138/427 (32%), Positives = 209/427 (48%), Gaps = 60/427 (14%) Query: 20 RQPIVLSHGKGATVWDIEGNSYIDCFAG-VAVNSIGHAHPKVALAICHQAQRLIHSSNIY 78 R+ +++ G+G + DI GN ++D +G V +G+ +A A+ Q + + + + Y Sbjct: 36 REQMIVVAGEGLRIRDIRGNEFLDATSGGVWSVMVGYGRESIARAVYEQLKVMPYFAGAY 95 Query: 79 YTREQVELA-KLLTAISPHDRVFFANSGAEANEGAIKLARKFT-------GKSEIIAAEN 130 ++ A KLL + D+V+F+NSG+EANE A K+ R + GK +I+ + Sbjct: 96 GNIPSIKFAAKLLELLPRLDKVYFSNSGSEANEKAFKMVRLASSIDPGRQGKYKILYRDR 155 Query: 131 SFHGRTLATVTATGQKKYSEPFRPLPEGFKHVP------------YGDIG-AMADAV--- 174 +HG TLAT++A GQ + + F P EGF VP Y D G A A AV Sbjct: 156 DYHGTTLATMSAGGQFERKQGFGPFAEGFVEVPHCLCYRCPHDRSYPDCGIACARAVEEV 215 Query: 175 ----GDETAA-IILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRTGAM 229 G ET ++EP+ GG+I P Y VQE+ R++ V LI+DEV GFGRTG Sbjct: 216 ILREGPETVGGFVVEPITAGGGIIPPVREYFPLVQEICRRHGVWLIMDEVVCGFGRTGRF 275 Query: 230 FASQLFGVEPDITTVAKAMGGGY-PIGAVLANERVAMAF-----EPGDHG------STFG 277 + + F V+PDI T+AK + Y + A + + F +P + ST+G Sbjct: 276 WGHEHFEVDPDIVTMAKGLASSYEALSATAVKQEIYDIFLNDPAKPEEAANFFRDISTYG 335 Query: 278 GNPWGCAAAIATIEVLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEI 337 G AAA+ + ++ DE+L E + +MG+ L +L Q L V D+RGVGL G+E+ Sbjct: 336 GCTAPMAAALESTRIIEDEELVENSREMGALLLEKL-QALTSLPVVGDVRGVGLFCGLEL 394 Query: 338 --DGECAGVVDAAREMGVLINCTAGKVI---------------RIVPPLVIKKEEIDAAV 380 D V A ++ N A KVI +VP L + EE+D V Sbjct: 395 VRDKGTKIPVSEAEMARLMANIMAEKVIVGRTNSSLPGLNTTLYLVPCLTVSAEELDTIV 454 Query: 381 DVLGHVI 387 + I Sbjct: 455 AAVSRAI 461 Lambda K H 0.320 0.138 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: 443 Number of extensions: 27 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: 390 Length of database: 472 Length adjustment: 32 Effective length of query: 358 Effective length of database: 440 Effective search space: 157520 Effective search space used: 157520 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: 51 (24.3 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