Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_092053439.1 BQ4888_RS01605 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_900111775.1:WP_092053439.1 Length = 449 Score = 197 bits (501), Expect = 5e-55 Identities = 137/407 (33%), Positives = 219/407 (53%), Gaps = 50/407 (12%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL-YYN 77 P+ + G+GA ++D +G YID V+ VN+ GH HP + A+ +Q ++ H + + Sbjct: 29 PIPIARGDGAYLYDFDGKGYIDGVSSWWVNLFGHNHPRLNRALSKQAGKVAHHIFAGFTH 88 Query: 78 EPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF---TGC---TKFIAFEGGF 131 EP A A L E AP L KVFF ++G+ +VE A+K++ ++ TG T+F++ + Sbjct: 89 EPAATLAARLCELAPPGLEKVFFTDNGSAAVEAALKMSFQYWRQTGQGEKTRFVSITEAY 148 Query: 132 HGRTMGALSATWKPEFREPFEPLV--------PEFEHVPYGDVN---------AVEKAID 174 HG T+GALS +++ ++PL+ P+ PYG A+E+ + Sbjct: 149 HGETLGALSVGGCGLYKDIYQPLLLDGFQVQGPDCFRCPYGCERESCNAECFAAMEEVVA 208 Query: 175 D---DTAAVIVEP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFA 230 + AAVI+EP +Q AG+RI P +L++LRELCD + I DE+ G GRTG+ FA Sbjct: 209 EHHRQIAAVIIEPLIQCAAGMRIYPPIYLKKLRELCDRWRIHYIADEIAVGFGRTGRLFA 268 Query: 231 FEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAF-------EPGDHGSTFGGNPLAC 282 EH V PD++CL+KG+ GG +P+ + R+E+ +AF + H ++ GNPLAC Sbjct: 269 NEHAGVSPDLLCLSKGITGGYMPLSVVLTRQEMYDAFYDDYATLKAFLHSHSYSGNPLAC 328 Query: 283 AAVCAAVSTVLEENLPEAAERKGKL--AMRILSEAEDVVEEVRGRGLMMGVEVGDDE--- 337 A C ++ EE + E K + + + EA V E R GL+ +E+ D+ Sbjct: 329 ALACEVLNIFTEEKILEKMVPKMAILASQKHRFEALPQVGEFRQLGLVGAIELVRDKVGK 388 Query: 338 --------RAKDVAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEK 376 R V R+ L++GAL+ G+V+ +PPL I + +L + Sbjct: 389 TPYPWQERRGYAVYRKALEKGALLR-PLGNVVYFMPPLTIEKADLSR 434 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: 423 Number of extensions: 25 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: 449 Length adjustment: 32 Effective length of query: 357 Effective length of database: 417 Effective search space: 148869 Effective search space used: 148869 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