Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_019866653.1 METMI_RS0112580 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUE8 (395 letters) >NCBI__GCF_000384075.1:WP_019866653.1 Length = 449 Score = 177 bits (450), Expect = 4e-49 Identities = 126/421 (29%), Positives = 221/421 (52%), Gaps = 59/421 (14%) Query: 27 MQTYGRQPLV-LSKGKGAVVQDIYGKEYIDCVAGIAVNNVGHCHPTVVKAIQAQAENLIH 85 M+ + P++ + G+G ++D GK Y+D V+ VN GH +P + A++ Q + L H Sbjct: 21 MKDHENLPMIPIKTGRGVWLEDFDGKRYLDAVSSWWVNLFGHANPIINAALKEQLDTLEH 80 Query: 86 VSNLYYT-EIQAEFAETLASIT--GMERVFFCNSGAESVEAAMKLA------RVATGKSA 136 V +T E + AE L IT G+ R F+ ++G+ +VE A+K++ T K+ Sbjct: 81 VIFAGFTHETGIKLAEKLVDITPAGLNRCFYADNGSAAVEVALKMSFHYWRNGGQTQKTK 140 Query: 137 FVAAEHSFHGRTIGALSVTHKSMYRDPFMPPVSSETTFVPYSDA---------------- 180 F+ E+S+HG T+GAL+V + ++Y++ + P + T VP D Sbjct: 141 FITLENSYHGETLGALAVGNVALYKETYAPLLMDVIT-VPGPDCYFREVGETWAEYSTRR 199 Query: 181 -EAIRQAISENTA---AVILEP-IQGEGGINIPDPGYLKEVREICDETGALLIFDEVQTG 235 + QA+ ++ AVI+EP +Q G + + DP YLK +R+ CD+ G LI DE+ G Sbjct: 200 FTLMEQALQQHAGTVCAVIIEPLVQCAGSMRMYDPVYLKLLRQACDKYGVHLIADEIAVG 259 Query: 236 FGRTGTWFCKEQFGVEPDIMSMSKAIGGGF-PMGAIAAHNGI---------NFGRGQHAS 285 FGRTGT F EQ + PD + +SK + GG+ P+ A+ + I H+ Sbjct: 260 FGRTGTLFACEQASISPDFLCLSKGLTGGYLPLSAVLTTDNIYQAFYADYTQLTAFLHSH 319 Query: 286 TFGGGPLACAAALASVKVIREEKLLERSKEMGAYFMKKLAGMVRD--DVVEVRGKGLMIG 343 ++ G LAC AALA++ + +++ ++ +++ + A + ++A D +V EVR G+++ Sbjct: 320 SYTGNALACRAALATIGIFQQDNVINKNQRLIAK-LAEVAVRFHDHPNVAEVRQTGMILA 378 Query: 344 VEI------KYPCG-------KFVDFAREQGVLVNCTSDSVLRLVPPLVITKEQIDTVVD 390 +E+ + P K +A QGVL+ +V+ +PP VIT+ +++ + + Sbjct: 379 IELVKNKATREPFAWQERRGLKVYQYALAQGVLLR-PLGNVIYFMPPYVITEAELELLAE 437 Query: 391 V 391 V Sbjct: 438 V 438 Lambda K H 0.319 0.135 0.391 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: 369 Number of extensions: 23 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: 395 Length of database: 449 Length adjustment: 32 Effective length of query: 363 Effective length of database: 417 Effective search space: 151371 Effective search space used: 151371 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 (21.7 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