Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_028487302.1 B076_RS0110635 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000483485.1:WP_028487302.1 Length = 430 Score = 155 bits (391), Expect = 3e-42 Identities = 135/432 (31%), Positives = 223/432 (51%), Gaps = 48/432 (11%) Query: 30 DFDT-YVMNTYGRFP-----IAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVR 83 +FD +V + Y + P I + + QGS + + + +D ++ G+ HP + + Sbjct: 9 EFDQRHVWHPYAKTPNPIAAIGVKKTQGSIITLADDREVVDGMSSWWAAVHGYNHPKISQ 68 Query: 84 AVSDQIQKLHHV--SNLYYIPEQGELAKWIVEHSCA--DRVFFCNSGAEANEAAIKLVRK 139 A+ QI + H+ L + P ELAK +++ + A D+VF +SG+ + E AIK+ + Sbjct: 69 AMHVQIDTMPHIMFGGLTHEPAI-ELAKRLIKITPAGLDKVFLADSGSISMEVAIKVALQ 127 Query: 140 YAHTVLDFLEQPVILTAKASFHGRTLATITATGQPKY-----------QQYFDPLVP-GF 187 Y + L+ ++ +L+ + +HG T AT+ A P+ Q +F P GF Sbjct: 128 YWIS-LELPQKNRLLSVRNGYHGDTFATM-AISDPENGMHSLFKDILTQHFFAPAPEAGF 185 Query: 188 DYVPYN-DIRSLENKVADLDEGNSRVAAIFLEPL-QGEGGVRPGDLAYFKRVREICDQND 245 D N DI++LE+ L ++ +AA+ +EP+ QG GG+R AY K++R++C Q D Sbjct: 186 DKESDNHDIQALESL---LQAHHTEIAAVTIEPIVQGAGGMRFYRPAYLKKLRQLCTQYD 242 Query: 246 ILLVFDEVQVGVGRTGKLWGYEHLGVEPDIFTSAKGLAGG-VPIGAMMC-KKFCDVFEPG 303 +LL+ DE+ G GRTGKL+ E + PDI K L GG + + AM+C + D G Sbjct: 243 VLLIADEIATGFGRTGKLFACEWADISPDILCVGKALTGGTMTMAAMLCTSQISDTISAG 302 Query: 304 N-----HASTFGGNPLACAAGLAVLKTIEGDRLLDNV-QARGEQLRSGLAEIKNQYPTL- 356 H TF GNPLAC+A +A + D LLD+ Q+R E++ + L N TL Sbjct: 303 TPGLLMHGPTFMGNPLACSASIASI-----DLLLDSPWQSRVEEIETHLKSSLNFLSTLP 357 Query: 357 -FTEVRGWGLINGLEISAESSLTSVEIVKAAMEQGLLLAPAGPKVLRFVPPLVVTEAEIA 415 E+R G I +++ E + EI AA+ G+ + P G K++ +P + ++ Sbjct: 358 GVEEIRVLGAIGVVQL--ERADLGPEIQAAALNNGVWVRPFG-KLIYIMPAFNIPHNQLQ 414 Query: 416 QAVEILRQAIAT 427 Q + + +AI T Sbjct: 415 QLTDGMSKAIQT 426 Lambda K H 0.320 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: 22 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: 429 Length of database: 430 Length adjustment: 32 Effective length of query: 397 Effective length of database: 398 Effective search space: 158006 Effective search space used: 158006 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