Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_013819183.1 METME_RS12875 acetylornithine transaminase
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000214665.1:WP_013819183.1 Length = 390 Score = 331 bits (848), Expect = 3e-95 Identities = 176/395 (44%), Positives = 250/395 (63%), Gaps = 15/395 (3%) Query: 23 YVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLH 82 ++M TY R V +GEG LWD+ GK YLD +AGIA C LGHAHPA+ QA+ Q Q L Sbjct: 4 HIMPTYARQTVTFDRGEGAWLWDSNGKRYLDALAGIAVCNLGHAHPAVHQALCKQSQTLI 63 Query: 83 HISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVI 142 H SNLY + Q LA + S D VFFCNSGAEANEAAIK+ RKY H ++ PVI Sbjct: 64 HTSNLYGVKLQAELADKLCRLSGMDNVFFCNSGAEANEAAIKIARKYGH--EQGIDAPVI 121 Query: 143 LSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRVA 202 L+ SFHGRT+ ++ATG K ++ F PL GF +VPYN+I A+ AI ++ + Sbjct: 122 LTMDKSFHGRTMGALSATGNTKIKQGFAPLLPGFVHVPYNNIDAIISAI----HADKNIV 177 Query: 203 AIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIEP 262 AI++E +QGEGGV D +Y +R +CDE+ +LL+LDE+Q G+GRTG++ Y+ I P Sbjct: 178 AILVEPVQGEGGVNIPDADYLNRIRALCDEHQLLLMLDEIQTGIGRTGEFLAYQRNQILP 237 Query: 263 DIFTSAKGLAGGIPIGAMMCK-DSCAVFNPGEHASTFGGNPFSCAAALAVVETLEQENLL 321 D+ T AK L G+PIGA M + + A+ G H STFGGNP +C+AALAV++TL +L+ Sbjct: 238 DVCTLAKALGNGVPIGACMARGKAAAILTAGNHGSTFGGNPLACSAALAVLDTLCSTDLI 297 Query: 322 ENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLLL 381 + + +G+++ + E P+ +R GL+ G+E+ A E+V A+E+GLL+ Sbjct: 298 ADADRKGKRICDAVTRQLEGNPHIVSIRHLGLMIGIELDAPCG----ELVGKALEQGLLI 353 Query: 382 APAGPKVLRFVPPLIVSAAEINEAIALLDQTLAAM 416 +R +PPL++ A+I+ LL +TL+A+ Sbjct: 354 NVTADNTIRLLPPLLIDDAQID----LLTETLSAL 384 Lambda K H 0.319 0.136 0.406 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: 414 Number of extensions: 23 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: 418 Length of database: 390 Length adjustment: 31 Effective length of query: 387 Effective length of database: 359 Effective search space: 138933 Effective search space used: 138933 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: 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