Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate aminotransferase
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__BFirm:BPHYT_RS22435 Length = 427 Score = 212 bits (540), Expect = 1e-59 Identities = 146/399 (36%), Positives = 208/399 (52%), Gaps = 34/399 (8%) Query: 28 DLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMP-QTLPT 86 D R + A +WD EG +ID G V N GH +P+++ A++ Q + Q +P Sbjct: 23 DFYAERAENAELWDVEGRRFIDFAAGIAVCNTGHRHPKILAAIRDQLDHFTHTAYQIVPY 82 Query: 87 PMRGEFYRTLTAILP---PELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGR 143 E L P P+ F +G EA E A+K ARA TGR +A GF GR Sbjct: 83 ASYVELAEKLNERAPGDHPKKTAFF--TTGAEAVENAIKIARAATGRPGVIAFTGGFHGR 140 Query: 144 TMGSLSVTWE-PKYREPFLPLVEPVEFIPYND-------------VEALKRA-VD-EETA 187 T+ +++T + Y+ F P V P+ + +E L +A +D + A Sbjct: 141 TLMGMALTGKVAPYKIGFGPFPSDVFHAPFPNPLHGVTTADSLKAIEFLFKADIDPKRVA 200 Query: 188 AVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVP 247 A+I EPVQGEGG PA EF+RA R++ E G LLI DE+QTG RTGK FA H+ +VP Sbjct: 201 AIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHHYDVVP 260 Query: 248 DILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLW 307 D++T+AK+L GG+PL + R +V + GG G T+ GNPLA+AA A + ++ +L Sbjct: 261 DLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAAHAVLDIIDEEKLC 320 Query: 308 ERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLEL-----KEKAAPYIARLEK---E 357 ERA LG KL A+ S P+I +VRG G MV +E E A + R++ E Sbjct: 321 ERATLLGDRVKAKLIALQSDVPQIADVRGPGGMVAVEFCKAGGTEPDAEFTKRVQTRALE 380 Query: 358 HRVLALQAG--PTVIRFLPPLVIEKEDLERVVEAVRAVL 394 +L L G V+RFL PL I+ + + + V+ Sbjct: 381 RGLLLLVCGVYSNVVRFLFPLTIQDAVFDEAMAILEDVI 419 Lambda K H 0.319 0.137 0.402 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: 433 Number of extensions: 24 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: 427 Length adjustment: 31 Effective length of query: 364 Effective length of database: 396 Effective search space: 144144 Effective search space used: 144144 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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