Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate Dsui_0883 Dsui_0883 transcriptional regulator with HTH domain and aminotransferase domain
Query= metacyc::MONOMER-6727 (397 letters) >FitnessBrowser__PS:Dsui_0883 Length = 475 Score = 163 bits (413), Expect = 9e-45 Identities = 112/391 (28%), Positives = 191/391 (48%), Gaps = 11/391 (2%) Query: 11 GKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQY 70 G+S + I E+L+ + P ++ F +PEL+P ++ A R A Sbjct: 87 GQSTALDVSDFIFEILESVKNPAVVPFGSSFASPELYPLDKLGRCLAAAARHLDPRATVT 146 Query: 71 SPTEGYAPLRA-----FVAEWIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSY 125 G LR +++ V P+E+++T+G+ + L+L + G V +E+P++ Sbjct: 147 DLPPGNEELRRQIALRYLSRGANVSPQEIVVTSGAMEGLNLCLQAVTRPGDLVAIESPTF 206 Query: 126 MGAIQAFRLQGPRFLTVPAG-EEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPA 184 +QA G + + +P EG L ALE+ L++ + + +F NP G Sbjct: 207 YANLQAIERLGLKVIEIPTHPREGISLAALEDALRQHPIKACLCMLNFSNPITGSLSDAR 266 Query: 185 RKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGL 244 + L+ ++ + ++EDD Y ELYFG+ + P+ + G V+++ SFSK L+PG Sbjct: 267 KAELVALLARYQVPLIEDDVYAELYFGD-QAPAHAKAEDRHGL--VLHVSSFSKSLAPGY 323 Query: 245 RVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEG-FSERLERVRRVYREKAQA 303 R+ + VA QK+ + K L T + Q+ + E LK G + L R+RR + + A Sbjct: 324 RIGW-VAGGRFTQKIQRLKLTTSLATTVPVQIALAEYLKHGGYDNHLRRLRRTFSLQEIA 382 Query: 304 MLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGG 363 M+ A++R P R RP GG F+W+ELP G+ L R AL++ ++ PG F A Sbjct: 383 MVGAVERHFPAGTRLARPSGGYFLWVELPPGVDTLALHRLALDQGISIAPGPIFSAKREY 442 Query: 364 ENTLRLSYATLDREGIAEGVRRLGRALKGLL 394 + LRL+Y + + LG+ + LL Sbjct: 443 GHCLRLNYGHPWTPATEKAIAVLGQIIDSLL 473 Lambda K H 0.320 0.139 0.401 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: 493 Number of extensions: 28 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: 397 Length of database: 475 Length adjustment: 32 Effective length of query: 365 Effective length of database: 443 Effective search space: 161695 Effective search space used: 161695 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 Sep 17 2021. The underlying query database was built on Sep 17 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:
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