Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate BWI76_RS24235 BWI76_RS24235 aminotransferase
Query= BRENDA::Q72LL6 (397 letters) >FitnessBrowser__Koxy:BWI76_RS24235 Length = 393 Score = 258 bits (659), Expect = 2e-73 Identities = 139/384 (36%), Positives = 221/384 (57%), Gaps = 7/384 (1%) Query: 14 AGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPT 73 AG ++ S +RELLK ++ PG++S GG+PAPELF E A +++ + A QY T Sbjct: 10 AGELKPSAVRELLKHSKLPGVISLGGGIPAPELFDTEGLNLAVQQVMNGRFNDAFQYGLT 69 Query: 74 EGYAPLRAFVAEWIGVR-----PEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGA 128 EGY PLR V+E R V IT+GSQQ+LD+V + LD G +++E P+Y+ A Sbjct: 70 EGYPPLRQAVSELCQARGVACPASHVYITSGSQQSLDIVARTLLDPGDAIVVERPTYLAA 129 Query: 129 IQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRL 188 +Q F+L L+V ++G ++ L ++L+ R + +YL+P+F NP G R+RL Sbjct: 130 LQVFQLAQANILSVDTDDDGMLVEQLADLLETTRVKAVYLVPTFGNPGGKTLSEARRRRL 189 Query: 189 LQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPG-VIYLGSFSKVLSPGLRVA 247 +++ + V++EDD Y E+ F + L++ A E G V+Y +FSK+L+PG+R+ Sbjct: 190 VELAKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVELGCEDQVVYTSTFSKILAPGMRIG 249 Query: 248 FAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLK-EGFSERLERVRRVYREKAQAMLH 306 + V Q+ V KQ ADLHT ML+Q++ E L ++ +R YR+K A+ Sbjct: 250 WIVMPDWLAQQTVIVKQAADLHTNMLSQVITAEYLSMNRLESQIALIREDYRKKCVALAD 309 Query: 307 ALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENT 366 AL+ ++ + + ++RPKGGMF+W ++ LE V +VPG F+ + T Sbjct: 310 ALESQLGEHLEFSRPKGGMFLWARFRYPFDTMEWMKKTLENGVVYVPGEAFYNDNPDTRT 369 Query: 367 LRLSYATLDREGIAEGVRRLGRAL 390 LRLSY+T+ +G+ V RL ++L Sbjct: 370 LRLSYSTVSADGLMTAVERLAKSL 393 Lambda K H 0.320 0.139 0.403 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: 375 Number of extensions: 18 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: 397 Length of database: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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 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