Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate 5207770 Shew_0291 branched-chain amino acid aminotransferase (RefSeq)
Query= BRENDA::P54691 (305 letters) >FitnessBrowser__PV4:5207770 Length = 307 Score = 176 bits (447), Expect = 5e-49 Identities = 106/289 (36%), Positives = 159/289 (55%), Gaps = 15/289 (5%) Query: 3 KFLPIAYFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDR 62 K + +F + +P+ DAK+ V +HALHYGT+ F G+R P+ P FRL H R Sbjct: 4 KTAELIWFNGEIMPWGDAKVHVMSHALHYGTSVFEGIRVYDTPQGPAG---FRLTDHVQR 60 Query: 63 LSKSAKFLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVYSS--GLGIAPRLHNLEK 118 L SAK + S ++ + D VK N+ D + YIRPLV+ G+GI P + + Sbjct: 61 LYDSAKIYRMPVPYSFDETMQACRDIVKSNKLDAA-YIRPLVFFGDVGMGITPP-KDAKC 118 Query: 119 DFLVYGLEMGDYLAAD----GVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVES 174 D +V G YL GV ++SW R + P K Y++S TEA + Sbjct: 119 DLMVAAFPWGAYLGEGSMERGVDVAVTSWNRLAPNTIPTGAKAGGNYLSSLQISTEAKRN 178 Query: 175 GFDEAILMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTC 234 GFDE I ++ G V E G N+F+V+ ++ TP IL GITRD+I+T+A DLG Sbjct: 179 GFDEGIALDVNGLVSEGAGANLFVVKKNKLYTPPATAAILLGITRDTIITLARDLGYEVV 238 Query: 235 QRPIDKSELMIADEVFLSGTAAKITPVKRIENFTL--GGDRPITEKLRS 281 + P+ + L +ADE+F++GTAA+I PV+ ++ + GG P+T+ L++ Sbjct: 239 EEPMSREFLYLADEIFMTGTAAEIVPVRSVDRIEVGAGGRGPVTQALQA 287 Lambda K H 0.320 0.138 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: 229 Number of extensions: 9 Number of successful extensions: 2 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: 305 Length of database: 307 Length adjustment: 27 Effective length of query: 278 Effective length of database: 280 Effective search space: 77840 Effective search space used: 77840 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: 48 (23.1 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