Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate WP_092347659.1 BLU87_RS10080 hypothetical protein
Query= CharProtDB::CH_012531 (298 letters) >NCBI__GCF_900107645.1:WP_092347659.1 Length = 287 Score = 211 bits (537), Expect = 2e-59 Identities = 104/278 (37%), Positives = 165/278 (59%), Gaps = 1/278 (0%) Query: 6 IFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIMLEI 65 ++LNG+FV D AKVSV+D G+LYGDG+FE R G +++ +H RL +SA+++ + Sbjct: 4 VYLNGKFVNSDLAKVSVFDQGFLYGDGIFESFRSVKGKLYQFSKHYQRLVQSAEALSYPL 63 Query: 66 PYSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQLSLFPQ 125 ++ ++ I++ +N N Y R+ ++RG G +G D ++ + Sbjct: 64 AFTQQQLEEILLTLCERNGWKNAYYRITITRGKGQIGFQRDMDNDLTCFIVGREFQGLDD 123 Query: 126 EYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVAE 185 EYY++GI V TRRN P+ +SP++KS++ LN++L ++EAK G E +MLN++ ++ E Sbjct: 124 EYYQQGIKVKVAQTRRNAPEAISPKIKSISNLNSLLGKLEAKALGTFEVIMLNNKEHICE 183 Query: 186 GSGDNVFIVKGNKLITPPSSAGALEGITRNAILEI-GEKLGYDVREELFTRHDVYVADEV 244 GS N+F + + TP +S G LEG+TR+ I+ + E+L V F D+ +DEV Sbjct: 184 GSASNIFWTRDQWVFTPGASTGLLEGVTRSTIMRLCEEELNLRVISGEFKLQDLQFSDEV 243 Query: 245 FLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRK 282 F+T T+ EVI V VD TI GQ GP RL +E + Sbjct: 244 FITSTSLEVIPVVQVDAFTINQGQVGPIAKRLRQELHR 281 Lambda K H 0.317 0.138 0.390 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: 200 Number of extensions: 5 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: 298 Length of database: 287 Length adjustment: 26 Effective length of query: 272 Effective length of database: 261 Effective search space: 70992 Effective search space used: 70992 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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