Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate WP_036257439.1 DL86_RS01600 D-amino-acid transaminase
Query= CharProtDB::CH_012531 (298 letters) >NCBI__GCF_000746085.1:WP_036257439.1 Length = 286 Score = 143 bits (360), Expect = 5e-39 Identities = 91/274 (33%), Positives = 142/274 (51%), Gaps = 9/274 (3%) Query: 7 FLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIMLEIP 66 ++NG++V +AKV + D GY + DGV+E V+ G + + H+ RL S + ++ P Sbjct: 6 YVNGQYVFSRDAKVHIEDRGYQFADGVYEVCEVFHGALIDEQRHMERLARSLAELRIDAP 65 Query: 67 YSLDEITNIVVETIRQNKLSNGYIRLVVSRG-AGNLGLDPDSCTKPNVVVIAEQLSLFPQ 125 + I+ E I +NK++NGY+ + V+RG A P+ +P++VV Q+ Sbjct: 66 LGAGALKVILREVIVRNKVTNGYVYIQVTRGVAPREHTFPEKPVRPSLVVTGRQIDPEKG 125 Query: 126 E-YYEKGIPVVTVATRR-NRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYV 183 E KGI VVT R R D +K+++ L N+L R AK G EA +++ +G V Sbjct: 126 ERAARKGISVVTTPDLRWKRVD-----IKTISLLPNVLARQTAKEQGAYEAWLIDSEGMV 180 Query: 184 AEGSGDNVFIV-KGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYVAD 242 EG+ N +I+ + +IT L G+TR ++EI G E F+ + + A Sbjct: 181 IEGAASNAWIIDRSGAIITRQLDHCVLRGVTRTTLIEIIAAEGLRFEERKFSVEEAFAAQ 240 Query: 243 EVFLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRL 276 E F+TG V+ V +DGR IG G GP RL Sbjct: 241 EAFVTGATTLVMPVIAIDGRKIGAGAPGPVAQRL 274 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: 223 Number of extensions: 11 Number of successful extensions: 3 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: 286 Length adjustment: 26 Effective length of query: 272 Effective length of database: 260 Effective search space: 70720 Effective search space used: 70720 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