Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_057687392.1 ABB28_RS16060 PLP-dependent aminotransferase family protein
Query= reanno::Koxy:BWI76_RS24235 (393 letters) >NCBI__GCF_001431535.1:WP_057687392.1 Length = 477 Score = 117 bits (293), Expect = 7e-31 Identities = 89/272 (32%), Positives = 132/272 (48%), Gaps = 25/272 (9%) Query: 71 GYPPLRQAVSE-LCQARGVACPASHVYITSGSQQSLDIVARTLLDPGDAIVVERPTYLAA 129 G+ PLR+AV+ L +RG++C V+IT+G + +L++V RTLL PGD E P YL A Sbjct: 153 GHEPLRRAVATYLGISRGISCTHDQVFITAGYRGALELVCRTLLQPGDVGWFEDPGYLFA 212 Query: 130 LQVFQLAQANILSVDTDDDGMLVEQLADLLETTRVKAVYLVPTFGNPGGKTLSEARRRRL 189 Q Q A + V D +G+ V+ R V PT +P G LS RR L Sbjct: 213 RQFLQRAGMRLAPVPVDAEGLHVDIAQRRAPDARFAVV--TPTHQSPTGVALSLPRRLEL 270 Query: 190 VELAKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVELGCEDQVVYTSTFSKILAPGMRIG 249 +E A++ IIEDD E + RPL L E +V+YT TFSK+L PG+R+ Sbjct: 271 LEWAQRQRSWIIEDDYDSEFRYHG---RPL-PALKSLDREQRVLYTGTFSKVLFPGLRLA 326 Query: 250 WIVMPDWLAQQTVIVKQAADLHT---------NMLSQVITAEYLSMNRLESQIALIREDY 300 ++V+P Q A H ++L Q A+++ + +R Y Sbjct: 327 YLVVPP---------SQVAAFHDTVNHLPGAGSILPQATVADFMDQGHFVRHLRRMRALY 377 Query: 301 RKKCVALADALESQLGEHLEFSRPKGGMFLWA 332 ++ L DAL + G+ L+ GG+ + A Sbjct: 378 AERRGYLVDALAREAGDWLQVQPQAGGIHVLA 409 Lambda K H 0.320 0.136 0.395 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: 449 Number of extensions: 33 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: 393 Length of database: 477 Length adjustment: 32 Effective length of query: 361 Effective length of database: 445 Effective search space: 160645 Effective search space used: 160645 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 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