Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011801465.1 PNAP_RS10420 PLP-dependent aminotransferase family protein
Query= reanno::Koxy:BWI76_RS24235 (393 letters) >NCBI__GCF_000015505.1:WP_011801465.1 Length = 395 Score = 295 bits (755), Expect = 2e-84 Identities = 147/394 (37%), Positives = 235/394 (59%), Gaps = 5/394 (1%) Query: 5 RLAARAGELKPSAVRELLKHSKLPGVISLGGGIPAPELFDTEGLNLAVQQVMNGRFNDAF 64 + A R ++ SA+REL K PG+IS GG P P +FD EG+ A + +N A Sbjct: 2 QFADRLNNVETSAIRELFKLLGKPGIISFAGGFPDPAMFDIEGIKEASSKALNEEPGGAL 61 Query: 65 QYGLTEGYPPLRQAVSELCQARGVACPASHVYITSGSQQSLDIVARTLLDPGDAIVVERP 124 QYG TEGY PLR+ +S +GV + +T+GSQQ+LD++ +TL++PGD ++VE P Sbjct: 62 QYGATEGYGPLREQLSSFMAGKGVTVQPEGLIVTTGSQQALDLLGKTLINPGDKVIVEGP 121 Query: 125 TYLAALQVFQLAQANILSVDTDDDGMLVEQLADLLETTRVKAVYLVPTFGNPGGKTLSEA 184 T+LA +Q F+L A ++S D G+ ++L L+ + K VYL+PTFGNP G L+ Sbjct: 122 TFLATIQCFRLYGAQVISAPIDAHGVKTDELEWLIAEHKPKFVYLIPTFGNPSGALLTLE 181 Query: 185 RRRRLVELAKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVEL-GCEDQVVYTSTFSKILA 243 RRR+++E+A +H +++EDDPYG++ F + L + + G + + + + SK+L+ Sbjct: 182 RRRQVLEMAVRHQTLVVEDDPYGDLYFGEAPPPSLLSLSDSVPGSRELLAHCGSLSKVLS 241 Query: 244 PGMRIGWIVMPDWLAQQTVIVKQAADLHTNMLSQVITAEYLSMNRLESQIALIREDYRKK 303 PG+RIGW++ P L V+ KQ +D HT+ +Q ++YL R+ + +A +R+ Y ++ Sbjct: 242 PGLRIGWMIAPPALLANAVMCKQFSDAHTSTFAQATASQYLKAGRMPATLAHVRKVYGQR 301 Query: 304 CVALADALESQLGEHLEFSRPKGGMFLWARFR----YPFDTMEWMKKTLENGVVYVPGEA 359 A+ +AL+ +LG + F +P+GG+F WA D E+ KK +E V +VPG Sbjct: 302 AAAMGNALKRELGAAVAFEQPQGGLFFWASLTGEGGKTRDAGEFAKKAIEQLVAFVPGAP 361 Query: 360 FYNDNPDTRTLRLSYSTVSADGLMTAVERLAKSL 393 FY NPD T RLS++T + + RL +++ Sbjct: 362 FYAANPDLATFRLSFATADVGKIEEGIARLGRAV 395 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: 405 Number of extensions: 23 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: 393 Length of database: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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 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