Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011605448.1 FRAAL_RS18885 PLP-dependent aminotransferase family protein
Query= reanno::Koxy:BWI76_RS24235 (393 letters) >NCBI__GCF_000058485.1:WP_011605448.1 Length = 401 Score = 299 bits (765), Expect = 1e-85 Identities = 160/389 (41%), Positives = 232/389 (59%), Gaps = 3/389 (0%) Query: 5 RLAARAGELKPSAVRELLKHSKLPGVISLGGGIPAPELFDTEGLNLAVQQVMNGRFNDAF 64 +LAARA ++ S VRE+L + P VIS GG+PAPEL D +G+ A QV+ Sbjct: 9 QLAARARAVRTSPVREILALTARPEVISFAGGLPAPELIDADGIRRAYDQVLTDEPRRVL 68 Query: 65 QYGLTEGYPPLRQAVSELCQARGVACPASHVYITSGSQQSLDIVARTLLDPGDAIVVERP 124 QY TEG P LR AV+ RG+ H+ +T+GSQQ+L ++A LL+PGDA+VVE P Sbjct: 69 QYSTTEGDPDLRAAVAARLARRGLPTEPDHLLVTTGSQQALTLLAAALLEPGDAVVVEDP 128 Query: 125 TYLAALQVFQLAQANILSVDTDDDGMLVEQLADLLETTRVKAVYLVPTFGNPGGKTLSEA 184 TYLA LQ F A A + + TDD G++ ++LADL+ R + +Y+VPTF NP G+T++ Sbjct: 129 TYLAVLQCFGFAGARVFAAPTDDQGIIPDRLADLVARERPRLLYVVPTFQNPTGRTMAAD 188 Query: 185 RRRRLVELAKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVELGCEDQVVYTSTFSKILAP 244 RRR + E+A + I+EDDPYGE+ + + + Y D+ V +FSK +AP Sbjct: 189 RRRAVAEVAARQGLWIVEDDPYGELRYEGTAQPWIASYP---AAADRTVLLGSFSKTMAP 245 Query: 245 GMRIGWIVMPDWLAQQTVIVKQAADLHTNMLSQVITAEYLSMNRLESQIALIREDYRKKC 304 GMR+GW+ P L + VI KQAADLHT+ + Q A YL+ L++ +A + YR++ Sbjct: 246 GMRLGWLRAPAALRRACVIAKQAADLHTSTVDQAAAARYLAEADLDAHLARMCAVYRERR 305 Query: 305 VALADALESQLGEHLEFSRPKGGMFLWARFRYPFDTMEWMKKTLENGVVYVPGEAFYNDN 364 A+ D L L ++RP+GGMF+WAR +D + + + V YVPG F+ Sbjct: 306 DAMLDGLVGALPPGSSWNRPEGGMFVWARLPAGYDATALLPAVVAHDVAYVPGAPFFAGA 365 Query: 365 PDTRTLRLSYSTVSADGLMTAVERLAKSL 393 PD LRLS++T + + + RLA++L Sbjct: 366 PDPAALRLSFTTHAPARIAEGMARLARAL 394 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: 453 Number of extensions: 13 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: 393 Length of database: 401 Length adjustment: 31 Effective length of query: 362 Effective length of database: 370 Effective search space: 133940 Effective search space used: 133940 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