Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011318729.1 AVA_RS09755 PLP-dependent aminotransferase family protein
Query= reanno::Koxy:BWI76_RS24235 (393 letters) >NCBI__GCF_000204075.1:WP_011318729.1 Length = 490 Score = 148 bits (374), Expect = 3e-40 Identities = 100/323 (30%), Positives = 158/323 (48%), Gaps = 8/323 (2%) Query: 71 GYPPLRQAVSE-LCQARGVACPASHVYITSGSQQSLDIVARTLLDPGDAIVVERPTYLAA 129 GY PLR+A++ L ++R V C A + I GSQQ LD++ R L+D GD IVVE P YL A Sbjct: 167 GYQPLREAIAAYLSRSRAVNCQAEQIIIVGGSQQGLDLITRILIDRGDGIVVEEPGYLGA 226 Query: 130 LQVFQLAQANILSVDTDDDGMLVEQLADLLETTRVKAVYLVPTFGNPGGKTLSEARRRRL 189 + F A++ V D G++V +L + +K VY+ P+ P G LS RR L Sbjct: 227 RRAFLAQGASLFPVPVDQSGLIVNKLKTSI-IPNLKLVYVTPSHQFPTGAVLSLPRRLEL 285 Query: 190 VELAKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVELGCEDQVVYTSTFSKILAPGMRIG 249 + A+K +IIEDD E + + RP+ L + V+Y TFSK+L P +R+G Sbjct: 286 LAWAQKAGVMIIEDDYDSEYRYGE---RPI-PALQGLDQGNSVIYVGTFSKVLFPALRLG 341 Query: 250 WIVMPDWLAQQTVIVKQAADLHTNMLSQVITAEYLSMNRLESQIALIREDYRKKCVALAD 309 ++V+P L K AD ++L Q ++++ LE I +R Y ++ L Sbjct: 342 YLVLPQNLVNIFARAKWLADRQCSLLEQYALTDFITEGHLERHIRKMRSLYNQRRQTLVQ 401 Query: 310 ALESQLGEHLEFSRPKGGMFLWARFRYPFDTMEWMKKTLENGV-VYVPGEAFYNDNPDTR 368 +L S G + GM L + E ++ +GV + + D+P + Sbjct: 402 SLFSHFGNRAKILGENAGMHLMVKIDTQISDDEIVQSAALSGVSIGAAYPQYLKDSPGSE 461 Query: 369 TLRLSYSTVSADGLMTAVERLAK 391 + Y+ ++ + V RLA+ Sbjct: 462 FI-FGYAELNEQQIQEGVRRLAR 483 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: 408 Number of extensions: 24 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: 490 Length adjustment: 32 Effective length of query: 361 Effective length of database: 458 Effective search space: 165338 Effective search space used: 165338 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 Jul 25 2024. The underlying query database was built on Jul 25 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