Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011604224.1 FRAAL_RS13430 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000058485.1:WP_011604224.1 Length = 396 Score = 343 bits (880), Expect = 5e-99 Identities = 169/387 (43%), Positives = 247/387 (63%), Gaps = 1/387 (0%) Query: 29 MKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGF 88 M ASEVR L + +++SLAGG+PA + P+E +A E++ A ALQYG+ +G Sbjct: 1 MIASEVRALFAVASRPEIVSLAGGMPAVDALPLETVAATVSELVLSRGAVALQYGSAQGD 60 Query: 89 TPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQ 148 LR + + M ++++T+GSQQALDL+ RVF++PGD+VV E PTY+ A+ Sbjct: 61 PGLRARICDVMAMEGITDAHPDNVVVTAGSQQALDLLTRVFVDPGDVVVTEGPTYVTAIN 120 Query: 149 AFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRR 208 F Y+ V +P+D +G+ L + L+ L EG +VKL+YT+PTFQNP G+T++ RR Sbjct: 121 TFAAYQARIVHVPMDGDGLSPSALAQTLERLAAEGARVKLLYTVPTFQNPGGITLTPPRR 180 Query: 209 KRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGW 268 +LE+ L+VEDNPYG L ++GEPV+ ++A D V+YLG+FSK LAPG R+GW Sbjct: 181 AEVLEICRRAGVLVVEDNPYGLLSFTGEPVRAMRA-DAPDDVVYLGSFSKTLAPGLRVGW 239 Query: 269 IAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKA 328 A + +L +A +S L + F+Q++ +Y+ + E Y+ RRDAML A Sbjct: 240 ALAPAPVTARLVLAAESAILSQSMFTQLVVERYLATQPWAEQVKVFREMYRERRDAMLDA 299 Query: 329 LEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTM 388 L E MP G WT+P+GG FVWVTLP G+DT+ ML +A+A VAYVPG F+A ++M Sbjct: 300 LAESMPAGATWTRPDGGFFVWVTLPGGVDTRAMLPRAIAARVAYVPGAGFYADGSGGSSM 359 Query: 389 RLNFTYVPEEKIREGIKRLAETIKEEM 415 RL+F Y P E+IR+G+ RL +++E+ Sbjct: 360 RLSFCYPPPERIRDGVGRLGRVVRDEL 386 Lambda K H 0.318 0.137 0.398 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: 443 Number of extensions: 25 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: 417 Length of database: 396 Length adjustment: 31 Effective length of query: 386 Effective length of database: 365 Effective search space: 140890 Effective search space used: 140890 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 (21.7 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