Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_083790034.1 TCUR_RS24380 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000024385.1:WP_083790034.1 Length = 410 Score = 345 bits (884), Expect = 2e-99 Identities = 173/389 (44%), Positives = 254/389 (65%), Gaps = 4/389 (1%) Query: 29 MKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGF 88 M SE+R L + +V+SLAGG+P P++++ ++ E+ + +ALQY + +G Sbjct: 1 MVPSEIRALFAVASRPEVVSLAGGMPNITALPLDVVGDMLGELTRRRGTEALQYASAQGD 60 Query: 89 TPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQ 148 LR + E M + S D+++T GSQQALD+I R+FI+PGD+V+ EAP+Y+ AL Sbjct: 61 PELRARICEVMALE-GVHGSPDDVIVTVGSQQALDMITRIFIDPGDVVLAEAPSYVGALG 119 Query: 149 AFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRR 208 F Y+ + V +PLD++G+ L E L+ L KEG++VK +YT+P FQNPAGVT+SE RR Sbjct: 120 TFAMYQADVVHVPLDEDGLIPAALRETLERLRKEGRRVKFLYTVPNFQNPAGVTLSETRR 179 Query: 209 KRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGW 268 +L + + + L+VEDNPYG L + EP++ ++A DD V+YLG+FSK APGFR+GW Sbjct: 180 AEILAICAAHQVLVVEDNPYGLLGFDREPMRALRA-DDPDNVIYLGSFSKTFAPGFRVGW 238 Query: 269 IAAEPHLIR-KLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLK 327 A PH IR KL +A +S LC + F+Q +Y+ I + Y RRDAML+ Sbjct: 239 ALA-PHAIRAKLVLAAESAILCHSSFTQFAVREYLATQPWQQQIKSFRVMYAERRDAMLE 297 Query: 328 ALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNT 387 +LE MP+G WT+P GG FVW+TLPEG+D+K M +A+A+ VAYVPG F+A + Sbjct: 298 SLEALMPDGCTWTRPGGGFFVWLTLPEGLDSKAMAPRAIAERVAYVPGTGFYADGQGRRH 357 Query: 388 MRLNFTYVPEEKIREGIKRLAETIKEEMK 416 MRL++ Y ++IREG++RLA I+ E++ Sbjct: 358 MRLSYCYPEPDRIREGVRRLAGVIERELQ 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: 469 Number of extensions: 30 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: 410 Length adjustment: 31 Effective length of query: 386 Effective length of database: 379 Effective search space: 146294 Effective search space used: 146294 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