Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012852598.1 TCUR_RS11130 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000024385.1:WP_012852598.1 Length = 486 Score = 167 bits (424), Expect = 5e-46 Identities = 121/370 (32%), Positives = 189/370 (51%), Gaps = 25/370 (6%) Query: 45 DVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLA-LAEWMRKRY 103 D+I L PA + E AE E L +H+ T G+ P LA L E + RY Sbjct: 117 DLIDLGCAAPAAPSCLAEAAAEAMAE-LPRHS-------TGHGYEPTGLAVLREAIAARY 168 Query: 104 D---IPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQI 160 P I++T+G+QQA+ L+ V + PGD V++E PTY AL+A + V + Sbjct: 169 TELGAPTRPDQIVVTTGAQQAISLLAHVLVTPGDAVLIERPTYPHALEALRRCGGRLVPV 228 Query: 161 PLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDF 220 + EG ++L+ +++ +L Y IP FQNP G + + R L+ A D Sbjct: 229 GVG-EGWDLELVAASMRQAA-----ARLAYLIPDFQNPTGHLLDDAGRAALVAAARSADA 282 Query: 221 LIVEDNPYGELRY--SGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRK 278 L++ D + EL + +P+ A D GRV+ +G+ SK++ G RIGWI A L+R+ Sbjct: 283 LLIVDESFSELSLDPAAPRPRPVAAHDTGGRVISIGSASKLMWGGLRIGWIRAGAPLVRR 342 Query: 279 LEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVR 338 L A+ SVDL + Q++AW+ +E ++ + RDA+ AL E +PE Sbjct: 343 LIAARASVDLASPVLEQLVAWRLLE--RIEQVRAERAQELTRSRDALAGALRELLPEW-E 399 Query: 339 WTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLNFTYVPEE 398 +T P GGM +WV L + T + E+A GV VPG F +++ +RL + +P + Sbjct: 400 FTLPRGGMSLWVRLEAPVATP-VAERAWRHGVRVVPGPVFGVDGVLEDCLRLPYV-LPPQ 457 Query: 399 KIREGIKRLA 408 +R ++RLA Sbjct: 458 TLRTAVERLA 467 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: 463 Number of extensions: 29 Number of successful extensions: 6 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: 486 Length adjustment: 33 Effective length of query: 384 Effective length of database: 453 Effective search space: 173952 Effective search space used: 173952 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: 51 (24.3 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