Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_083529261.1 AS188_RS05075 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_001482365.1:WP_083529261.1 Length = 412 Score = 276 bits (707), Expect = 6e-79 Identities = 154/404 (38%), Positives = 233/404 (57%), Gaps = 8/404 (1%) Query: 13 APTL-DYEKYFSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEV 71 AP L D F+++A G + S VR + ++ +ISLAGG P P ++A + Sbjct: 12 APGLPDPAALFARRAEGFRPSPVRAVFEIAMRPGMISLAGGNPDTGALPHAVLAGTAARL 71 Query: 72 LEKHAAQALQYGTTKGFTPLRLALAEWMRKRYDIPISKVD---IMITSGSQQALDLIGRV 128 L + ++ LQYG+ G L E + + D+ + D I IT+GSQ +DL+ ++ Sbjct: 72 LAERGSEVLQYGSGAGIE----RLPELVCRLMDLEGAATDPGRIQITAGSQAGIDLVVKL 127 Query: 129 FINPGDIVVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKL 188 F +PGD+VV E PTY+ AL F YE + +DD+G+ + + E++ L G+ VKL Sbjct: 128 FCDPGDVVVAEGPTYVGALGVFGSYEVAVSHVDVDDDGLDPEAVAERIDALRATGRTVKL 187 Query: 189 VYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEG 248 VYT+PTF NP GVT+ E+RR+RL+ + +E +++ED+PYG L + E P D Sbjct: 188 VYTVPTFHNPTGVTLGEERRRRLVAVCAERGVVVLEDDPYGLLGFDREHRLPSLYSLDPE 247 Query: 249 RVMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLD 308 V++LG+FSKI +PG R+GWIAA P + +L+IA ++V + + Q +A +YV G H Sbjct: 248 TVVHLGSFSKIFSPGLRVGWIAASPAVRARLQIAAEAVTIHPSVLGQELAAEYVGGEHWR 307 Query: 309 NHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAK 368 + + Y+ R AM+ ALEE MPEGVRWT+P GG F W+ L +L +A+ Sbjct: 308 PALDRAVARYRSRCAAMMAALEEHMPEGVRWTRPAGGFFTWLDLDPARAHGDLLHRAIDH 367 Query: 369 GVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIK 412 GV VPG A +A ++RL F+ EE I EG++RL ++ Sbjct: 368 GVVVVPGGACYADGRPSTSLRLAFSAAAEEDIAEGVRRLGRMLR 411 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: 458 Number of extensions: 19 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: 417 Length of database: 412 Length adjustment: 31 Effective length of query: 386 Effective length of database: 381 Effective search space: 147066 Effective search space used: 147066 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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