Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_040536608.1 L248_RS11710 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000469325.1:WP_040536608.1 Length = 402 Score = 267 bits (682), Expect = 5e-76 Identities = 147/394 (37%), Positives = 223/394 (56%), Gaps = 9/394 (2%) Query: 20 KYFSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQA 79 K F+++ L + + + + +++D+IS AGG P FP + + KE + Sbjct: 3 KQFAERTLKATEAGIADAFAVSDNADLISFAGGFPDAGLFPNAEMGDAFKEAFG-NTQNL 61 Query: 80 LQYGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVE 139 LQY G+ PLR LA+ + P DI++T G+QQA+DL+ R+ INPGD +VVE Sbjct: 62 LQYHGDHGYQPLREQLAQRLSND-GTPTQPDDIILTQGAQQAIDLVARMLINPGDGLVVE 120 Query: 140 APTYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPA 199 APTY AL AF Y+P + +IP+ +GM + L + L KL+YTIP FQNP Sbjct: 121 APTYFGALGAFDNYDPTYYEIPMQADGMDMHALRKALM-----AHSFKLIYTIPDFQNPT 175 Query: 200 GVTMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKI 259 GV MS +R+ LL LA EY+ +++ED+PY LR++GE + ++A D + RV+ LG+FSKI Sbjct: 176 GVVMSLAKRQELLRLAREYNVVVLEDSPYRWLRFTGEQLPTLRALDTDDRVISLGSFSKI 235 Query: 260 LAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYK 319 LAPG R+GW + I + K DL + + V Y+ LD H+ + Y+ Sbjct: 236 LAPGLRLGWASGGQKWIAAIAALKNGADLESPFMTMVAVSNYLAHNDLDAHLAKLRAVYQ 295 Query: 320 PRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAV--AKGVAYVPGEA 377 ++DAM++ L + +P G P+GG FVW+T P G+D ++L+ + +AY+P + Sbjct: 296 AKKDAMVRVLHQELPAGFSADDPQGGFFVWLTAPAGVDMGVLLKDEILPQDHIAYIPSKN 355 Query: 378 FFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETI 411 + + V N RLNFT IR GI RL+ + Sbjct: 356 LYPSKRVVNAARLNFTGEDAATIRTGIARLSAAL 389 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: 418 Number of extensions: 20 Number of successful extensions: 4 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: 402 Length adjustment: 31 Effective length of query: 386 Effective length of database: 371 Effective search space: 143206 Effective search space used: 143206 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