Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_013721656.1 ALIDE2_RS06730 aspartate aminotransferase family protein
Query= BRENDA::Q9SR86 (481 letters) >NCBI__GCF_000204645.1:WP_013721656.1 Length = 442 Score = 196 bits (497), Expect = 2e-54 Identities = 133/403 (33%), Positives = 212/403 (52%), Gaps = 12/403 (2%) Query: 89 AKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQLKLINHSTILYLNHTISDFA 148 AK V D+ GR LD G + GH HP +V +V + + H + ++ A Sbjct: 28 AKGCVVTDDTGREILDFTSGQMCATIGHNHPAIVQAVQEAGEKAYHMFSGMIPEVVARLA 87 Query: 149 EALVST-LPGDLKVVFFTNSGTEANELAMMMARLYTGCNDIVSLRNSYHGNAAATMGATA 207 + + +P L F N+G+E+NE+A+ MA++YT +I+++ S+HG A A+ Sbjct: 88 QTMARDWMPQGLSKSIFINTGSESNEVALRMAKMYTQGFEILAVGGSWHGVTGAASAASF 147 Query: 208 QSNWK-FNVVQSGVHHAINPDPYRG-IFGSDGEKYASDVHDL----IQFGTSGQVAGFIG 261 S+ K + V GV P+ YR I G DGE A ++ ++G+ + I Sbjct: 148 ASDRKGYGVHVPGVFVMPEPNMYRPYIQGMDGEASALACLEIGLKMYDMASTGRRSAIII 207 Query: 262 ESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWGFQSHGVIPDIV 321 E I GG++ Y+ A + G + I DE Q+ F R G H GV PDI+ Sbjct: 208 EPIISAGGVLVPPKSYMQALRKAADERGMLLIFDEAQTAFGRIG-HRHAADFFGVTPDIM 266 Query: 322 TMAKGIGNGIPLGAVVTTPEIAGVLSRR--SYFNTFGGNPMCTAAGHAVLRVLHEEKLQE 379 ++K +G G+PL AV TTPEI + + +++ + +P+ G AVLR + +E+L E Sbjct: 267 AVSKTMGGGLPLAAVSTTPEIEEDIHAKGFTFYTSHVSDPLPATVGLAVLRTIQQERLIE 326 Query: 380 NANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAETLHLMDQMKE 439 A +G++L+RRL L+++YE IGDVRG G++LGVE VK R+ + P A + E Sbjct: 327 RAQSMGAYLRRRLEELQSRYEAIGDVRGEGMLLGVELVKSRETREPYHALGAITTQRCYE 386 Query: 440 MGVL--VGKGGFYGNVFRITPPLCFTLSDADFLVDVMDHAMSK 480 +G+ + + G+V+RI PPL T + D VD++D A+ + Sbjct: 387 LGLSMNIRRRPERGSVWRIAPPLTATQGEIDRGVDMLDEALRR 429 Lambda K H 0.320 0.136 0.406 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: 486 Number of extensions: 27 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: 481 Length of database: 442 Length adjustment: 33 Effective length of query: 448 Effective length of database: 409 Effective search space: 183232 Effective search space used: 183232 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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