Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_015943022.1 DHAF_RS03890 aspartate aminotransferase family protein
Query= BRENDA::Q9SR86 (481 letters) >NCBI__GCF_000021925.1:WP_015943022.1 Length = 399 Score = 191 bits (485), Expect = 4e-53 Identities = 133/406 (32%), Positives = 206/406 (50%), Gaps = 40/406 (9%) Query: 83 PLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQLKLINHSTILYLNH 142 P+ IV+ K V+D G++YLD G+A S GH HP VV ++ KQ + I H++ LY Sbjct: 24 PMAIVKGKGTTVWDIEGKQYLDFVTGLAVSSLGHSHPAVVEAIQKQAEEILHTSNLYWIP 83 Query: 143 TISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMMARLYTGCN------DIVSLRNSYH 196 AE LV D VFF NSG EANE A+ +AR Y + +I++L NS+H Sbjct: 84 NQIALAEKLVEHSFADQ--VFFCNSGAEANEAAIKIARKYAKEHYSEDKYEILTLVNSFH 141 Query: 197 GNAAATMGATAQSNWKFNVVQSGVHHAINPDPYRGIFGSDGEKYASDVHDLIQFGT--SG 254 G AT+ AT Q+ + Q G +A P+ + + ++DL Q + Sbjct: 142 GRTLATLTATGQTKY-----QKG--YAPLPEGFTYV----------PINDLAQLEEKMNP 184 Query: 255 QVAGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWGFQSH 314 +VA + E IQG GG+ L +L A + G + I DE+Q G RTG F ++ Sbjct: 185 KVAAVMLEPIQGEGGVFPLEVEFLAKARKLCDDYGALLIFDEIQVGLGRTGKLF-AYEWS 243 Query: 315 GVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAVLRVLHE 374 V+PDI+T+AK +G G+P+G ++ ++A + +TFGGNP+ TA G AV+ VL E Sbjct: 244 NVVPDIMTLAKALGGGVPIGVMLAKEKVASTFKPGDHASTFGGNPLATAVGCAVMDVLTE 303 Query: 375 EKLQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAETLHLM 434 E E+ + K+ L L +KY+ ++RG+G +LG P ++ Sbjct: 304 EGFLEDVQKRAQYFKQELQKLADKYQTGTEIRGQGFILG----------WPLDRLGAEIV 353 Query: 435 DQMKEMGVLVGKGGFYGNVFRITPPLCFTLSDADFLVDVMDHAMSK 480 + +E G+L+ G G R PPL + + D + ++D ++ Sbjct: 354 EGAREKGLLINFVG--GKALRFLPPLNVSYQEIDEAITILDQIFAE 397 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: 422 Number of extensions: 22 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: 399 Length adjustment: 32 Effective length of query: 449 Effective length of database: 367 Effective search space: 164783 Effective search space used: 164783 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