Align L-allo-threonine aldolase (EC 4.1.2.49) (characterized)
to candidate GFF2934 Psest_2990 Threonine aldolase
Query= BRENDA::O07051 (338 letters) >FitnessBrowser__psRCH2:GFF2934 Length = 341 Score = 369 bits (947), Expect = e-107 Identities = 196/335 (58%), Positives = 241/335 (71%), Gaps = 4/335 (1%) Query: 1 MRYIDLRSDTVTQPTDAMRQCMLHAEVGDDVYGEDPGVNALEAYGADLLGKEAALFVPSG 60 M IDLRSDTVTQPT MR+ M AE GDDVYGEDP V+ LE A LG AA+FVPSG Sbjct: 1 MSDIDLRSDTVTQPTADMREAMFRAETGDDVYGEDPTVSRLERQLAGDLGFSAAMFVPSG 60 Query: 61 TMSNLLAVMSHCQRGEGAVLGSAAHIYRYEAQGSAVLGSVALQPVPMQADGSLALADVRA 120 TMSNLLA+M+HC+RG+ ++G AH Y+YE G+AVLGS+ QP+ M+ADG+L L + A Sbjct: 61 TMSNLLALMAHCERGDEYIVGQQAHTYKYEGGGAAVLGSIQPQPIEMEADGTLDLRRIEA 120 Query: 121 AIAPDDVHFTPTRLVCLENTHNGKVLPLPYLREMRELVDEHGLQLHLDGARLFNAVVASG 180 AI PD+ HF +RL+ LENT +GKVLPL YL R+ + L LHLDGARLFNA V G Sbjct: 121 AIKPDNFHFARSRLLVLENTMHGKVLPLDYLAAARDFTRQRDLALHLDGARLFNAAVKLG 180 Query: 181 HTVRELVAPFDSVSICLSKGLGAPVGSLLVGSHAFIARARRLRKMVGGGMRQAGILAQAG 240 RE+ FD+VS+CLSKGLGAPVGS+L G AFIA+ARRLRKMVGGGMRQAGILA AG Sbjct: 181 CDAREITRHFDTVSVCLSKGLGAPVGSVLCGDDAFIAKARRLRKMVGGGMRQAGILAAAG 240 Query: 241 LFALQQHVVRLADDHRRARQLAEGLAALPGIRLDLAQVQTNMVFLQLTSGESAPLLAFMK 300 L+AL+ ++ RLADDHRRA L LAAL G ++ VQTNMV++++ ++ L AF Sbjct: 241 LYALEHNIDRLADDHRRAEWLGNELAAL-GFAVE--PVQTNMVYVEM-GAQATALTAFCA 296 Query: 301 ARGILFSGYGELRLVTHLQIHDDDIEEVIDAFTEY 335 RGI + LRLVTHL +HD+ + V+ AF E+ Sbjct: 297 QRGIRLTPAARLRLVTHLDVHDEHVPRVVGAFAEF 331 Lambda K H 0.322 0.137 0.396 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: 390 Number of extensions: 13 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: 338 Length of database: 341 Length adjustment: 28 Effective length of query: 310 Effective length of database: 313 Effective search space: 97030 Effective search space used: 97030 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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