Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate GFF4229 PS417_21665 threonine aldolase
Query= BRENDA::P75823 (333 letters) >FitnessBrowser__WCS417:GFF4229 Length = 334 Score = 379 bits (972), Expect = e-110 Identities = 189/324 (58%), Positives = 246/324 (75%), Gaps = 1/324 (0%) Query: 1 MIDLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQ 60 +IDLRSDTVT+P+ M +AM A GDDVYG+DP+VN L+ A+ G AA+F+PTGT Sbjct: 3 VIDLRSDTVTQPTPGMRDAMATAVSGDDVYGEDPSVNRLEAELAKRLGFAAALFVPTGTM 62 Query: 61 ANLVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKI 120 +NL+AL++HCERGEEYIVGQ AH Y +E GGAAVLGSIQPQP++ ADG+L LD+V I Sbjct: 63 SNLLALMAHCERGEEYIVGQQAHTYKYEGGGAAVLGSIQPQPLEVQADGSLDLDQVLAAI 122 Query: 121 KPDDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYGCE 180 KPDD HFART+LL+LENT GKVLP +YL +A FTRE +LALH+DGAR++NA V G + Sbjct: 123 KPDDFHFARTRLLALENTMQGKVLPLDYLAKARAFTREHDLALHLDGARLYNAAVKLGVD 182 Query: 181 LKEITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSGILAAAGIY 240 +EI Q+ DS ++CLSKGLG P+GS+L G+ I +A R RKM GGGMRQ+G LAAAG+Y Sbjct: 183 AREIAQHFDSVSVCLSKGLGAPIGSVLCGSTALIAKARRLRKMVGGGMRQAGSLAAAGLY 242 Query: 241 ALKNNVARLQEDHDNAAWMAEQLREAGADVMRQDTNMLFVRVGEENAAALGEYMKARNVL 300 AL + V RL EDH NA W+ + LR+AG +V TNM++V++G++ A AL + R + Sbjct: 243 ALDHQVQRLAEDHANAHWLGDALRQAGYEVEPVQTNMVYVQIGDQ-AQALKAFAAERGIT 301 Query: 301 INASPIVRLVTHLDVSREQLAEVA 324 ++A+P +R+VTHLDVSR Q+ VA Sbjct: 302 LSAAPRLRMVTHLDVSRAQIERVA 325 Lambda K H 0.319 0.134 0.391 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: 345 Number of extensions: 10 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: 333 Length of database: 334 Length adjustment: 28 Effective length of query: 305 Effective length of database: 306 Effective search space: 93330 Effective search space used: 93330 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: 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