Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate 3608752 Dshi_2144 Threonine aldolase (RefSeq)
Query= BRENDA::P75823 (333 letters) >FitnessBrowser__Dino:3608752 Length = 344 Score = 273 bits (697), Expect = 6e-78 Identities = 154/331 (46%), Positives = 201/331 (60%), Gaps = 4/331 (1%) Query: 3 DLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQAN 62 DLRSDTVTRP M AM A VGDD YG+DPTV L+ AE + K A +F PTG +N Sbjct: 16 DLRSDTVTRPCAGMRAAMADAEVGDDCYGEDPTVLRLEAVLAERTDKAAGLFFPTGCMSN 75 Query: 63 LVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKIKP 122 L AL++ C RGEE IVG+ H Y EA A+VLG++ PI A DG L ++ +KP Sbjct: 76 LAALMAQCARGEEVIVGRDYHVYADEAASASVLGALSLVPIPVAEDGGLEPAEIRAALKP 135 Query: 123 DDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYGCELK 182 +D+H+AR++LL LENT G+ +P + A RE L++H+DGAR FNAV A G Sbjct: 136 EDVHYARSRLLCLENTVGGRAVPLARMAAAVRTGREAGLSVHLDGARFFNAVTALGSSEA 195 Query: 183 EITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSGILAAAGIYAL 242 E+ D+ ++CLSKGLG P G++LVG I A R RK+ GGGMRQSG+LAAAG++AL Sbjct: 196 ELAGLADTVSLCLSKGLGAPAGTVLVGPTPVIAEARRLRKLLGGGMRQSGVLAAAGLWAL 255 Query: 243 KNNVARLQEDHDNAAWMAEQLREAGADVMRQDTNMLFVRVGEENAAALGEYMKARNVLIN 302 ++ + RL EDH AA +A L G +RQ TNM+F +N AAL M + V I+ Sbjct: 256 EHQLPRLAEDHARAARLARALIPLG--TVRQGTNMVFFTPPVQNRAALAARMAGQGVRIS 313 Query: 303 --ASPIVRLVTHLDVSREQLAEVAAHWRAFL 331 +RLV H DV L A + + L Sbjct: 314 DPGEGAIRLVVHRDVDDAALTAAIAAFESCL 344 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: 308 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: 333 Length of database: 344 Length adjustment: 28 Effective length of query: 305 Effective length of database: 316 Effective search space: 96380 Effective search space used: 96380 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 Apr 09 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