Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate GFF2934 Psest_2990 Threonine aldolase
Query= BRENDA::P75823 (333 letters) >FitnessBrowser__psRCH2:GFF2934 Length = 341 Score = 360 bits (924), Expect = e-104 Identities = 182/329 (55%), Positives = 239/329 (72%), Gaps = 1/329 (0%) Query: 2 IDLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQA 61 IDLRSDTVT+P+ M EAM A GDDVYG+DPTV+ L+ A G AA+F+P+GT + Sbjct: 4 IDLRSDTVTQPTADMREAMFRAETGDDVYGEDPTVSRLERQLAGDLGFSAAMFVPSGTMS 63 Query: 62 NLVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKIK 121 NL+AL++HCERG+EYIVGQ AH Y +E GGAAVLGSIQPQPI+ ADGTL L ++ IK Sbjct: 64 NLLALMAHCERGDEYIVGQQAHTYKYEGGGAAVLGSIQPQPIEMEADGTLDLRRIEAAIK 123 Query: 122 PDDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYGCEL 181 PD+ HFAR++LL LENT +GKVLP +YL A +FTR+R+LALH+DGAR+FNA V GC+ Sbjct: 124 PDNFHFARSRLLVLENTMHGKVLPLDYLAAARDFTRQRDLALHLDGARLFNAAVKLGCDA 183 Query: 182 KEITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSGILAAAGIYA 241 +EIT++ D+ ++CLSKGLG PVGS+L G+ +I +A R RKM GGGMRQ+GILAAAG+YA Sbjct: 184 REITRHFDTVSVCLSKGLGAPVGSVLCGDDAFIAKARRLRKMVGGGMRQAGILAAAGLYA 243 Query: 242 LKNNVARLQEDHDNAAWMAEQLREAGADVMRQDTNMLFVRVGEENAAALGEYMKARNVLI 301 L++N+ RL +DH A W+ +L G V TNM++V +G + A AL + R + + Sbjct: 244 LEHNIDRLADDHRRAEWLGNELAALGFAVEPVQTNMVYVEMGAQ-ATALTAFCAQRGIRL 302 Query: 302 NASPIVRLVTHLDVSREQLAEVAAHWRAF 330 + +RLVTHLDV E + V + F Sbjct: 303 TPAARLRLVTHLDVHDEHVPRVVGAFAEF 331 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: 364 Number of extensions: 8 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: 341 Length adjustment: 28 Effective length of query: 305 Effective length of database: 313 Effective search space: 95465 Effective search space used: 95465 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