Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate Ac3H11_4475 Low-specificity L-threonine aldolase (EC 4.1.2.48)
Query= BRENDA::P75823 (333 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4475 Length = 355 Score = 325 bits (832), Expect = 1e-93 Identities = 175/338 (51%), Positives = 229/338 (67%), Gaps = 22/338 (6%) Query: 1 MIDLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQ 60 M D RSDTVT+P+ AM EAM AP+GDDV+ DDP+VNALQD+AAEL G EAA+F P+GTQ Sbjct: 1 MPDFRSDTVTQPTPAMREAMFKAPLGDDVFADDPSVNALQDHAAELLGFEAALFAPSGTQ 60 Query: 61 ANLVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKI 120 NL+AL HC+RG+E IVGQ+ H Y +EAGG AVLGSIQPQP++ DGTL + +A I Sbjct: 61 TNLIALWGHCQRGDEAIVGQSWHTYRWEAGGMAVLGSIQPQPVETQPDGTLRVADIAAAI 120 Query: 121 KPDDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYG-- 178 KPDD HFART+L+ LENT G+VLP Y+ + + R R LA+H+DGAR+FNA A Sbjct: 121 KPDDPHFARTRLVVLENTTGGQVLPPAYIADVAQLARSRGLAMHLDGARMFNAATANAAR 180 Query: 179 ------CELKEITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSG 232 E + + + DS ++CLSKGLG PVGSL++G+RD+I++A R RK+ GGGMRQ+G Sbjct: 181 NGTDVYAEARALCSHFDSASLCLSKGLGAPVGSLVLGSRDFIRQARRTRKILGGGMRQAG 240 Query: 233 ILAAAGIYALKNNVARLQEDHDNAAWMAEQLREAGAD---------VMRQDTNMLFVRVG 283 +LAAAG YAL+++V RL +DH N +A+ L EA V+ TN+LF + Sbjct: 241 VLAAAGSYALQHHVRRLADDHANLDRLAQGLAEANRSHPVLKDKITVLPWQTNILFTDLH 300 Query: 284 EENAAALGEYMKARNVLINAS-----PIVRLVTHLDVS 316 E A A ++ V + +S +R VTHLDVS Sbjct: 301 AEVAPAFTAWLAQHGVRVTSSLYGGATRLRWVTHLDVS 338 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: 388 Number of extensions: 14 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: 355 Length adjustment: 29 Effective length of query: 304 Effective length of database: 326 Effective search space: 99104 Effective search space used: 99104 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