Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate 6938343 Sama_2462 threonine aldolase (RefSeq)
Query= BRENDA::P75823 (333 letters) >FitnessBrowser__SB2B:6938343 Length = 336 Score = 336 bits (862), Expect = 4e-97 Identities = 184/328 (56%), Positives = 228/328 (69%), Gaps = 5/328 (1%) Query: 3 DLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQAN 62 D RSDTVT+P+ AM +AM A VGDDVYGDDPTVN L+ AAE+ G +AA+F +GTQAN Sbjct: 4 DFRSDTVTQPTAAMRQAMSQAQVGDDVYGDDPTVNRLEAMAAEMLGFDAALFTSSGTQAN 63 Query: 63 LVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKIKP 122 L+AL+SHCERG+EYI GQ AHNY FE GGAAVLGSIQPQP+ ADGT+ L + IKP Sbjct: 64 LLALMSHCERGDEYICGQDAHNYRFEGGGAAVLGSIQPQPLLNQADGTIALGDIEAAIKP 123 Query: 123 DDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYGCELK 182 DD+H+ART+LLSLENT GKVLP YL A R L +H+DGAR+ NA VA + Sbjct: 124 DDVHYARTRLLSLENTIGGKVLPMGYLANAQALAFNRGLKIHLDGARLANAAVALNKPMA 183 Query: 183 EITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSGILAAAGIYAL 242 EI + DS ++CLSKGL PVGSLL+G+ IK+A RWRKM GGGMRQ+GILAAAGI AL Sbjct: 184 EIAGHFDSVSLCLSKGLCAPVGSLLLGDDRLIKKARRWRKMLGGGMRQAGILAAAGIIAL 243 Query: 243 KNNVARLQEDHDNAAWMAEQLREAG---ADVMRQDTNMLFVRVGEE-NAAALGEYMKARN 298 ++ RL EDHDNAA + +L + TNM+F RV E + + + + Sbjct: 244 ESQWQRLAEDHDNAALLGRELSMIDGFEVNTASIQTNMVFARVAEHIDIKHVAAELASLG 303 Query: 299 VLINASPIVRLVTHLDVSREQ-LAEVAA 325 +I+ + +RLVTH D+SR+ LA VAA Sbjct: 304 FIISPAKNLRLVTHNDISRDAVLAFVAA 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: 367 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 333 Length of database: 336 Length adjustment: 28 Effective length of query: 305 Effective length of database: 308 Effective search space: 93940 Effective search space used: 93940 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