Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate WP_017599524.1 D471_RS0115815 threonine aldolase
Query= BRENDA::Q9X266 (343 letters) >NCBI__GCF_000341125.1:WP_017599524.1 Length = 337 Score = 249 bits (636), Expect = 7e-71 Identities = 147/336 (43%), Positives = 199/336 (59%), Gaps = 11/336 (3%) Query: 1 MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTM 60 MIDLRSDTVT+PT MR+A+A+AEVGDDVYGEDPT+ LE A GKEAA++VPSG M Sbjct: 1 MIDLRSDTVTRPTAAMRRAIAEAEVGDDVYGEDPTVRALEEETAALLGKEAAVYVPSGHM 60 Query: 61 GNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDP--DDVRKA 118 NQ+++ T+ G+EV H+ E GA AVLS V P G D D + Sbjct: 61 ANQIALYVSTRSGEEVWAHEHHHLIGSEQGAAAVLSRVQPRLYSGAPFPSDDVLADWTRG 120 Query: 119 IRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIA 178 + H +L+ +ENT G+VVPL + + A +HG+ H+DGAR++NA+ A Sbjct: 121 AGEGDAHRAEPALLWLENTFT---GQVVPLAEQRRVVAFAHDHGMRAHLDGARLWNAAAA 177 Query: 179 SGVPVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAA 238 E A D+V C SKGL APVGS + GD + RAR+ARK+LG GMRQAG++AA Sbjct: 178 LDAAPAEVAAGFDTVSVCFSKGLGAPVGSALAGDAATVRRARRARKLLGAGMRQAGIIAA 237 Query: 239 AGIIALTKMVDRLKEDHENARFLALKLKEI-GYSVNPEDVKTNMVILRTDNLKVNAHGFI 297 + AL +R+ EDH A LA ++ G S +TNMV+L+T + +A + Sbjct: 238 GALHALRHHRERIPEDHTRAMLLAERIGAAPGLSAR---ARTNMVLLQTP--EGSAARLV 292 Query: 298 EALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALN 333 E L +GV A A+ + IRL H D++ D++EA N Sbjct: 293 ELLARNGVGAVAIGPSLIRLTVHLDITDGDVDEAAN 328 Lambda K H 0.319 0.135 0.384 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: 289 Number of extensions: 10 Number of successful extensions: 3 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: 343 Length of database: 337 Length adjustment: 28 Effective length of query: 315 Effective length of database: 309 Effective search space: 97335 Effective search space used: 97335 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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