Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate WP_015798122.1 AFER_RS03495 aromatic amino acid beta-eliminating lyase/threonine aldolase
Query= BRENDA::Q9X266 (343 letters) >NCBI__GCF_000023265.1:WP_015798122.1 Length = 335 Score = 231 bits (588), Expect = 3e-65 Identities = 142/330 (43%), Positives = 189/330 (57%), Gaps = 6/330 (1%) Query: 2 IDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMG 61 IDLRSDTVT+PT+ MR+AMA A GDD YGEDPT+ ELE AA G EAALFV SGTM Sbjct: 3 IDLRSDTVTQPTDAMRRAMASARCGDDGYGEDPTVRELEERAAGLLGMEAALFVASGTMA 62 Query: 62 NQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRP 121 NQV++ T G V++ A +H+ +E GA A + V H + +GA D V A+ Sbjct: 63 NQVALRTLTTPGSVVVVGARAHLCQFERGASARNALVQLHTLADDDGAPTADAVADAVAT 122 Query: 122 RNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGV 181 + +LIAIENTH SGG PL+ ++ ++IDGAR++NAS+A GV Sbjct: 123 YRAIGVQPALIAIENTHMPSGG--TPLDPVRTGALADAATATPLYIDGARLWNASVALGV 180 Query: 182 PVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGI 241 A +V C SKGL AP+GSVV G D +ERAR R+ LGG +RQAG++AAA + Sbjct: 181 EPSVLTERATAVSTCFSKGLGAPMGSVVAGSADLVERARWERQALGGRLRQAGIIAAAAL 240 Query: 242 IALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALR 301 +AL + L DHE A L ++ TNMV++ D + LR Sbjct: 241 VALDEWRSVLARDHERAAVLRDRVAAELGDARVRWGGTNMVLVDAD----RPVEMLARLR 296 Query: 302 NSGVLANAVSDTEIRLVTHKDVSRNDIEEA 331 +GVLANA+ +R V H+D+S ++ A Sbjct: 297 EAGVLANAIGPRTLRFVVHRDLSDAEVTVA 326 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: 280 Number of extensions: 9 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: 335 Length adjustment: 28 Effective length of query: 315 Effective length of database: 307 Effective search space: 96705 Effective search space used: 96705 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