Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate WP_012103076.1 CKL_RS13380 low-specificity L-threonine aldolase
Query= BRENDA::Q9X266 (343 letters) >NCBI__GCF_000016505.1:WP_012103076.1 Length = 342 Score = 328 bits (840), Expect = 2e-94 Identities = 176/339 (51%), Positives = 234/339 (69%), Gaps = 4/339 (1%) Query: 2 IDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMG 61 I+LRSDT T+PT+ MR AM +AEVGDDVYG+DPT+ ELE+ AA+ GKEAALFVPSGT G Sbjct: 4 IELRSDTATEPTQAMRDAMYKAEVGDDVYGDDPTVVELEKYAAKLMGKEAALFVPSGTFG 63 Query: 62 NQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRP 121 NQ+++ H +RG EVIL DSHI +EVGA AV++GV + K G MD +VR AIR Sbjct: 64 NQLALFTHCRRGTEVILGEDSHIVVHEVGAPAVIAGVQLRTLKTKGGEMDIYEVRDAIRC 123 Query: 122 R-NIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASG 180 + +IH+P TSLI +EN + S GRV+ L+N+ E+ AK++ + VH+DGARIFNA+ Sbjct: 124 KEDIHYPETSLICMENAY--SDGRVLSLKNMNEVFNEAKKYNLPVHLDGARIFNAAAYLE 181 Query: 181 VPVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAG 240 V VK+ Y DSVMFCLSKGLCAPVGS++ G + FI+RA+K RK++GGGMRQAG LAAAG Sbjct: 182 VDVKDITKYCDSVMFCLSKGLCAPVGSILAGSKYFIQRAKKGRKLMGGGMRQAGFLAAAG 241 Query: 241 IIALTKMVDRLKEDHENARFLALKLKEI-GYSVNPEDVKTNMVILRTDNLKVNAHGFIEA 299 I+AL M RL+ED+ENA FL +L +I G VN ED+ NMV ++ +E Sbjct: 242 IVALKHMSGRLREDYENALFLGKELSKIPGIKVNLEDIHINMVFFDMSETGYDSSKLVEE 301 Query: 300 LRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKL 338 G+ N + ++R VT+ VS+ DI + +++ Sbjct: 302 FYKKGIKINPEENGKMRFVTNYWVSKEDIPYVVKTLKEI 340 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: 324 Number of extensions: 17 Number of successful extensions: 4 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: 342 Length adjustment: 29 Effective length of query: 314 Effective length of database: 313 Effective search space: 98282 Effective search space used: 98282 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 Sep 24 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