Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate WP_084544078.1 GY23_RS09030 alcohol dehydrogenase catalytic domain-containing protein
Query= SwissProt::Q8U259 (348 letters) >NCBI__GCF_001939075.1:WP_084544078.1 Length = 349 Score = 185 bits (470), Expect = 1e-51 Identities = 111/335 (33%), Positives = 185/335 (55%), Gaps = 15/335 (4%) Query: 18 ELVEVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIRPPQIMGHEVAGEVVEVG 77 ++VEV +P E+L+++ +CGTD IY+ + I P+I+GHE +G + +VG Sbjct: 17 KVVEVPIPVINEDELLVRVSYAGVCGTDNRIYQGTKI----IEGPRIIGHEFSGVIEKVG 72 Query: 78 PGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGVFAEYAVVP----- 132 V+ VGD+V+V I CG CY CK G+ ++C N K G + DG FA+Y +P Sbjct: 73 TNVQSFSVGDHVTVYPMISCGDCYTCKTGRKNICVNRKTIGYEIDGGFAQYIKIPKIAIN 132 Query: 133 AQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPI-AGKSVLITGAGPLGLLGIAVAKASG 191 NV+K N+ + + EP+ A++ + I G V+I GAGP+GL + +AK Sbjct: 133 MGNVFKVSSNLDQKVVAITEPIAAALNGIKRANIQQGDCVVIIGAGPIGLFHVQLAKLKE 192 Query: 192 AYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFSGAPKALE 251 ++V EP +R +A K+GA + INPF+E+ + ++TDG G DV + G PK +E Sbjct: 193 PGILVVIEPDHAKREIALKLGATHTINPFDENPEIRLKELTDGEGADVVIIDVGIPKIIE 252 Query: 252 QGLQAVTPAGRVSLLGLFP--GKVSIDFNNLIIFKALTVYGITGRHLWETWYTVSRLLQS 309 + ++ V G + P K+S+D NLI +K + + G + E V L++S Sbjct: 253 ESIEYVKKGGTYVIFAGAPHGSKISLD-PNLIHYKEINLTG-SSAATPELHQEVLDLVES 310 Query: 310 GKLNIDPIITHKYKGFDKYEEAFELMRAGKTGKVV 344 G++++ +I+ + G D++E A E+ + + KV+ Sbjct: 311 GQVDVTLLIS-EVVGLDEWERALEMKNSFQKIKVI 344 Lambda K H 0.318 0.138 0.417 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: 306 Number of extensions: 15 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: 348 Length of database: 349 Length adjustment: 29 Effective length of query: 319 Effective length of database: 320 Effective search space: 102080 Effective search space used: 102080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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