Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate Echvi_4558 Echvi_4558 putative phosphonate catabolism associated alcohol dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >FitnessBrowser__Cola:Echvi_4558 Length = 358 Score = 74.3 bits (181), Expect = 4e-18 Identities = 84/346 (24%), Positives = 151/346 (43%), Gaps = 39/346 (11%) Query: 20 VEVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIRPPQIMGHEVAGEVVEVGPG 79 + V P GE+L++ L +IC +DLH + + + ++GHE+ G + + Sbjct: 21 LSVAFPSLQKGEILVRNLYATICASDLHTFH----GRRKSCHHSVLGHEIVGRIEALAE- 75 Query: 80 VEG--------IEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDT-------DGV 124 EG +E GD ++ + +G ++ +G + +G Sbjct: 76 -EGAKDYHGRPLEKGDRITWSVYAHDPASPTSLKGFPQKSEDLYKYGHEQIDDHYQLNGG 134 Query: 125 FAEYAVV-PAQNVWKNPKNIPPEYATLQEPLGNAVDTV-----LAGPIAGKSVLITGAGP 178 F+ + + +++K P+ + A PL T+ LAG ++GK+VL+ GAG Sbjct: 135 FSTHCHLRKGTSLFKLPEALTDREAA---PLNCTHATIAGAMRLAGSLSGKTVLVNGAGM 191 Query: 179 LGLLGIAVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVD 238 LGL A+AK GA V + S + AK GAD +DV + + D Sbjct: 192 LGLSACAMAKEKGASHVWACDLSIEKATHAKAFGADTAFEAESKDVPHRIF---GPDKAD 248 Query: 239 VFLEFSGAPKALEQGLQAVTPAGRVSLLG-LFPGKVSIDFNNLIIFKALTVYGITGRHLW 297 + +E SG P+A+E L + G + L+G +FP + ++ LT+ G+ Sbjct: 249 IIIETSGMPEAMENCLHMLGIGGTIILVGAVFPQRNLSINAEFLVRNLLTIKGLHNYIPE 308 Query: 298 ETWYTVSRLLQS-GKLNIDPIITHKYKGFDKYEEAFELMRAGKTGK 342 + +S L ++ K D ++ ++ ++ + AFE AG GK Sbjct: 309 DLATAISFLTKAKAKYPFDSLVGREF-SLEQLDSAFE---AGSHGK 350 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: 253 Number of extensions: 18 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: 2 Length of query: 348 Length of database: 358 Length adjustment: 29 Effective length of query: 319 Effective length of database: 329 Effective search space: 104951 Effective search space used: 104951 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 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