Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate Dsui_2228 Dsui_2228 Zn-dependent alcohol dehydrogenase
Query= curated2:Q6AAR3 (345 letters) >FitnessBrowser__PS:Dsui_2228 Length = 340 Score = 118 bits (296), Expect = 2e-31 Identities = 108/347 (31%), Positives = 162/347 (46%), Gaps = 19/347 (5%) Query: 1 MKALVKTRPEPGLELVEVPDPVAGPNDVIVKVMRTGICGTDVHIDKWDGWAAKTVHTPLV 60 MKA V L + EVP P P V+VKV+ +G+C TD+H D W K P + Sbjct: 5 MKAAVVHEFGKPLVIEEVPVPEVPPGQVLVKVVASGVCHTDLHAADGD-WPVKP-SLPFI 62 Query: 61 LGHEFCGEIVELGSEVNDLEVGQFVSGEG-HYVCGRCRACLAGKRHLCRNTQGIGYAVNG 119 GHE G + +G+ V ++ G V H CG C C+ G LC + Q GY VNG Sbjct: 63 PGHEGVGYVAAVGAGVTHVKEGDRVGVPWLHTACGHCEHCITGWETLCDSQQMTGYTVNG 122 Query: 120 AYCQYFVMPAGNVWVHHIPD-LDPDVAAIFDPFGNAVHTALQ-FPCLAED-VLVSGAGPI 176 Y +Y + G +V +PD L+ AA G V+ L+ C D V +SG G + Sbjct: 123 GYAEYVLADPG--YVGKLPDTLEFAPAAPVLCAGVTVYKGLKVLECKPGDWVAISGIGGL 180 Query: 177 GIMAALVAQFQGARNVVVTDLSDERLELAQQLGLKNAVNVSREGLETVWDRFDMKEGFDI 236 G MA A+ G +V+ D++DE+L LA+ LG +N +R ++ V + +G Sbjct: 181 GHMAVQYAKAMGF-HVIAVDVADEKLALAKTLGADVTLNAAR--VDPVAEIQKQIKGAHG 237 Query: 237 GLEMSGSGTALTSMIDNMTHGGRIALLGTPSTDITLDFSKIIFNMITIQG--VTGRQIFE 294 L + S +A + + G ++L+G P D L ++ N T++G V R+ E Sbjct: 238 ILVTAVSRSAFGQALGMLHKRGTMSLVGLPPGDFGLPIFDVVLNAKTVRGSIVGTRKDLE 297 Query: 295 TWYTMASLIRSGLDISGIITDRYPITEFREAFDVAGSGH-GGKVVMN 340 A G + TDR I + F +GH G++V+N Sbjct: 298 EALAFAG---EGKVKTHYSTDR--IENINDIFGRMKAGHIDGRIVLN 339 Lambda K H 0.322 0.140 0.436 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: 319 Number of extensions: 17 Number of successful extensions: 2 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: 345 Length of database: 340 Length adjustment: 29 Effective length of query: 316 Effective length of database: 311 Effective search space: 98276 Effective search space used: 98276 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 (21.9 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