Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate CCNA_02479 CCNA_02479 aryl-alcohol dehydrogenase
Query= curated2:Q72L62 (343 letters) >FitnessBrowser__Caulo:CCNA_02479 Length = 366 Score = 119 bits (298), Expect = 1e-31 Identities = 113/373 (30%), Positives = 169/373 (45%), Gaps = 60/373 (16%) Query: 8 APEEGLTLVDRPVPEPGPGEILVRVEAASICGTDLHIWKWDAWARGRIRP---PLVTGHE 64 +P +L + P GEILVRV A +C TD+ + R + P P+V GHE Sbjct: 10 SPSGPFSLEALDIEPPRAGEILVRVVATGVCHTDMVM-------RDQHLPTPQPVVLGHE 62 Query: 65 FSGVVEAVGPGVKRPQVGDHVSLESHVVCHACPAC--RTGNY-HVCLNTKILGVDRDGG- 120 +GVVE VGPGV + VGDHV + + C CP+C Y H +G DG Sbjct: 63 GAGVVEQVGPGVAKVAVGDHVVMTFNS-CGRCPSCSDHAPTYCHEFFPRNFMGAREDGSS 121 Query: 121 ------------------FAEYVVVPAENAWVNPKDLPFEVAAILEPFGNAVHTVYAGSG 162 FA Y + NA K P E L P G V T G+G Sbjct: 122 GLSKGSEVIHANIFGQSSFATYALCHERNAVKVDKTAPLER---LGPLGCGVMT---GAG 175 Query: 163 V--------SGKSVLITGAGPIGLMAAMVARASGAGPILVSDPNPYRLAFARPY-ADRLV 213 +G+S+++ GAG +GL A + A+A GAGPI+ D NP RLA A AD + Sbjct: 176 AVMNALKVPAGRSLVVFGAGAVGLSAVLAAKAIGAGPIIAIDINPERLALALELGADHAL 235 Query: 214 NPLEEDLLEVVRRVTGSGVEVLLEFSGNEAAIHQGLMALIPGGEARILG-------IPSD 266 N E ++E ++ +TG+G ++ + N + Q + L G ++G +P D Sbjct: 236 NGAEGGVVEKIQAITGTGAHFSIDTTANLKVMRQAVDCLGARGVCGLVGASKMGDELPLD 295 Query: 267 PIRFDLAGELVMRGITAFGIAGRRLWQTWMQGTALVYSGRVDLSPLITHRLPLSRYREAF 326 + ++G V+RG+ G A ++ + AL +GR LI PL+ +A Sbjct: 296 AVSV-MSGGKVVRGVVE-GDADPDVFIPEL--IALHLAGRFPFDRLIQF-YPLAEINQAV 350 Query: 327 GLLASGQAVKVIL 339 +G+ +K ++ Sbjct: 351 SDGETGRVIKPVV 363 Lambda K H 0.321 0.140 0.432 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: 385 Number of extensions: 23 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: 366 Length adjustment: 29 Effective length of query: 314 Effective length of database: 337 Effective search space: 105818 Effective search space used: 105818 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 (21.8 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