Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate H281DRAFT_05508 H281DRAFT_05508 Alcohol dehydrogenase, class IV
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Burk376:H281DRAFT_05508 Length = 383 Score = 197 bits (502), Expect = 3e-55 Identities = 118/353 (33%), Positives = 196/353 (55%), Gaps = 4/353 (1%) Query: 30 GFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNC 89 G L+V+D + G+ L I + + +P+ V A +L + + Sbjct: 30 GVNSVLLVSDRGVKNAGLLEAPMAHLRTSGIAVECFFDVEADPSAATVQAAAQLARSSGV 89 Query: 90 DSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRSAKPQLPMIAINTTAGTASEMTRF 149 D V+++GGGSP D AK AL+A +G D+ D G+ ++ P+L ++ + TTAGT SE T Sbjct: 90 DCVVAIGGGSPMDVAKLAALLAKSGVDLEDIYGIHKTEGPRLRLVLVPTTAGTGSEATPI 149 Query: 150 CIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSLTAATGMDALTHAIEAYVSIA-A 208 I+T A K +V + P ++V D+ L IG+PK ++AATG+DA+ HAIEAY S + Sbjct: 150 SIVTTGAGE-KKGVVCPVLLPDIAVLDAELTIGLPKHVSAATGIDAMVHAIEAYTSRSLK 208 Query: 209 TPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQFLAGMAFNNASLGYVHAMAHQ 268 P++D A +A+ ++ +L G + + R+AM LAGMAF NA + VHA+A+ Sbjct: 209 NPLSDCLAREALRLLGPHLERVCAQGHDVETRQAMLLGANLAGMAFANAPVAAVHALAYP 268 Query: 269 LGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAMGVNVTGKNDAEGAEACINAIR 328 +G +++PHG+ N+++LP V FN A + + A+ + N G + E A + + Sbjct: 269 IGARFHVPHGLSNSLMLPAVLRFNMTSAESLYAELASLLVPNAIGSPE-ELTRALLAYLT 327 Query: 329 ELAKKVDIPAGLRDLNVKEEDFAVLATNALKDA-CGFTNPIQATHEEIVAIYR 380 EL K+ +P LRD+ + ED LA +A+K + NP + +++ +A+Y+ Sbjct: 328 ELPVKLGLPVRLRDVGITAEDLPDLAIDAMKQSRLLVNNPREVGYDDALAMYQ 380 Lambda K H 0.318 0.131 0.373 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: 361 Number of extensions: 16 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: 383 Length of database: 383 Length adjustment: 30 Effective length of query: 353 Effective length of database: 353 Effective search space: 124609 Effective search space used: 124609 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 (21.8 bits) S2: 50 (23.9 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