Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF759 PGA1_c07730 putative zinc-binding alcohol dehydrogenase
Query= reanno::Phaeo:GFF3379 (342 letters) >FitnessBrowser__Phaeo:GFF759 Length = 326 Score = 89.7 bits (221), Expect = 9e-23 Identities = 87/290 (30%), Positives = 128/290 (44%), Gaps = 41/290 (14%) Query: 11 EGLWMVQAPVPEIGPDEVLIKIRTTGICGTDIHIWNWDEWASHTVPVPMITGHEFAGEIV 70 E L P+ P E LI+I +GICG+D+H + + + P P+I GHE AG I Sbjct: 10 ETLVFRDVPMVAARPGEHLIRIHASGICGSDMHAYLGHD---NRRPAPLILGHEAAGTIE 66 Query: 71 E---IGRNVT--DLAVGQRCSGEGHLIQTDSRQSRAGKFHLDPGTRGIGVN-EQGAFAQY 124 + GR VT L C+ AG+ +L + I + +GAFAQ+ Sbjct: 67 DGPQAGRRVTINPLVTCGSCAA-----------CAAGRENLCASRQIISMPPREGAFAQF 115 Query: 125 LKLPAFNVVPLPEDIPDEIGAILDPLGNAVHTA-LSFDLLGEDV----LITGAGPIGVMA 179 + +P N+V +PED+P A+ +PL + H A L+ L D+ L+ G G IG+ A Sbjct: 116 VAMPERNLVTVPEDVPLSKAALAEPLAVSWHAARLALKALHPDMERRALVIGGGAIGLAA 175 Query: 180 AAVARHAGARHVVITDINPDRLA-LAEHVVPAVRAVNVAEEDLQDVVRELGLKQGFDVGL 238 A R G V + + N R A LA+H A + Q +V + L Sbjct: 176 ALALRAMGVEDVAVQEPNAARRAFLADH------CGQQAVAEFQGIV---------PLVL 220 Query: 239 EMSGSQAALDQMVEALVMGGKIALLGIPPGKSPVDWSRIVFKAITIKGVY 288 + G A A GG IA +G+ +D R+ + IT G Y Sbjct: 221 DAVGYAATRAAASAAAAPGGVIAHVGLGEDAGGLDIRRMTLQEITFIGTY 270 Lambda K H 0.320 0.139 0.421 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: 267 Number of extensions: 13 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: 342 Length of database: 326 Length adjustment: 28 Effective length of query: 314 Effective length of database: 298 Effective search space: 93572 Effective search space used: 93572 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