Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate BWI76_RS00645 BWI76_RS00645 lactaldehyde reductase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Koxy:BWI76_RS00645 Length = 382 Score = 326 bits (835), Expect = 8e-94 Identities = 169/376 (44%), Positives = 240/376 (63%) Query: 8 IPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDG 67 +P +++ GA ++ D + ++A + + LIVTD L KLG+ + A++E+ + ++D Sbjct: 7 LPKISLHGAGAIGDMVKLVAGKRWGKALIVTDGQLVKLGLLDSLFAAMDEQQMAYHLFDE 66 Query: 68 TQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRSA 127 PNPT V G E CD +I+ GGGSP D AK + ++ AN G Y GV + Sbjct: 67 VFPNPTEALVQKGYAAYCEAGCDYLIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVT 126 Query: 128 KPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSL 187 P +P++AINTTAGTA+EMT +I D R +K I+D ++ P ++V+D+S+M+ +P ++ Sbjct: 127 NPGVPLVAINTTAGTAAEMTSNAVIIDAERQVKEVIIDPNIIPDIAVDDASVMLDIPPAI 186 Query: 188 TAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQ 247 TAATGMDALTHAIEA+VS+ A P+TDA A +A+ +I LP AV+DG N +ARE MA+ Q Sbjct: 187 TAATGMDALTHAIEAFVSVGAHPLTDANAQEAIRLINLWLPKAVDDGHNLEAREQMAFGQ 246 Query: 248 FLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAM 307 +LAGMAFN+A LG VHA+AHQ G +NLPHGVCNA+LLP ++ FN A +R A AM Sbjct: 247 YLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIIENFNRPNAVSRFARVAQAM 306 Query: 308 GVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTNP 367 GV+ G +D + INAIR L+K+V IP G L V + D AL D C NP Sbjct: 307 GVDTRGMSDEAASMEAINAIRALSKRVGIPQGFSQLGVSKADIEGWLDKALADPCAPCNP 366 Query: 368 IQATHEEIVAIYRAAM 383 A+ +E+ +Y A+ Sbjct: 367 RAASRDEVRELYLEAL 382 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: 383 Number of extensions: 13 Number of successful extensions: 1 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: 382 Length adjustment: 30 Effective length of query: 353 Effective length of database: 352 Effective search space: 124256 Effective search space used: 124256 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