Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 15894 b1776 predicted oxidoreductase, Zn-dependent and NAD(P)-binding (NCBI)
Query= BRENDA::P07913 (341 letters) >FitnessBrowser__Keio:15894 Length = 358 Score = 164 bits (414), Expect = 4e-45 Identities = 113/364 (31%), Positives = 190/364 (52%), Gaps = 32/364 (8%) Query: 1 MKALSKL-KAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPM 59 MKAL++ KA G M DVP P G D++I+I+ AICG D+ YN D S + Sbjct: 1 MKALARFGKAFGGYKMIDVPQPMCGPEDVVIEIKAAAICGADMKHYNVDSGSDE---FNS 57 Query: 60 VVGHEYVGEVVGIGQEVKGFKIGDRV--SGEGHITCGHCRNCRGGRTHLCRNTIGVGVNR 117 + GHE+ G + +G++VK +K+G RV GH+ CG C C G C + +G++ Sbjct: 58 IRGHEFAGCIAQVGEKVKDWKVGQRVVSDNSGHV-CGVCPACEQGDFLCCTEKVNLGLDN 116 Query: 118 ---PGCFAEYLVIPA-------FNAFKIPDNISDDLAAIFDPFGNAVHTAL--SFDLVGE 165 G F++Y ++P ++IPD + + AA+ DP NA + S L G+ Sbjct: 117 NTWGGGFSKYCLVPGEILKIHRHALWEIPDGVDYEDAAVLDPICNAYKSIAQQSKFLPGQ 176 Query: 166 DVLVSGAGPIGIMAAAVAKHVGARNVVITDVNE---YRLELARKMGITRAVNVAKENLND 222 DV+V G GP+G+ + +A+ +GA N+V+ + E R +A+++G T VN + E++ Sbjct: 177 DVVVIGTGPLGLFSVQMARIMGAVNIVVVGLQEDVAVRFPVAKELGATAVVNGSTEDVVA 236 Query: 223 VMAELGMTEGFDVGLEMSGAPPAFRTMLDTMNHGGRIAM--LGIPPSDMSIDWTKVIFKG 280 ++ + + +E SGA A + ++ + G + +G P D SI+ Sbjct: 237 RCQQICGKDNLGLVIECSGANIALKQAIEMLRPNGEVVRVGMGFKPLDFSINDITA---- 292 Query: 281 LFIKGIYGREMFE--TWYKMAALIQSG-LDLSPIITHRFSIDDFQKGFDAMRSGQSGKVI 337 + K I G ++ +W L+ SG + + P+ITHR + +++GFDAM + KVI Sbjct: 293 -WNKSIIGHMAYDSTSWRNAIRLLASGAIKVKPMITHRIGLSQWREGFDAMVDKTAIKVI 351 Query: 338 LSWD 341 +++D Sbjct: 352 MTYD 355 Lambda K H 0.322 0.140 0.433 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: 345 Number of extensions: 22 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: 341 Length of database: 358 Length adjustment: 29 Effective length of query: 312 Effective length of database: 329 Effective search space: 102648 Effective search space used: 102648 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