Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate CA265_RS08610 CA265_RS08610 alcohol dehydrogenase
Query= BRENDA::P07913 (341 letters) >FitnessBrowser__Pedo557:CA265_RS08610 Length = 339 Score = 120 bits (302), Expect = 4e-32 Identities = 80/251 (31%), Positives = 125/251 (49%), Gaps = 8/251 (3%) Query: 21 PELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMVVGHEYVGEVVGIGQEVKGFK 80 PEL + +IKI++ ICGTD+H + E +Q P V+GHE GE+V GFK Sbjct: 20 PELKKDHAIIKIKRIGICGTDLHAF---EGTQPFFNYPRVLGHELSGELVE-ADGADGFK 75 Query: 81 IGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGCFAEYLVIPAFNAFKIPDNIS 140 IG+ V+ + CG C CR + + C GV+ G EYL +P+ + +S Sbjct: 76 IGEAVTFIPYFNCGECIACRMNKPNCCVKMQVCGVHVDGGMREYLQVPS-RTLLHGEGLS 134 Query: 141 DDLAAIFDPFGNAVHTALSFDL-VGEDVLVSGAGPIGIMAAAVAKHVGARNVVITDVNEY 199 D A+ +P H D+ GE VLV GAGPIG+ A+ GA NV+ D+NE Sbjct: 135 YDELALVEPLAIGAHGVRRADVQPGEFVLVIGAGPIGLGTMEFARIAGA-NVIALDINED 193 Query: 200 RLELAR-KMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMSGAPPAFRTMLDTMNHGGR 258 RL + K+ + VN ++ ++++ + V ++ +G A ++ M HG R Sbjct: 194 RLAFCKDKLKVAHVVNALSPDVVQQLSDITNGDMPTVVIDATGNQKAINNAINYMAHGAR 253 Query: 259 IAMLGIPPSDM 269 ++G+ D+ Sbjct: 254 FVLIGLQKGDL 264 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: 270 Number of extensions: 13 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: 339 Length adjustment: 28 Effective length of query: 313 Effective length of database: 311 Effective search space: 97343 Effective search space used: 97343 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