Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_094578795.1 CEV32_RS19735 alcohol dehydrogenase AdhP
Query= BRENDA::P07913 (341 letters) >NCBI__GCF_002252475.1:WP_094578795.1 Length = 344 Score = 137 bits (345), Expect = 4e-37 Identities = 106/343 (30%), Positives = 161/343 (46%), Gaps = 12/343 (3%) Query: 1 MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60 MKA + + + + +VP+P+ G + + I+ + +C TD+H D W K P P + Sbjct: 5 MKAAVVREFGKPLTIDEVPIPQPGDGQIQVAIQASGVCHTDLHAAEGD-WPVKPNP-PFI 62 Query: 61 VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHIT-CGHCRNCRGGRTHLCRNTIGVGVNRPG 119 GHE VG V +G+ VK K GDRV T CGHC +C GG LC + G + G Sbjct: 63 PGHEGVGFVSAVGKGVKHVKEGDRVGIPWLYTACGHCVHCLGGWETLCEEQLNTGYSVNG 122 Query: 120 CFAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSF--DLVGEDVLVSGAGPIGI 177 FA+Y+V +P NI + A G V+ L G+ V++SG G +G Sbjct: 123 GFADYVVADPNFVGHLPKNIEFNEIAPILCAGVTVYKGLKVTDTKPGDWVVISGIGGLGH 182 Query: 178 MAAAVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGL 237 MA AK +G NV D+++ +L+LAR++G T VN N + G L Sbjct: 183 MAVQYAKAMGL-NVAAVDIDDKKLDLARRLGATVTVNAKTHNDPAAYIKKETDGGAQGVL 241 Query: 238 EMSGAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYK 297 + +P AF + GG IA+ G+P D + ++ G+ ++G + T Sbjct: 242 VTAVSPKAFEQAIGMAARGGTIALNGLPAGDFPLSIFNMVLNGVTVRG----SIVGTRLD 297 Query: 298 MAALIQSGLDLSPIITHRF-SIDDFQKGFDAMRSGQ-SGKVIL 338 + I D T R ID+ FD MR+GQ G+V++ Sbjct: 298 LQESIDFAADGKVKATIRTDKIDNINAIFDEMRAGQIEGRVVM 340 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: 303 Number of extensions: 23 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: 341 Length of database: 344 Length adjustment: 29 Effective length of query: 312 Effective length of database: 315 Effective search space: 98280 Effective search space used: 98280 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 24 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