Align mannitol 2-dehydrogenase (NADP+) (EC 1.1.1.138) (characterized)
to candidate RR42_RS22860 RR42_RS22860 l-threonine 3-dehydrogenase
Query= BRENDA::Q1ACW3 (345 letters) >FitnessBrowser__Cup4G11:RR42_RS22860 Length = 351 Score = 136 bits (343), Expect = 7e-37 Identities = 87/277 (31%), Positives = 139/277 (50%), Gaps = 11/277 (3%) Query: 7 MKAL-RYDKPESYAVVEVPLPTLRDNDVLIKVKACGVCGTDLHIHEGEFIAK----FPLI 61 MKAL + ++ + +VP P + NDV+I+++ +CGTD+HI + + A+ P+ Sbjct: 1 MKALAKLERAPGLTLTDVPEPEVGHNDVMIRIRQTAICGTDIHIWKWDEWAQNTIPVPMQ 60 Query: 62 PGHETVGVVAAIGKDVKGFTVGERVCADNSELCNECFYCRRGQLLLCEKFEAHGVTMDGG 121 GHE VG + AIG++V+G +G+RV + C C CR G+ LC GV G Sbjct: 61 VGHEYVGEIVAIGQEVRGLAIGDRVSGEGHITCGFCRNCRAGRRHLCRNSVGVGVNRAGA 120 Query: 122 FAEYCAYPAGKVFKI-HNLSDVDATLLEPASCAAHGLEKIAPKIGSSVLMFGAGPTGLCL 180 FAEY PA F+I ++ D A + +P A H +G VL+ GAGP G+ Sbjct: 121 FAEYLVIPAFNAFRIPDDIPDEIAAIFDPFGNATHTALSF-NLVGEDVLITGAGPIGIMA 179 Query: 181 AQLP-HNGASHVVIAAPEGLKMDLAKKLDCADIYVPLSRSNPQAQFDQIKSDNPYGFDIV 239 A + H GA +VVI ++ LA+K+ A V + N + ++ GFD+ Sbjct: 180 AAIARHVGARNVVITDVNEYRLALARKMG-ATRAVNVQHENLKDVAAELHMTE--GFDVG 236 Query: 240 VEATGSPKILEDAINYVRRGGKLVVYGVYSDAARVSW 276 +E +G P + ++ GGK+ + G+ + W Sbjct: 237 MEMSGVPTAFATMLEHMNHGGKIAMLGIPPSKMAIDW 273 Lambda K H 0.320 0.138 0.420 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: 302 Number of extensions: 21 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: 345 Length of database: 351 Length adjustment: 29 Effective length of query: 316 Effective length of database: 322 Effective search space: 101752 Effective search space used: 101752 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