Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 7026324 Shewana3_3466 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__ANA3:7026324 Length = 292 Score = 119 bits (298), Expect = 7e-32 Identities = 80/259 (30%), Positives = 131/259 (50%), Gaps = 23/259 (8%) Query: 16 LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDV-GEGAARE------LDGTFER 68 L G+ L+TG GIG A LA+ G + + L P+ G A E + F Sbjct: 34 LKGKVGLITGSTSGIGLATAHVLAEQGCHLILHGLMPEAEGRRLAAEFAEQYHIHTYFSN 93 Query: 69 LNVTDADAVADL----ARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWC 124 ++ D +++ + L +D+LVNNAGI P D W ++++NL F Sbjct: 94 ADLRDPESIHAFMDAGVKALGSIDILVNNAGIQHTENVAHFPIDKWNDIIAINLSSAFHT 153 Query: 125 CREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVR 184 ++ M + G I++ AS+ GL+++ +AAY A+K ++ LT+ +A E A +G+ Sbjct: 154 IQQAVPAMAEKRWGRIINIASVHGLVAS--VNKAAYCAAKHGIVGLTKVVAIECAEQGIT 211 Query: 185 VNAVAPGYTATPL---------TRRGLETPEWR-ETWLKETPLGRLAEPREIAPAVLYLA 234 VNA+ PG+ TPL + +GL E + + + PL + +PR+I VL+L Sbjct: 212 VNAICPGWVDTPLINKQIEAIASNKGLSYDEAKYQLVTAKQPLPEMLDPRQIGEFVLFLC 271 Query: 235 SDAASFVTGHTLVVDGGYT 253 S AA +TG +L +DG +T Sbjct: 272 SSAARGITGASLAMDGAWT 290 Lambda K H 0.319 0.134 0.408 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: 174 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: 255 Length of database: 292 Length adjustment: 25 Effective length of query: 230 Effective length of database: 267 Effective search space: 61410 Effective search space used: 61410 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: 47 (22.7 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