Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 6936328 Sama_0517 D-beta-hydroxybutyrate dehydrogenase (RefSeq)
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__SB2B:6936328 Length = 266 Score = 124 bits (310), Expect = 3e-33 Identities = 81/259 (31%), Positives = 135/259 (52%), Gaps = 23/259 (8%) Query: 16 LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNP-DVGEGAARELDGTFE-RLNVTD 73 L+G+ L+TG GIG A+ LA+ G + + L P D G+ A + + R ++ Sbjct: 8 LEGKVGLITGSTSGIGLATAQVLAEQGCNLILHGLLPEDEGQSMAADFAAQYRIRTFFSN 67 Query: 74 ADA---------VADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWC 124 AD +A+ + L +D+L+NNAGI P + W ++++NL F Sbjct: 68 ADLRQPESIHRFMAEGTKALGSIDILINNAGIQHTDSVASFPIEKWNDIIAINLSSAFHT 127 Query: 125 CREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVR 184 ++ M + G I++ AS+ GL+++ +AAY A+K ++ LT+ +A E A +G+ Sbjct: 128 MQQAVPAMAQKRWGRIINIASVHGLVAS--VNKAAYCAAKHGIVGLTKVVAIECAEQGIT 185 Query: 185 VNAVAPGYTATPL---------TRRGLETPEWR-ETWLKETPLGRLAEPREIAPAVLYLA 234 VNA+ PG+ TPL +GL+ E R + + PL + +PR+I L+L Sbjct: 186 VNAICPGWVDTPLINKQIEAVANTKGLDYHEARYQLVTAKQPLPEMLDPRQIGEFALFLC 245 Query: 235 SDAASFVTGHTLVVDGGYT 253 DAA +TG +L +DGG+T Sbjct: 246 GDAARGITGASLAMDGGWT 264 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: 152 Number of extensions: 11 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: 266 Length adjustment: 24 Effective length of query: 231 Effective length of database: 242 Effective search space: 55902 Effective search space used: 55902 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