Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate Dsui_2312 Dsui_2312 3-hydroxybutyrate dehydrogenase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__PS:Dsui_2312 Length = 260 Score = 127 bits (318), Expect = 3e-34 Identities = 91/259 (35%), Positives = 132/259 (50%), Gaps = 23/259 (8%) Query: 16 LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDV-GEGAARELDGTF------ER 68 L G+ ALVTG GIG +AR LA+ GA V + P EG + F Sbjct: 2 LSGKIALVTGSTSGIGLAVARALARNGAAVMLNGSRPAAEAEGLRAAMAAEFGVKVAYTS 61 Query: 69 LNVTDADAVADLA----RRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWC 124 ++ DA +V LA ++L VD+LVNNAGI A ++ P++ W ++++NL VF Sbjct: 62 ADLADAASVRALAAAAEKQLGVVDILVNNAGIQHVAAVDEFPEEKWDQLIAINLSSVFHA 121 Query: 125 CREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVR 184 + M AR G IV+ AS GL+++ +A Y ASK AV+ ++++A E A G+ Sbjct: 122 TKAVLPGMKARNWGRIVNIASAHGLVAS--PFKAPYTASKHAVVGFSKAVALEVAETGIT 179 Query: 185 VNAVAPGYTATPLTRRGL----------ETPEWRETWLKETPLGRLAEPREIAPAVLYLA 234 NAV PGY TPL + + E R+ L P R E ++A VL+L Sbjct: 180 CNAVCPGYVRTPLVEKQVAAQAKVHNLPEDQVIRDVILAAQPNKRFLEADDLAEFVLFLC 239 Query: 235 SDAASFVTGHTLVVDGGYT 253 S A + +TG L +DG +T Sbjct: 240 SPAGAGMTGAALPMDGAWT 258 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: 154 Number of extensions: 12 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: 260 Length adjustment: 24 Effective length of query: 231 Effective length of database: 236 Effective search space: 54516 Effective search space used: 54516 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