Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate Ac3H11_148 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30)
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_148 Length = 260 Score = 157 bits (396), Expect = 3e-43 Identities = 88/255 (34%), Positives = 146/255 (57%), Gaps = 12/255 (4%) Query: 11 NITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIK-EDVKDVAAQINPSRTLA--LQV 67 +++ +VA +TGA+SG+G A + GA VVL + E +K++ A+I A +++ Sbjct: 6 DLSGRVAFITGASSGLGAQFARTLARAGAGVVLASRRIEKLKELRARIEGEGGDAHVIEL 65 Query: 68 DITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMA 127 D+T +I+ VA + IDIL N++GV+ ++ +D+ E +D + N+KG+F +A Sbjct: 66 DVTDHASIKSAVAHAETEMGSIDILINNSGVSTTQRLQDVTPEDYDFIFDTNVKGAFFVA 125 Query: 128 QIIGREMIATG---------GGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEW 178 Q +G+ M+A GG+I+N+AS A + L + AYC SKAA+V MT+ +AMEW Sbjct: 126 QEVGKRMLARSRGAAPGSFTGGRIINIASMAGLKVLPQIGAYCMSKAAVVQMTRAMAMEW 185 Query: 179 APYNINVNAISPTVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAAS 238 + IN NAI P I TE+ W + G+ + ++P R G P+++ A + L SD + Sbjct: 186 GKFGINTNAICPGYIDTEINHHHWDTEQGQKLIAMLPRKRVGSPQDLDALLVMLASDQSH 245 Query: 239 LITGENLIIDGGYTI 253 I G + D G+ + Sbjct: 246 FINGAVIAADDGFAV 260 Lambda K H 0.316 0.133 0.369 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: 162 Number of extensions: 6 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: 254 Length of database: 260 Length adjustment: 24 Effective length of query: 230 Effective length of database: 236 Effective search space: 54280 Effective search space used: 54280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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