Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2257 Length = 267 Score = 157 bits (396), Expect = 3e-43 Identities = 89/245 (36%), Positives = 143/245 (58%), Gaps = 8/245 (3%) Query: 10 FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKD--VAAQINPSRTLALQV 67 F T +V +VTG A GIG+A F+ +GA V++D+ +D + +AA++ L ++ Sbjct: 16 FGHTGRVCIVTGGAQGIGEACVRRFAAEGAKPVIVDV-DDARGQALAAELG---ALYVRC 71 Query: 68 DITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMA 127 D+ K ++ +VA++ + +ID+L N+AG+ ++ E +D + +NLKGSFL+ Sbjct: 72 DVGDKAQVDALVAQVLAAHGRIDVLVNNAGIFRAADFLEVTEADFDAVLRVNLKGSFLVG 131 Query: 128 QIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNA 187 Q + R M+ +GGG IVNM+S V+A+ +Y SK + +T+V+A+ A NI VNA Sbjct: 132 QAVARAMVTSGGGAIVNMSSVNGVLAIPNIASYNVSKGGVNQLTRVMALALADKNIRVNA 191 Query: 188 ISPTVILTELGKKA--WAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENL 245 ++P I TEL KA + + + P R G P E+A +L SDAAS +TGE + Sbjct: 192 VAPGTIATELAAKAVLTSDEAKRKIMSRTPMKRLGQPSEIADVVAWLASDAASYVTGEIV 251 Query: 246 IIDGG 250 +DGG Sbjct: 252 TVDGG 256 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: 168 Number of extensions: 8 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: 267 Length adjustment: 24 Effective length of query: 230 Effective length of database: 243 Effective search space: 55890 Effective search space used: 55890 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