Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 16923 b2842 2-deoxy-D-gluconate 3-dehydrogenase (NCBI)
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Keio:16923 Length = 253 Score = 145 bits (367), Expect = 6e-40 Identities = 88/246 (35%), Positives = 141/246 (57%), Gaps = 5/246 (2%) Query: 10 FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINP--SRTLALQV 67 F++ KVAVVTG +G+G+ MA ++ G +V ++I E + + Q+ R L+L Sbjct: 6 FSLEGKVAVVTGCDTGLGQGMALGLAQAGCDIVGINIVEPTETIE-QVTALGRRFLSLTA 64 Query: 68 DITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMA 127 D+ K + I ++ + IDIL N+AG+ E A + E+ WD M LN+K F M+ Sbjct: 65 DLRKIDGIPALLDRAVAEFGHIDILVNNAGLIRREDALEFSEKDWDDVMNLNIKSVFFMS 124 Query: 128 QIIGREMIATG-GGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVN 186 Q + IA G GGKI+N+AS S + +Y ASK+ ++ +T+++A EWA +NINVN Sbjct: 125 QAAAKHFIAQGNGGKIINIASMLSFQGGIRVPSYTASKSGVMGVTRLMANEWAKHNINVN 184 Query: 187 AISPTVILTELGKKAWAG-QVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENL 245 AI+P + T ++ A Q ++ IPAGR+G P ++ +FL S A+ + G + Sbjct: 185 AIAPGYMATNNTQQLRADEQRSAEILDRIPAGRWGLPSDLMGPIVFLASSASDYVNGYTI 244 Query: 246 IIDGGY 251 +DGG+ Sbjct: 245 AVDGGW 250 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: 152 Number of extensions: 8 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: 254 Length of database: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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