Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 3607131 Dshi_0553 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Dino:3607131 Length = 255 Score = 174 bits (442), Expect = 1e-48 Identities = 97/247 (39%), Positives = 151/247 (61%), Gaps = 4/247 (1%) Query: 10 FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKED-VKDVAAQINPS--RTLALQ 66 F++ DK A+VTGA+SGIG+A+AE+F++ GA +V D + D+ AQI + + A+ Sbjct: 7 FSLQDKTALVTGASSGIGRAIAEVFADAGADIVGQGRDLDRLTDLGAQIKTTGRQFAAIT 66 Query: 67 VDITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLM 126 D+ + + V + KIDIL NSAG+A+ + + W +T+ +NL F++ Sbjct: 67 GDLADPDQTQNVADRALAAFGKIDILVNSAGIAVTGPVTNYDLDDWQRTLAVNLTAPFIL 126 Query: 127 AQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVN 186 ++ + M+ GKI+N++SQ VIAL H AY SK + ++T+ L E AP+N+ VN Sbjct: 127 SKAVMPGMMQRKQGKIINISSQTGVIALKDHAAYATSKGGLNALTKSLMTEAAPHNVQVN 186 Query: 187 AISPTVILTELGKKAWAGQVGED-MKKLIPAGRFGYPEEVAACALFLVSDAASLITGENL 245 AI PTV+LTE+GK+ W+ +D P GRFG P E+A AL+L S A+ L+ G + Sbjct: 187 AICPTVVLTEMGKELWSAPERKDPFIARTPLGRFGEPIEIADMALYLASPASDLVNGAVM 246 Query: 246 IIDGGYT 252 +I+GGY+ Sbjct: 247 MIEGGYS 253 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: 169 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: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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