Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 200848 SO1683 3-oxoacyl-(acyl-carrier-protein) reductase, putative (NCBI ptt file)
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__MR1:200848 Length = 252 Score = 121 bits (304), Expect = 1e-32 Identities = 84/252 (33%), Positives = 140/252 (55%), Gaps = 16/252 (6%) Query: 11 NITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKED-VKDVAAQINPSRTL-ALQVD 68 ++ DKV V+TG A G+G AMA F++ GA + L+D+ +D ++ A + S + +D Sbjct: 2 DLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYALD 61 Query: 69 ITKKENIEKVVAEIKKVYPKIDILANSAGV---ALLEKAED------LPEEYWDKTMELN 119 IT +E++ A I + + KI++L N+AG+ +L KA+D + + + + +N Sbjct: 62 ITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVN 121 Query: 120 LKGSFLMAQIIGREMIATG-GGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEW 178 L G+FL + MI +G G IVN++S A + + Y ASKA + +M+ A E Sbjct: 122 LTGTFLCGREAAAAMIESGQAGVIVNISSLAKAGNVGQS-NYAASKAGVAAMSVGWAKEL 180 Query: 179 APYNINVNAISPTVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAAS 238 A YNI A++P VI TE+ A + E ++KL+P GR G+ EE+A+ F++ + Sbjct: 181 ARYNIRSAAVAPGVIATEM-TAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEN--D 237 Query: 239 LITGENLIIDGG 250 + G +DGG Sbjct: 238 YVNGRVFEVDGG 249 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: 176 Number of extensions: 11 Number of successful extensions: 5 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: 252 Length adjustment: 24 Effective length of query: 230 Effective length of database: 228 Effective search space: 52440 Effective search space used: 52440 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: 46 (22.3 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