Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 5209125 Shew_1603 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__PV4:5209125 Length = 248 Score = 135 bits (340), Expect = 8e-37 Identities = 81/242 (33%), Positives = 131/242 (54%), Gaps = 1/242 (0%) Query: 9 DFNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLALQVD 68 + ++T KVA+VTGA+ GIG+A+AE E GA V+ E + + L ++ Sbjct: 4 NLDLTGKVALVTGASRGIGRAVAETLVEAGALVIGTATSERGAAAIQEYLGDKGHGLVLN 63 Query: 69 ITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQ 128 +T E+I+ + A IK+ ++DIL N+AG+ + E+ W ++ NL + ++ Sbjct: 64 VTDSESIDHLFASIKEKVGEVDILVNNAGITRDNLLMRMKEDEWTDIIDTNLTSLYRTSK 123 Query: 129 IIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAI 188 + R M+ G+I+N+ S + YCA+KA ++ T+ LA E A I VNAI Sbjct: 124 QVLRAMMKKRSGRIINIGSVVGTMGNAGQTNYCAAKAGLIGFTKSLAREVASRQITVNAI 183 Query: 189 SPTVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLIID 248 +P I T++ + Q M + +P R G P+E+A LFL SD+A+ ITGE L ++ Sbjct: 184 APGFIQTDMTDELTEEQQKGIMSQ-VPMERLGQPQEIANAVLFLASDSAAYITGETLHVN 242 Query: 249 GG 250 GG Sbjct: 243 GG 244 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: 142 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: 248 Length adjustment: 24 Effective length of query: 230 Effective length of database: 224 Effective search space: 51520 Effective search space used: 51520 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