Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_027723082.1 H589_RS0116710 3-oxoacyl-ACP reductase FabG
Query= SwissProt::Q92EU6 (254 letters) >NCBI__GCF_000425265.1:WP_027723082.1 Length = 240 Score = 115 bits (288), Expect = 8e-31 Identities = 78/242 (32%), Positives = 132/242 (54%), Gaps = 13/242 (5%) Query: 15 KVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKED---VKDVAAQINP--SRTLALQVDI 69 K+A++TGA+ GIG A+A +E G Y + L+ + D A QI + L+ D+ Sbjct: 3 KIALITGASKGIGAAIAVQLAEDG-YDIWLNYRSDDAGAHKTAEQIKQHGQQCTLLKFDV 61 Query: 70 TKKENIEKVVAEI-KKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQ 128 T ++ +E+ ++ + +K P I + N+AG + W+K ++++L G F + + Sbjct: 62 TDEKAVEENLSSLLEKKVPYI--VVNNAGFTRDSIMMMMDSSDWNKVLQVHLTGFFNVTK 119 Query: 129 IIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAI 188 + M+ G+I+N+AS + + YCA+KA ++ T+ LAME A NI VNA+ Sbjct: 120 PVVSRMLRKRTGRIINIASTSGETGVAGQTNYCAAKAGLIGATKSLAMEVAKRNILVNAV 179 Query: 189 SPTVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLIID 248 +P I T++ + +++K IP R G P+EVA FL SD AS ITG+ + ++ Sbjct: 180 TPGFIDTDMLSELPV----DEIKNTIPLKRLGTPKEVAGVVSFLCSDKASYITGQTIAVN 235 Query: 249 GG 250 GG Sbjct: 236 GG 237 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: 133 Number of extensions: 10 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: 240 Length adjustment: 24 Effective length of query: 230 Effective length of database: 216 Effective search space: 49680 Effective search space used: 49680 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 Apr 09 2024. 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