Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate Echvi_2940 Echvi_2940 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Cola:Echvi_2940 Length = 251 Score = 141 bits (356), Expect = 1e-38 Identities = 89/248 (35%), Positives = 138/248 (55%), Gaps = 14/248 (5%) Query: 14 DKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPS---RTLALQVDIT 70 +K ++TG ASGIG AM + F+E+G V +D + + A+ S R LQ D++ Sbjct: 3 NKTILITGGASGIGLAMTKRFAEEGGNVYFIDYDQKTGEKVAEELTSKGHRVTFLQGDVS 62 Query: 71 KKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQII 130 + E +++ ++ I ID+L N+AG++ + E+ EE +D+ ++N+KG + + Sbjct: 63 QTEEMKQTISSISG---SIDVLVNNAGISHVGNLENTAEEDFDRLYQVNVKGIY-NCSLA 118 Query: 131 GREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAISP 190 + GG I+NMAS AS + L AY +K A+ SMT +A ++ YNI VN+I+P Sbjct: 119 SLPKMKEKGGSIINMASVASTMGLPDRFAYSMTKGAVFSMTLSMARDYVEYNIRVNSIAP 178 Query: 191 ----TVILTELGKKAWAGQVGEDMKKLI---PAGRFGYPEEVAACALFLVSDAASLITGE 243 T + K + G+ E KL P GR G PEE+AA A++L SD AS +TG Sbjct: 179 GRVHTPFVDGFLAKNYPGKEKEMFDKLAATQPIGRMGKPEEIAAMAVYLSSDEASFLTGG 238 Query: 244 NLIIDGGY 251 N IDGG+ Sbjct: 239 NYPIDGGF 246 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: 183 Number of extensions: 7 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: 251 Length adjustment: 24 Effective length of query: 230 Effective length of database: 227 Effective search space: 52210 Effective search space used: 52210 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