Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate N515DRAFT_1006 N515DRAFT_1006 3-oxoacyl-[acyl-carrier protein] reductase
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Dyella79:N515DRAFT_1006 Length = 248 Score = 115 bits (289), Expect = 7e-31 Identities = 78/244 (31%), Positives = 127/244 (52%), Gaps = 12/244 (4%) Query: 15 KVAVVTGAASGIGKAMAELFSEKGAYVVL--LDIKEDVKDVAAQINPS--RTLALQVDIT 70 KVA+VTGA+ GIG +A+ + +GA VV+ K V I + + +A++ D+ Sbjct: 7 KVALVTGASKGIGAGIAKALAAEGAAVVVNYASSKAGADAVVDAITKAGGKAVAVKGDVA 66 Query: 71 KKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQII 130 + + + + K + ++DIL N++GV E + E+++ K +N+ G L Q Sbjct: 67 QAADAQAIADAAVKEFGRLDILVNNSGVYEFAPLEQITEDHFHKQFNVNVLGLLLTTQAA 126 Query: 131 GREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAISP 190 + M GG I+N+ S + I Y A+K A+ ++T VL+ E P I VNA++P Sbjct: 127 AKHM--GEGGSIINIGSLVTRIVPPGGSVYTATKGAVDAITGVLSRELGPRKIRVNALNP 184 Query: 191 TVILTELGKKAWAGQVGEDMKK----LIPAGRFGYPEEVAACALFLVSDAASLITGENLI 246 ++ TE AG +G D + P GR G P+++A A+FL SD + +TGE L Sbjct: 185 GMVETE--GTVTAGFIGSDFHQEAIAHTPLGRIGQPQDIATIAVFLASDDSYWLTGEKLY 242 Query: 247 IDGG 250 GG Sbjct: 243 AAGG 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: 159 Number of extensions: 12 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: 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