Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 6936328 Sama_0517 D-beta-hydroxybutyrate dehydrogenase (RefSeq)
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__SB2B:6936328 Length = 266 Score = 124 bits (310), Expect = 3e-33 Identities = 88/259 (33%), Positives = 130/259 (50%), Gaps = 18/259 (6%) Query: 11 NITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKED------VKDVAAQINPSRTLA 64 ++ KV ++TG+ SGIG A A++ +E+G ++L + + D AAQ RT Sbjct: 7 SLEGKVGLITGSTSGIGLATAQVLAEQGCNLILHGLLPEDEGQSMAADFAAQYR-IRTFF 65 Query: 65 LQVDITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSF 124 D+ + E+I + +AE K IDIL N+AG+ + P E W+ + +NL +F Sbjct: 66 SNADLRQPESIHRFMAEGTKALGSIDILINNAGIQHTDSVASFPIEKWNDIIAINLSSAF 125 Query: 125 LMAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNIN 184 Q M G+I+N+AS ++A AYCA+K IV +T+V+A+E A I Sbjct: 126 HTMQQAVPAMAQKRWGRIINIASVHGLVASVNKAAYCAAKHGIVGLTKVVAIECAEQGIT 185 Query: 185 VNAISPTVILTELGKK---AWAGQVGEDMKKL--------IPAGRFGYPEEVAACALFLV 233 VNAI P + T L K A A G D + P P ++ ALFL Sbjct: 186 VNAICPGWVDTPLINKQIEAVANTKGLDYHEARYQLVTAKQPLPEMLDPRQIGEFALFLC 245 Query: 234 SDAASLITGENLIIDGGYT 252 DAA ITG +L +DGG+T Sbjct: 246 GDAARGITGASLAMDGGWT 264 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: 145 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: 266 Length adjustment: 24 Effective length of query: 230 Effective length of database: 242 Effective search space: 55660 Effective search space used: 55660 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: 47 (22.7 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