Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate GFF3147 PGA1_c31980 short chain dehydrogenase
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Phaeo:GFF3147 Length = 253 Score = 137 bits (344), Expect = 3e-37 Identities = 88/251 (35%), Positives = 133/251 (52%), Gaps = 9/251 (3%) Query: 12 ITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDV-----KDVAAQINPSRTLALQ 66 + K A+VTG ASG G + F +GA V++ DI D DV P R +A Sbjct: 3 LAGKCAIVTGGASGFGAGIVTKFLTEGARVMIADINADAAAAAASDVCETYGPDRAIAQT 62 Query: 67 VDITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKA-EDLPEEYWDKTMELNLKGSFL 125 VD++ + +++++ + +IDIL N+AGV+ L ED+ EE +D+ + +N+K +L Sbjct: 63 VDVSDRASVDQMAQAALNHFGQIDILVNNAGVSHLPTPLEDVSEEDFDRVVAVNMKSVYL 122 Query: 126 MAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINV 185 A+ + M + G I+N+AS A V Y ASK +++ T+ +A+E AP + V Sbjct: 123 TARALVPHMKSRQSGAILNVASTAGVSPRPNLNWYNASKGWMITATRTMAVELAPAGVRV 182 Query: 186 NAISPTVILTELGKKAWAGQVGEDMKKL---IPAGRFGYPEEVAACALFLVSDAASLITG 242 NAI+P T L K E K IP GRF PE++ A +L SD AS++TG Sbjct: 183 NAINPVAGETPLLKTFMGEDTPEVRAKFLSTIPIGRFSTPEDMGNAACYLCSDEASMVTG 242 Query: 243 ENLIIDGGYTI 253 L +DGG I Sbjct: 243 VALEVDGGRCI 253 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: 164 Number of extensions: 8 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: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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