Align glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate SMc02038 SMc02038 glycerol dehydrogenase
Query= CharProtDB::CH_017124 (365 letters) >FitnessBrowser__Smeli:SMc02038 Length = 364 Score = 327 bits (838), Expect = 3e-94 Identities = 170/358 (47%), Positives = 230/358 (64%), Gaps = 3/358 (0%) Query: 1 MDRAIQSPGKYVQGADALQRLGDYLKPLADSWLVIADKFVLGFAEDTIRQSLSKAGLAMD 60 M RA P KY+Q A + +L YL PL LV+ D+ + + I +S + L + Sbjct: 1 MARAFGGPNKYIQRAGEIDKLAAYLAPLGKRALVLIDRVLFDALSERIGKSCGDS-LDIR 59 Query: 61 IVAFNGECSQGEVDRLCQLATQNGRSAIVGIGGGKTLDTAKAVAFFQKVPVAVAPTIAST 120 F GEC E++R+ ++A ++G +VG+GGGKT DTAK VA + +APTIAST Sbjct: 60 FERFGGECCTSEIERVRKVAIEHGSDILVGVGGGKTADTAKIVAIDTGARIVIAPTIAST 119 Query: 121 DAPCSALSVLYTDEGEFDRYLMLPTNPALVVVDTAIVARAPARLLAAGIGDALATWFEAR 180 DAPCSA++V YT+ G ++ L LP NP VVVD+A+VA APAR L AGIGDAL+TWFEAR Sbjct: 120 DAPCSAIAVRYTEHGVYEEALRLPRNPDAVVVDSALVAAAPARFLVAGIGDALSTWFEAR 179 Query: 181 A--ASRSSAATMAGGPATQTALNLARFCYDTLLEEGEKAMLAVQAQVVTPALERIVEANT 238 + SR+ G PAT+ + +AR C D L + KA +AV+A ++TPA+E I+EANT Sbjct: 180 SNIESRTDNYVAGGFPATEAGMAIARHCQDVLTRDAVKAKIAVEAGLLTPAVENIIEANT 239 Query: 239 YLSGVGFESGGVAAAHAVHNGLTAVAETHHFYHGEKVAFGVLVQLALENASNAEMQEVMS 298 LSG+GFE+ G +AAH +H+GLT + E H ++HGEKVAFG L L LEN AE++ ++ Sbjct: 240 LLSGLGFENCGCSAAHGIHDGLTVLEEVHGYFHGEKVAFGTLCLLMLENRDRAEIEAMIR 299 Query: 299 LCHAVGLPITLAQLDITEDIPTKMRAVAELACAPGETIHNMPGGVTVEQVYGALLVAD 356 C +VGLP LA L I +D+P K+ VAE AC PG I+ P +TV V A+L D Sbjct: 300 FCRSVGLPTKLADLGIVDDVPAKIGRVAEAACRPGNIIYATPVTITVPAVRDAILALD 357 Lambda K H 0.319 0.133 0.380 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: 381 Number of extensions: 17 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: 365 Length of database: 364 Length adjustment: 29 Effective length of query: 336 Effective length of database: 335 Effective search space: 112560 Effective search space used: 112560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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