Align glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_038856588.1 AFK65_RS14270 oxidoreductase
Query= CharProtDB::CH_017124 (365 letters) >NCBI__GCF_001277175.1:WP_038856588.1 Length = 362 Score = 178 bits (451), Expect = 2e-49 Identities = 127/371 (34%), Positives = 186/371 (50%), Gaps = 28/371 (7%) Query: 3 RAIQSPGKYVQGADALQRLGDYLKP--LADSWLVIADKFVLGFAEDTIRQSLSKAGLAMD 60 R + P Y AL RLGD+ P LA + V ++ + A + ++ G Sbjct: 7 RVVPGPANYYSHPGALARLGDFYTPAQLARAVWVYGER-AMAAARPFLTDAIDAPGATR- 64 Query: 61 IVAFNGECSQGEVDRLCQLATQNGRSAIVGIGGGKTLDTAKAVAFFQKVPVAVAPTIAST 120 + F G CS+ +V+ L A + R+ ++G+GGG LDTAKA+A +PV PTIA+T Sbjct: 65 -ILFRGHCSESDVNALAAQAGDD-RAVVIGVGGGALLDTAKALARRLGLPVVAIPTIAAT 122 Query: 121 DAPCSALSVLYTDEGEFDRYLMLPTNPALVVVDTAIVARAPARLLAAGIGDALATWFEAR 180 A + LSV Y D G+ + + LV+V+ I+ RAPA L AGIGD LA W+E Sbjct: 123 CAAWTPLSVWYNDAGQALHFEIFDDANHLVLVEPEIILRAPAEYLLAGIGDTLAKWYE-- 180 Query: 181 AASRSSAATMAGGPAT-----QTALNLARFCYDTLLEEGEKAMLAVQAQVVTPALERIVE 235 A +A PAT + LN A D LLE+ E+A+ + +T +V+ Sbjct: 181 ------AVVLAPAPATLPLTVRLGLNAALAIRDVLLEQSEEALASQHRGALTQDFRDVVD 234 Query: 236 A----NTYLSGVGFESGGVAAAHAVHNGLTAVAETHHFYHGEKVAFGVLVQLALENASNA 291 A + G+G VAAAHAVHNGLT + +T + HG KVA+G+LVQ AL Sbjct: 235 AIIAGGGMVGGLGERYTRVAAAHAVHNGLTVLPQTEKYLHGTKVAYGILVQSALLGQDEV 294 Query: 292 EMQEVMSLCHAVGLPITLAQLDITEDIPTKMRAVAELACAPGETIHNMPGGVTVEQVYGA 351 + +++ LP TLA+LD+ ++ V P E+IH +P ++ A Sbjct: 295 -LAQLIDAWRRFRLPTTLAELDVDIHNAAELDRVIAHTLRPVESIHALPVALSP----AA 349 Query: 352 LLVADQLGQHF 362 L A + +HF Sbjct: 350 LRAAFEKVEHF 360 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: 370 Number of extensions: 16 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: 362 Length adjustment: 29 Effective length of query: 336 Effective length of database: 333 Effective search space: 111888 Effective search space used: 111888 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 24 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