Align sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_038017555.1 HA49_RS11675 L-idonate 5-dehydrogenase
Query= metacyc::MONOMER-17164 (369 letters) >NCBI__GCF_000757425.2:WP_038017555.1 Length = 343 Score = 169 bits (428), Expect = 1e-46 Identities = 101/314 (32%), Positives = 158/314 (50%), Gaps = 15/314 (4%) Query: 40 IVQVIVTGLCGSDIHYWQHGRIGRYVVEAPIVLGHESAGIVVECGSKSGFAIGDRVALEP 99 +V++ G+CGSD+HY+QHG++G + V+ P++LGHE G VV+ + +VA+ P Sbjct: 31 LVRITRGGICGSDLHYYQHGKVGSFAVKMPMILGHEVIGYVVKSDNPE-LQENQKVAVNP 89 Query: 100 GIACNTCHHCRAGRYNLCSAMRFAATPPY----DGTLATYYRLPAECCYKLPAHVSLQHG 155 C C +C AG+ N C+ MRF + Y DG + Y + C + Sbjct: 90 SKPCGHCKYCEAGQENQCTTMRFFGSAMYFPHVDGGFSQYKIVDTAQCIPFNHQADDRVM 149 Query: 156 ALVEPLSVAVHSCRLAGDMQQKSVVVFGAGPVGLLCASVSRAFGASTVVVVDINSDRLSV 215 EPL+V +H+ AGD+Q K V + G GP+G L A+ ++A GA+ VV DI+ LS+ Sbjct: 150 VFAEPLAVCIHATHQAGDLQDKKVFISGVGPIGCLIAAAAKARGAAEVVCADISPRSLSM 209 Query: 216 AQKYGATHTYKMSNESPEHNAARILEEMELDNG-AHIVLDATGAEPCMNCGISVLASGGT 274 A+ GAT T +N D G + +A+G + + V + GT Sbjct: 210 AEAMGATQTIDAANGD--------FTPFLADKGYFDVSFEASGHPASLTRCLEVTRAKGT 261 Query: 275 FVQVGLGKPNPSLPVGQICDKEAIFRGSFRYGPGDYRTAIGLLSSGRVVLEGLVTHEFPF 334 VQVG+G P P+ + KE GSFR+ ++ TA+ L G + L + EF + Sbjct: 262 LVQVGMGGDVPGFPIMMLIAKEINLVGSFRF-THEFATAVEWLEKGTINPLPLYSGEFDY 320 Query: 335 TQAEEAFKNVGNRQ 348 + + A G++Q Sbjct: 321 HEIDAALNFAGDKQ 334 Lambda K H 0.321 0.137 0.420 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: 330 Number of extensions: 15 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: 369 Length of database: 343 Length adjustment: 29 Effective length of query: 340 Effective length of database: 314 Effective search space: 106760 Effective search space used: 106760 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