Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_011384968.1 AMB_RS13020 KR domain-containing protein
Query= reanno::Phaeo:GFF1301 (257 letters) >NCBI__GCF_000009985.1:WP_011384968.1 Length = 256 Score = 125 bits (315), Expect = 7e-34 Identities = 78/253 (30%), Positives = 123/253 (48%), Gaps = 3/253 (1%) Query: 4 LSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTARAEATAAQIGAAAIAVELDVTD 63 L+G+ AL+TG RGIGAA A GA V I D R +A A +G +A+A +DVTD Sbjct: 7 LAGRHALVTGGGRGIGAAIARQMLALGAVVTITGRDQGRLDAAATSLGCSAVA--MDVTD 64 Query: 64 QASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREAYQRTFDINVSGTLFMMQAAA 123 +I +R + G + IL+NNA + AAP + + +++G QAA Sbjct: 65 APAIQNGFARAAQVQGPITILVNNAGIAKAAPFAKTDLGLWDDILRTDLTGAFLCTQAAL 124 Query: 124 QQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGINVNAIAP 183 M+ G G +++N+AS AG G + YCA K +I LT++ + L S + VNA+ P Sbjct: 125 PGMLEAGWG-RVVNVASTAGLTGLAYCAAYCAAKHGLIGLTRALAVELASKPVTVNAVCP 183 Query: 184 GVVDGEHWDGVDAFFAKYEGKAPGQKKAEVAQSVPYGRMGTAADLTGMAVFLASEDADYV 243 G + + A G+ P + A + + P R+ ++ +L + + Sbjct: 184 GYTETDIVADTIANIVAKTGRTPEEALAGLVAANPQKRLIKPEEVAEAVAWLCLPGSASI 243 Query: 244 VAQTYNVDGGQWM 256 Q+ V GG+ M Sbjct: 244 TGQSIAVAGGELM 256 Lambda K H 0.317 0.130 0.365 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: 133 Number of extensions: 7 Number of successful extensions: 2 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: 257 Length of database: 256 Length adjustment: 24 Effective length of query: 233 Effective length of database: 232 Effective search space: 54056 Effective search space used: 54056 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 (21.7 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