Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate GFF356 Psest_0357 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >FitnessBrowser__psRCH2:GFF356 Length = 255 Score = 164 bits (416), Expect = 1e-45 Identities = 100/255 (39%), Positives = 147/255 (57%), Gaps = 11/255 (4%) Query: 4 RLQDKVAILTGAASGIGEAVARRYLDEGARCVLVDVKPADSFGDSLRATY--GDRVLTVS 61 RLQ++VA++TG+ GIG +A R +EGA V+ + + +SL + G RV ++ Sbjct: 2 RLQNQVALVTGSTQGIGRGIALRLAEEGADIVINGRQDDEQARESLEQVHARGRRVCFIA 61 Query: 62 ADVTRRDDIQRIVASTLERFGQIDILFNNAALFDMRPILEESWDVFDRLFAVNVKGMFFL 121 ADV + QR+V +E+ G++DIL NNA + L+ D +D++ VN++G FFL Sbjct: 62 ADVGDVEQCQRLVREGIEQMGRLDILVNNAGVQRHAAFLDAQADDYDQVLNVNLRGPFFL 121 Query: 122 MQAVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHKINV 181 QA A+ + E G GG+IIN SS + YCA+K + ++ A+ LAP I V Sbjct: 122 AQAFARYLREHGRGGRIINNSSVHEELPHPNFTAYCASKGGLKMLMRNIAIELAPLGITV 181 Query: 182 NGIAPGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFLASA 241 N +APG V+TP+ E+ N+P EK + + +P GR+G P D+ G FLAS Sbjct: 182 NNVAPGAVETPINREL-------MNQP--EKLASLLQNIPAGRLGRPHDVAGVVAFLASP 232 Query: 242 DADYITAQTLNVDGG 256 DA+YIT TL VDGG Sbjct: 233 DAEYITGTTLVVDGG 247 Lambda K H 0.321 0.135 0.393 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: 156 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: 260 Length of database: 255 Length adjustment: 24 Effective length of query: 236 Effective length of database: 231 Effective search space: 54516 Effective search space used: 54516 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 (21.9 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