Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate 351439 BT1911 7-alpha-hydroxysteroid dehydrogenase (NCBI ptt file)
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >FitnessBrowser__Btheta:351439 Length = 259 Score = 127 bits (319), Expect = 2e-34 Identities = 92/258 (35%), Positives = 133/258 (51%), Gaps = 17/258 (6%) Query: 4 RLQDKVAILTGAASGIGEAVARRYLDEGARCVLVDV--KPADSFGDSLRATYGDRVLTVS 61 R ++KV ++TGAA GIGEA RR + EG + V+ D+ + AD L D V + Sbjct: 3 RFENKVVVITGAAGGIGEATTRRIVSEGGKVVIADLSQERADKLAAELTQAGAD-VRPIY 61 Query: 62 ADVTRRDDIQRIVASTLERFGQIDILFNNAALFD-MRPILEESWDV--FDRLFAVNVKGM 118 T + +V ++ +GQID+L NN D R + E D+ FD +F +N+ Sbjct: 62 FSATELQSCKELVDFAMKEYGQIDVLINNVGGTDPKRDLNIEKLDIDYFDEVFHLNLCCT 121 Query: 119 FFLMQAVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHK 178 +L Q V M G GG I+N++S +G +A + Y A+KA V++ T+ A + Sbjct: 122 MYLSQQVIPIMTTHG-GGNIVNVASISGLTADANGTLYGASKAGVINLTKYIATQMGKKN 180 Query: 179 INVNGIAPGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFL 238 I N +APG+V TP +D L N LG+ A P +G P+D+ FL Sbjct: 181 IRCNAVAPGLVLTPA--ALDNLNEEVRNIFLGQC------ATPY--LGEPEDVAATIAFL 230 Query: 239 ASADADYITAQTLNVDGG 256 AS DA YIT QT+ VDGG Sbjct: 231 ASNDARYITGQTIVVDGG 248 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: 180 Number of extensions: 14 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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