Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate 5210422 Shew_2863 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >FitnessBrowser__PV4:5210422 Length = 248 Score = 130 bits (326), Expect = 3e-35 Identities = 87/258 (33%), Positives = 135/258 (52%), Gaps = 16/258 (6%) Query: 1 MAARLQDKVAILTGAASGIGEAVARRYLDEGARCVLVDVKPADSFGDSLRATYGDRVLTV 60 M + + KV ++TGAASG G+ +A+R +GA+ VL D+ D+ D+L + G+ + + Sbjct: 1 MQSNFEGKVVLITGAASGFGKLLAQRLAPQGAKLVLGDIN--DTALDALCSELGECAVGL 58 Query: 61 SADVTRRDDIQRIVASTLERFGQIDILFNNAALF-DMRPILEESWDVFDRLFAVNVKGMF 119 DV+ + + E FG++DI NNA + M+ +L + D FA+N KG+F Sbjct: 59 RCDVSIEAEQLALAQLAEESFGRLDIAINNAGISAPMKSLLATTEADMDLSFAINTKGVF 118 Query: 120 FLMQAVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHKI 179 F M+A M + CG I+N++S AG G ++ Y A K AV+ T++AAL A I Sbjct: 119 FGMKAQIPLMQKHKCGA-ILNVASMAGINGAPKLTPYVAAKHAVVGITRTAALEFAAQGI 177 Query: 180 NVNGIAPGVVDTPMWNE-VDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFL 238 VN I P TPM E VD R AVP+ R+ P+++ A L + Sbjct: 178 QVNAICPFFTPTPMVTEGVDPALIEQLTR-----------AVPMRRLADPNEVVSAMLHM 226 Query: 239 ASADADYITAQTLNVDGG 256 + D ++T Q + +DGG Sbjct: 227 VNPDNGFMTGQAIAIDGG 244 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: 142 Number of extensions: 8 Number of successful extensions: 5 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: 248 Length adjustment: 24 Effective length of query: 236 Effective length of database: 224 Effective search space: 52864 Effective search space used: 52864 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