Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate Dsui_3259 Dsui_3259 dehydrogenase of unknown specificity, short-chain alcohol dehydrogenase like protein
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >FitnessBrowser__PS:Dsui_3259 Length = 256 Score = 112 bits (281), Expect = 6e-30 Identities = 86/267 (32%), Positives = 132/267 (49%), Gaps = 32/267 (11%) Query: 8 KVAILTGAASGIGEAVARRYL------------DEGARCVLVDVKPADSFGDSLRATYGD 55 K ++TG + GIG A R D A LV +S DS R G Sbjct: 3 KTLLITGGSRGIGAATVRLAARAGYAVCFSYRQDAAAAQQLVAEVTRESSRDSGRE--GA 60 Query: 56 RVLTVSADVTRRDDIQRIVASTLERFGQIDILFNNAALFDMRPILEE-SWDVFDRLFAVN 114 +L AD++R ++I+ + A+ +RFG I L NNA + +++ +E+ D R+FA N Sbjct: 61 PILAFQADISREEEIRALFAAAEQRFGPITALVNNAGILELQTRVEDMDGDRLQRIFATN 120 Query: 115 VKGMFFLMQAVAQKMVEQ--GCGGKIINMSSQAGRRGEA-LVSHYCATKAAVLSYTQSAA 171 V G F + +++ + G GG I+N+SS+A R G A Y A+KAA+ + T A Sbjct: 121 VIGTFLCCREAVRRLSTRHGGHGGAIVNLSSRAARLGAAGEYVDYAASKAAIDTLTLGLA 180 Query: 172 LALAPHKINVNGIAPGVVDTPMWNEVDALFARYENRPLGEKKRL--VGEAVPLGRMGVPD 229 +A I VN +APG++DT + + GE R+ + +P+ R G P+ Sbjct: 181 REVAAEGIRVNAVAPGLIDTDI------------HASGGEPGRVERLRTGIPMQRGGTPE 228 Query: 230 DLTGAALFLASADADYITAQTLNVDGG 256 ++ A L+L S DA Y T L+V GG Sbjct: 229 EVAKAILWLLSEDASYTTGAILDVAGG 255 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: 153 Number of extensions: 11 Number of successful extensions: 6 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: 256 Length adjustment: 24 Effective length of query: 236 Effective length of database: 232 Effective search space: 54752 Effective search space used: 54752 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