Align TreU, component of Trehalose porter (characterized)
to candidate 3609748 Dshi_3131 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q97ZC1 (267 letters) >FitnessBrowser__Dino:3609748 Length = 265 Score = 103 bits (256), Expect = 5e-27 Identities = 73/252 (28%), Positives = 121/252 (48%), Gaps = 6/252 (2%) Query: 14 IYFLFPLYILVLLAFNSPKYTVLAKFPSLLPVSLTLNNLLTALQGTAFIDPFIKSLETAT 73 ++ + P+Y LV ++F + +LA F +L P + TL++ +T + +I S+ + Sbjct: 13 LFLMLPIYWLVTMSFKTTN-EILAGF-TLFPQTFTLDSYITIFTDPTWYWGYINSIIYVS 70 Query: 74 LVGIITIALAIPAGYGLSRLPRAIAYSIIILLLVTNMMPAIVIGIPIAVDFLKLHLFESV 133 L ++++A+A+PA Y SR + LL M PA V +P + + +F++ Sbjct: 71 LNTVLSVAVALPAAYAFSRYRFLGDKQLFFWLLTNRMAPAAVFALPFFQLYSSVKIFDTH 130 Query: 134 VGLALAQTLITLPLATFILQGTFSSIPIDLEHQARVDGANLFNRLFSVLLPLAAPGIAAA 193 + +ALA TL +PLA +IL+G SIP +L+ A VDG + + LP G+ A Sbjct: 131 LAVALAHTLFNVPLAVWILEGFMRSIPKELDETAYVDGYSFPRFFIKIFLPNIGAGVGVA 190 Query: 194 FLISWMFSWDEFTYAILLIPYHSTLPVTIYQDVTRGNLLAGIAFSLIFTLPVI-ILTFAL 252 +MFSW E A L + I +TR AG L+ + I+ A+ Sbjct: 191 AFFCFMFSWVEMLLAKTLTAVEAK---PIAAVMTRTASSAGYELGLLAAAGTLTIIPGAI 247 Query: 253 QKYLRGEYLAGG 264 Y Y+A G Sbjct: 248 VIYFVRNYIARG 259 Lambda K H 0.330 0.146 0.431 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: 206 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: 267 Length of database: 265 Length adjustment: 25 Effective length of query: 242 Effective length of database: 240 Effective search space: 58080 Effective search space used: 58080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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