Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate HSERO_RS01335 HSERO_RS01335 sugar ABC transporter permease
Query= reanno::Smeli:SM_b20327 (276 letters) >FitnessBrowser__HerbieS:HSERO_RS01335 Length = 283 Score = 148 bits (374), Expect = 1e-40 Identities = 83/272 (30%), Positives = 142/272 (52%), Gaps = 5/272 (1%) Query: 8 RTAFYALVAVIILVAVFPFYYAILTSLKSGTALFRIDYW--PTDIS-LANYAGIFSHGTF 64 R + A + V +L+ + P A++TS++S L +YW P D + L NY + Sbjct: 14 RALYRASLPVALLIWLLPMLAALVTSIRSNDELMAGNYWGWPQDFAMLENYREALTASPM 73 Query: 65 VRNLGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAGLF 124 + NS L+ V ++ LA A +AL+ +FRG +L T ++ + PQ ++ + Sbjct: 74 LHYFWNSCLITIPSVIGAISLAAMAGFALSTYQFRGNTVLFATFVACNFVPQQILMIPVR 133 Query: 125 ELIRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVITRV 184 +L +G+FNT ++ ++ F L F++ LP E+ EAA ++GAS W V R+ Sbjct: 134 DLSLSLGLFNTITGMMLFHIAMQTGFCTLFLRNFIKQLPFEMIEAARIEGASEWTVFYRI 193 Query: 185 FMPLMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWGNIM 244 +PL+ PAL +L F WN++ +AL T + + V +A L G Q+ W + Sbjct: 194 VLPLIRPALAALAVLVFTFVWNDYFWALVLTQGDDVAPITVGVAALRG--QWTTAWNLVS 251 Query: 245 AASVIVTVPLVVLVLIFQRRIISGLTAGGVKG 276 A S++ +P V+L + Q++ ++GLT G KG Sbjct: 252 AGSILAALPSVILFFVMQKQFVAGLTFGASKG 283 Lambda K H 0.332 0.143 0.426 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: 199 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: 276 Length of database: 283 Length adjustment: 26 Effective length of query: 250 Effective length of database: 257 Effective search space: 64250 Effective search space used: 64250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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