Align ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized)
to candidate H281DRAFT_00167 H281DRAFT_00167 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= reanno::Smeli:SMc04258 (302 letters) >FitnessBrowser__Burk376:H281DRAFT_00167 Length = 312 Score = 239 bits (610), Expect = 6e-68 Identities = 124/287 (43%), Positives = 177/287 (61%), Gaps = 4/287 (1%) Query: 8 SARPNQWLRNLNAKIASIPMILTAMVIFVGGTAWTVVYSFTNSKLLPRLAFVGFDQYERL 67 +A ++W+ K+ P ++ ++V G A T S +NS+L+PR FVG D+Y L Sbjct: 22 AALADRWI----PKLVLAPSVVISLVFVYGFIAITGYLSLSNSRLMPRYEFVGLDRYREL 77 Query: 68 WAAPRWLVSIQNLAVFGCLSLVFSLVIGFVLAALMDQKIRFENTFRTIMLYPFALSFIVT 127 + + S NL FG + + +G LA L+DQ+IR E R + LYP ALSFIVT Sbjct: 78 FDNDVFWTSAANLGWFGIPFIGICIGLGLFLAILLDQQIRNEGALRAVFLYPMALSFIVT 137 Query: 128 GLVWQWLLNPQYGIQSIVRSLGWTSFSFDPLYNSNIVIYGILIAALWQGTGLVMCLMLAG 187 G WQW++ P G++ + GWTSFSF L + + I+ ++IAA+WQ TG VM L LAG Sbjct: 138 GTAWQWIMTPSIGLEKVFHDWGWTSFSFSWLGDPDKAIFCVVIAAVWQSTGFVMALFLAG 197 Query: 188 LRGIDEDIWKAARVDGIPMWKTYVLIIIPMMRGVFITTLVIIASGIVKVYDLVVAQTSGG 247 LRG+D +I+KAA++DG + Y I+IP MR VF + L+I+ +K +DLVVA T+GG Sbjct: 198 LRGVDGEIFKAAQMDGANLPTIYRKIVIPSMRPVFFSVLLILCHITIKTFDLVVALTAGG 257 Query: 248 PGIASEVPAKYVYDYMFQAQNLGQGFAASTMMLVTVAIIIVPWAYLE 294 PG +S +PA ++Y + F LG G A+S MML TV ++VP YLE Sbjct: 258 PGTSSSLPAIFMYTFSFNRGQLGVGAASSMMMLATVVAVLVPLMYLE 304 Lambda K H 0.329 0.142 0.449 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: 318 Number of extensions: 17 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: 302 Length of database: 312 Length adjustment: 27 Effective length of query: 275 Effective length of database: 285 Effective search space: 78375 Effective search space used: 78375 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: 48 (23.1 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