Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate AO353_03845 AO353_03845 ABC transporter permease
Query= reanno::Smeli:SM_b20327 (276 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03845 Length = 282 Score = 91.3 bits (225), Expect = 2e-23 Identities = 71/223 (31%), Positives = 109/223 (48%), Gaps = 17/223 (7%) Query: 14 LVAVIILVAVFPFYYAILTSLKSGTALFRIDYWPTDISLANYAGIFSHGTFV-------- 65 L VI+ +AV P I+ S + L D+ P+ SL Y + TFV Sbjct: 23 LSGVILFLAVLPILTMIVMSFSGSSNL---DFPPSSYSLQWYKAAWH--TFVSPDASDVL 77 Query: 66 ---RNLGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAG 122 + + SL+V+ + + + L+AV AAYAL R+ FRG+ + L + +FP + + Sbjct: 78 SLGKAMSTSLMVSFMAMIFATLVAVPAAYALTRLEFRGKAMALQLMSLPLVFPMVVLGLA 137 Query: 123 LFELIRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVIT 182 L + + T L+ +++I LPF V T M + E+EEAA + GASP I Sbjct: 138 LLLVFDSLPFQMTVSRLVIAHVILALPFVVKNCTAAMLSIGSEVEEAAQMLGASPTRAIV 197 Query: 183 RVFMPLMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPV 225 V +PLM ++ LLAFI ++NEF F + TVP+ Sbjct: 198 DVVVPLMKSGILAGMLLAFIVSFNEFTVTY-FLYTIDVMTVPI 239 Score = 22.7 bits (47), Expect = 0.009 Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 2/54 (3%) Query: 119 VLAGLFELIRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIV 172 +LAG+ L+ F+ FN F Y I + +W+ + + L + A++ Sbjct: 208 ILAGM--LLAFIVSFNEFTVTYFLYTIDVMTVPIWMFSRTVSSLDPTVFSFAVL 259 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: 184 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 276 Length of database: 282 Length adjustment: 26 Effective length of query: 250 Effective length of database: 256 Effective search space: 64000 Effective search space used: 64000 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