Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)
Query= reanno::Smeli:SMc04257 (305 letters) >FitnessBrowser__Dyella79:N515DRAFT_3133 Length = 273 Score = 124 bits (312), Expect = 2e-33 Identities = 84/281 (29%), Positives = 147/281 (52%), Gaps = 22/281 (7%) Query: 31 IVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPL---EITFEPWVKAWAEACT 87 +V G LI L + PL M+ S E + PPL T + + + A Sbjct: 9 LVNGLLIGSTLVAVFPLLWMLSVSFMRPGE---ASALPPPLLPTHATLANYHELFERA-- 63 Query: 88 GLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILIVGAFIPYQ 147 G+ R NS+ ++ ++S+A + GYA A RF G + F +L+ G IP Q Sbjct: 64 -----GMGRYLLNSLGVSSAITLLSLAFNLMAGYAFAKLRFSGRERLFQVLLGGLVIPAQ 118 Query: 148 VMIYPIVIVLREMGVYGTLTGLII--VHTIFGMPILTLLFRNYFAGLPEELFKAARVDGA 205 V + P+ ++L+ +G+ + +++ + TIFG+ L R Y G+P++L +AAR+DGA Sbjct: 119 VAMLPLFLLLKYLGLVNSYAAVVVPAMATIFGI----FLVRQYARGIPDDLMEAARIDGA 174 Query: 206 GFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVV-FTRPEYYPMTVQLNNIVNSVQ 264 G I+ +I+LP+ PI V I WNDF++ ++ T E+Y + + L ++ S + Sbjct: 175 GELRIFVQIVLPLLKPIMVTLAIFTFLTAWNDFMWPLIALTGQEHYTLPIALASL--SRE 232 Query: 265 GVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305 V++ + MA +++T L L ++ R +++G+ G+VKG Sbjct: 233 HVQDSELMMAGSVVTVLPVLVLFLALQRYYLQGLLLGSVKG 273 Lambda K H 0.329 0.145 0.450 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: 197 Number of extensions: 10 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: 305 Length of database: 273 Length adjustment: 26 Effective length of query: 279 Effective length of database: 247 Effective search space: 68913 Effective search space used: 68913 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