Align ABC transporter for Glycerol, permease component 2 (characterized)
to candidate WP_086511010.1 BZY95_RS16615 carbohydrate ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_794 (270 letters) >NCBI__GCF_002151265.1:WP_086511010.1 Length = 275 Score = 129 bits (323), Expect = 9e-35 Identities = 87/269 (32%), Positives = 127/269 (47%), Gaps = 8/269 (2%) Query: 8 KRTLFLIAYLLFALL---PIYWMVNMSFKTNAEILSTFSFFPQHFTWDNYKTIFTDESWY 64 + TL +I +L A L P+ FKTNAE+ + + P + NY IF D +++ Sbjct: 7 RNTLRVIVLILVASLVIGPLLASFFGGFKTNAELRTNPLWLPDAWNPQNYVAIFLDGNFW 66 Query: 65 SGYINSLIYVSINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVFLLPFFQ 124 NS S+ +++TL V AAY FS+ F G + + +LL M P A +LP F Sbjct: 67 RYMGNSFFISSMTVLLTLVVGAAAAYVFSQIRFFGSRMIHSYLLLGLMFPFAAAILPLFI 126 Query: 125 LYTTVGLMDTHIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPRFFMTIF 184 +GL+DT+ AV L F + LA+ + + F +P+E+ E AY+DG S+ RFF + Sbjct: 127 KVRDLGLLDTYWAVILPQTAFGLSLAILLFKAFFDQLPKELFEAAYVDGCSYLRFFWSFT 186 Query: 185 LPLIKAGVGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASG---MDWATLAA 241 LPL + F F+ SW LL L +N + I + G W + A Sbjct: 187 LPLSTPILATVGVFVFVQSWNNFLL--PLVVLNDRSIYTWPLGMMQFQGEYLTQWNMILA 244 Query: 242 AGVLTIVPGAIVIWFVRHYIAKGFAMGRV 270 LTI P I + YI G G V Sbjct: 245 FVTLTITPAVIFFLAAQKYIVAGLTGGSV 273 Lambda K H 0.332 0.141 0.451 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: 246 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: 270 Length of database: 275 Length adjustment: 25 Effective length of query: 245 Effective length of database: 250 Effective search space: 61250 Effective search space used: 61250 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 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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