Align ABC transporter for Glycerol, permease component 2 (characterized)
to candidate RR42_RS13775 RR42_RS13775 sugar ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_794 (270 letters) >FitnessBrowser__Cup4G11:RR42_RS13775 Length = 277 Score = 468 bits (1205), Expect = e-137 Identities = 223/262 (85%), Positives = 246/262 (93%) Query: 9 RTLFLIAYLLFALLPIYWMVNMSFKTNAEILSTFSFFPQHFTWDNYKTIFTDESWYSGYI 68 R +FL+ YL+FA+LPIYWM+NMSFK+N EI+ST S +P FT ++YKTIFTD SWYSGYI Sbjct: 16 RAVFLVVYLVFAILPIYWMLNMSFKSNEEIVSTLSLWPNDFTLEHYKTIFTDPSWYSGYI 75 Query: 69 NSLIYVSINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVFLLPFFQLYTT 128 NS+IYV++N VI++TVALPAAYAFSRY F+GDKHVFFWLLTNRMTPPAVFLLPFFQLYTT Sbjct: 76 NSMIYVAMNTVISITVALPAAYAFSRYRFIGDKHVFFWLLTNRMTPPAVFLLPFFQLYTT 135 Query: 129 VGLMDTHIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPRFFMTIFLPLI 188 +GLMDTH+ VALAHL+F+VPLAVWILEGFMSG+PREIDETAY+DGYSF RFF+TIFLPLI Sbjct: 136 IGLMDTHLGVALAHLVFNVPLAVWILEGFMSGVPREIDETAYVDGYSFGRFFITIFLPLI 195 Query: 189 KAGVGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDWATLAAAGVLTIV 248 KAGVGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDW LAAAGVLTIV Sbjct: 196 KAGVGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDWGVLAAAGVLTIV 255 Query: 249 PGAIVIWFVRHYIAKGFAMGRV 270 PG IVIWFVRHYIAKGFAMGRV Sbjct: 256 PGGIVIWFVRHYIAKGFAMGRV 277 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: 386 Number of extensions: 14 Number of successful extensions: 1 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: 277 Length adjustment: 25 Effective length of query: 245 Effective length of database: 252 Effective search space: 61740 Effective search space used: 61740 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 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