Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate SM_b20486 SM_b20486 sugar ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Smeli:SM_b20486 Length = 333 Score = 201 bits (510), Expect = 3e-56 Identities = 118/314 (37%), Positives = 180/314 (57%), Gaps = 3/314 (0%) Query: 51 EWFTVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTA 110 E+ +A+IVV ++ FF FDLL+ + +FA+G LVVL +GGID+SF Sbjct: 11 EFSLLAVIVVISTVLSFATANFFSLGNAFDLLNISAVNIIFAVGLLVVLIAGGIDISFAV 70 Query: 111 IAALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIGTQY 170 A++ YG A+ + +L+ G+LG V+LG N L+HR + S++ TI T Sbjct: 71 AASVVQYGTAIALGWIGGGGWISGLLIAGSLG-VLLGCFNAFLIHRFRIISIVATISTFN 129 Query: 171 LYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWWL 230 +Y GLL+ F ++P + R+ LF DG + + VL ++ + TW L Sbjct: 130 IYFGLLMFFTRGVSIYDLPDWLT--DRVILFEREMPDGTWIEITLPVLVMIVCVIATWTL 187 Query: 231 LNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFD 290 + RT GR +YA G + A R G N+ A+ FG+ G++AGI G++ + P Sbjct: 188 ITRTTTGRQLYAFGDNPEGARRFGINIGAMQFIAFGWLGLMAGIGGLIQAHYAQEVVPNA 247 Query: 291 LVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGAF 350 L G ELDV+AAV+LGGAR+ GG GTV+G +LGV+L+++ ++ L L+GV K+IIGA Sbjct: 248 LYGRELDVLAAVVLGGARLGGGKGTVLGCVLGVLLISITQNGLNLMGVSPFAFKMIIGAI 307 Query: 351 ILLAGTLFALQRKR 364 IL+A TL + + +R Sbjct: 308 ILIAITLSSTRIER 321 Lambda K H 0.328 0.141 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: 298 Number of extensions: 15 Number of successful extensions: 3 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: 364 Length of database: 333 Length adjustment: 29 Effective length of query: 335 Effective length of database: 304 Effective search space: 101840 Effective search space used: 101840 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 (21.7 bits) S2: 49 (23.5 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