Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate HSERO_RS16730 HSERO_RS16730 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21105 (288 letters) >FitnessBrowser__HerbieS:HSERO_RS16730 Length = 293 Score = 161 bits (408), Expect = 1e-44 Identities = 93/269 (34%), Positives = 143/269 (53%), Gaps = 10/269 (3%) Query: 22 LFLAMLVICLPGLWIVLSSLRPTVEIMAKP--PVWIPETLSLDAYRAMFSGAGQGGVPVW 79 L + + V+ P W+V+++ +P E++++ P W+ + +F P W Sbjct: 31 LLIFLFVLLFPFYWMVITAFKPDNELLSQSGNPFWVIAPTLAHFKKLLFDTQ----YPAW 86 Query: 80 DYFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLPLFM 139 N++IVSV ST +LA + YA R RF+ + LG L +P L +PL Sbjct: 87 --LLNTVIVSVVSTFASLAASVFAAYAIERLRFQGSKQVGLGIFLAYLIPPSILFIPLAA 144 Query: 140 LYARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFWQVE 199 + + G+ DT ++LILTY +PF WL+ G+FR +P +L E A IDG T W+ ++ Sbjct: 145 IVFKLGLFDTRWALILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDGATRWEILVKII 204 Query: 200 FPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFTI-DWRGMCAL 258 PLA PG+ SAGIFAF SWNE+ A S KT+PVG++ E + W + A Sbjct: 205 LPLAVPGLISAGIFAFTLSWNEFIYALTFISSSEVKTVPVGIVTELVEGDVYHWGALMAG 264 Query: 259 AVVMIVPALTLTFIIQKHLVSGLTFGAVK 287 A++ +P + ++ VSG+T GAVK Sbjct: 265 ALLGSLPVAVVYSFFVEYYVSGMT-GAVK 292 Lambda K H 0.328 0.141 0.442 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: 279 Number of extensions: 11 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: 288 Length of database: 293 Length adjustment: 26 Effective length of query: 262 Effective length of database: 267 Effective search space: 69954 Effective search space used: 69954 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