Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate RR42_RS18605 RR42_RS18605 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21105 (288 letters) >FitnessBrowser__Cup4G11:RR42_RS18605 Length = 295 Score = 154 bits (390), Expect = 2e-42 Identities = 95/281 (33%), Positives = 149/281 (53%), Gaps = 14/281 (4%) Query: 11 RRLLKVAHLAGLFLAMLVICLPGLWIVLSSLRPTVEIMAKP--PVWIPETLSLDAYRAMF 68 RR + + G+F+ V+ P W+ +++ +P E++ + P W+ + +F Sbjct: 24 RRWVTIYIPLGIFV--FVLLFPFYWMAITAFKPDGELLMRSANPFWVMAPTFAHFKKLLF 81 Query: 69 SGAGQGGVPVWDYFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAV 128 P ++ N++IVS ST +LA + YA R RF+ + L L + Sbjct: 82 D------TPYPEWLLNTVIVSTISTFASLAASVLAAYAIERLRFQGAKQVGLAVFLAYLI 135 Query: 129 PGIALSLPLFMLYARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDG 188 P L +PL + + G+ DT ++LILTY +PF WL+ G+FR +P +L E A IDG Sbjct: 136 PPSILFIPLASIVFQLGLFDTRWALILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDG 195 Query: 189 CTPWQAFWQVEFPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEF 248 T W+ ++ PLA PG+ SAGIFAF SWNE+ A S KT+PVG++ E Sbjct: 196 ATRWEILVKIILPLAVPGLISAGIFAFTLSWNEFIYALTFISSSEVKTVPVGIVTELIEG 255 Query: 249 TI-DWRGMCALAVVMIVP-ALTLTFIIQKHLVSGLTFGAVK 287 + W + A A++ +P AL +F ++ + VSG+T GAVK Sbjct: 256 DVYHWGALMAGALLGSLPVALVYSFFVE-YYVSGMT-GAVK 294 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: 288 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: 288 Length of database: 295 Length adjustment: 26 Effective length of query: 262 Effective length of database: 269 Effective search space: 70478 Effective search space used: 70478 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