Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized)
to candidate RR42_RS22880 RR42_RS22880 ABC transporter permease
Query= reanno::Smeli:SMc02872 (315 letters) >FitnessBrowser__Cup4G11:RR42_RS22880 Length = 301 Score = 123 bits (309), Expect = 5e-33 Identities = 88/296 (29%), Positives = 146/296 (49%), Gaps = 27/296 (9%) Query: 18 RWHILVFLLPALVVYTAVMILPLFETLRQSFYNTVDGQ--LTFVGLGNFKVLFGDPRWAA 75 RW + L PAL+ ++ +P ++ S + G + FVGL NF+ + +P Sbjct: 14 RWLGALMLAPALIYIALLLGIPFLLSIYYSLSDITVGTRAMHFVGLANFQRIVQNPT--- 70 Query: 76 DFWNALKNNFVFFLIHMAVQNPIGIALAAMLSVPKLRFGA---FYRTAIFLPTLLSFVIV 132 FW +L N VF L+ A+ + LA +L++ LR R I LP + + Sbjct: 71 -FWRSLGNALVFTLVSQALV----VVLAKILALALLRDFRGKWLVRLLILLPWVAPISLG 125 Query: 133 GFIWKLILSPIWGVAPYLLDTVGLRSLFGP-----WLGKPDTALIAVSLISVWQYIGIPM 187 W I P++ + + L +GL FGP WLG+PD A+ +V L+ VW+ + + Sbjct: 126 SIGWLWIFDPVYSIINWTLRALGL---FGPQTWPVWLGQPDLAMASVILVDVWRLLPLAT 182 Query: 188 MLIYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGIVSILTFVGNFNAFDLIY 247 ++I A L IP ++ +AA +DG W +I +PL++P + + + V F D+I Sbjct: 183 VIILAGLHGIPQDIHDAAAMDGAGFWRHLLRINIPLVMPIMLVALLFGIV--FTLTDMII 240 Query: 248 TVQGALAGPDKSTDILGTLLYRTFFGFQLQLGDRSMGATIAAIMFLIILAGVALYL 303 GP +T +L +L + T +Q GD + GA I+ +F +++A VAL L Sbjct: 241 IFVLTRGGPYDTTQVLASLAFFT----GIQGGDLAEGAAISLFLFPLLVAVVALLL 292 Lambda K H 0.331 0.146 0.461 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: 353 Number of extensions: 25 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: 315 Length of database: 301 Length adjustment: 27 Effective length of query: 288 Effective length of database: 274 Effective search space: 78912 Effective search space used: 78912 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 (21.9 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