Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate WP_011842090.1 RSPH17029_RS15650 amino acid ABC transporter permease
Query= reanno::Smeli:SMc02119 (397 letters) >NCBI__GCF_000015985.1:WP_011842090.1 Length = 221 Score = 68.9 bits (167), Expect = 1e-16 Identities = 51/162 (31%), Positives = 80/162 (49%), Gaps = 15/162 (9%) Query: 232 LPLVTFLVTGAPITFDIPVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRG 291 L L+ F+ +G P G + P F ++ +A +A+ AEI RAGI+ Sbjct: 74 LVLLIFIYSGLPFA-------------GLAISP-FAAVAVAFFLNNSAYYAEIYRAGIQS 119 Query: 292 VSKGQTEAAHALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVA 351 V GQTEAA A G+ T VV+PQA+R ++P L S + + K +SLA + A+L+ Sbjct: 120 VPAGQTEAARACGLTTGQTLAHVVLPQAVRNVLPDLLSNTVEVVKLTSLASVVSLAELLY 179 Query: 352 VGGTILNQTGQSIEIVSIWLIVYLSLSLATSLFMNWYNARMA 393 + T + +V + +VYL L ++ Y R+A Sbjct: 180 SANMARSLTYNASPLV-LAALVYLVLLWPLVRLVSRYQRRLA 220 Score = 38.5 bits (88), Expect = 2e-07 Identities = 27/89 (30%), Positives = 45/89 (50%), Gaps = 8/89 (8%) Query: 89 LLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIPPLLVIFFW 148 L+ G T+ + I + G + +G LSH + + A ++ R +PPL+++ F Sbjct: 21 LMQGLWMTVKLCAAVIALGLVGGLFLALGALSHRRWLRWPAFAVIDFLRALPPLVLLIFI 80 Query: 149 YSGV----LSILPQARDALALPFDIFLSN 173 YSG+ L+I P A A+A FL+N Sbjct: 81 YSGLPFAGLAISPFAAVAVA----FFLNN 105 Lambda K H 0.327 0.141 0.412 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: 220 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 397 Length of database: 221 Length adjustment: 26 Effective length of query: 371 Effective length of database: 195 Effective search space: 72345 Effective search space used: 72345 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: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. 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