Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate GFF3539 PS417_18125 polar amino acid ABC transporter permease
Query= reanno::Smeli:SMc02119 (397 letters) >FitnessBrowser__WCS417:GFF3539 Length = 258 Score = 87.4 bits (215), Expect = 4e-22 Identities = 68/214 (31%), Positives = 105/214 (49%), Gaps = 20/214 (9%) Query: 191 LLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLGLIIGLPL---VTFLVTGAPITFD 247 LL V+ +AA++ R ++ L LPV + V L+ G PL + FL T Sbjct: 35 LLGCVLGLAAALL--RLSKNPLL----HLPVRFYVW-LMRGTPLLVQIVFLYTA------ 81 Query: 248 IPVAGKFNLTG----GSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAHAL 303 + G F G VV + +AL A++AEI+RAGI V KGQ EA +L Sbjct: 82 LAAGGIFRFEDIDLFGLVVPGNIQAAIIALGLNEGAYMAEIIRAGIGAVDKGQYEAGRSL 141 Query: 304 GIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQTGQS 363 G+ A R +V+PQA R+I+PPL +++ + KN++L IG +L+ + + T + Sbjct: 142 GMGFAKLMRRIVLPQAFRVIVPPLGNEFNVMLKNTTLVSVIGVQELLLSTQMVTSATFRV 201 Query: 364 IEIVSIWLIVYLSLSLATSLFMNWYNARMALVER 397 E+ + I +L L+ F W AR +R Sbjct: 202 FELYLVVAIYFLMLTTLWGFFQRWLEARFGQSDR 235 Score = 32.7 bits (73), Expect = 1e-05 Identities = 18/63 (28%), Positives = 32/63 (50%) Query: 90 LVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIPPLLVIFFWY 149 L G T L+A++ ++ ++G + RLS N ++ YV + R P L+ I F Y Sbjct: 20 LTGLWLTCLIAVSAMLLGCVLGLAAALLRLSKNPLLHLPVRFYVWLMRGTPLLVQIVFLY 79 Query: 150 SGV 152 + + Sbjct: 80 TAL 82 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: 237 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: 258 Length adjustment: 28 Effective length of query: 369 Effective length of database: 230 Effective search space: 84870 Effective search space used: 84870 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 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