Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate GFF3909 PGA1_65p00120 putative amino-acid ABC transporter, permease protein
Query= reanno::Smeli:SMc02119 (397 letters) >FitnessBrowser__Phaeo:GFF3909 Length = 224 Score = 67.0 bits (162), Expect = 5e-16 Identities = 56/197 (28%), Positives = 92/197 (46%), Gaps = 23/197 (11%) Query: 189 YTLLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLGLII----GLPLVTFLVT---G 241 Y L +AV A V A + R+PVL ++ L I G PL+ L G Sbjct: 19 YVPLTLFMAVVAMVLALVLASLLAVERVLRIPVLDQLVVLFISFFRGTPLLVQLFLFYYG 78 Query: 242 APITFDIPVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAH 301 P + V + N +++G L+ + AA++AE +RA I GV + Q EAA Sbjct: 79 LPQV--LSVLTQINGVSAAIMG---------LTLHFAAYMAESIRAAILGVDRSQWEAAQ 127 Query: 302 ALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVA-----VGGTI 356 ++G+ R +V+PQA RI P L + ++++ K +SLA +G +++ G+ Sbjct: 128 SIGMTRGQMMRRIVLPQAARIAAPTLVNYFIDMIKGTSLAFTLGVTEMMGATQKEAAGSF 187 Query: 357 LNQTGQSIEIVSIWLIV 373 L + V W++V Sbjct: 188 LYFEAFLVVAVIYWILV 204 Score = 37.0 bits (84), Expect = 5e-07 Identities = 18/66 (27%), Positives = 38/66 (57%), Gaps = 3/66 (4%) Query: 96 TLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIPPLLVIFFWYSG---V 152 TL +A+ ++ A ++ ++ + R+ ++ +L + ++ FR P L+ +F +Y G V Sbjct: 23 TLFMAVVAMVLALVLASLLAVERVLRIPVLDQLVVLFISFFRGTPLLVQLFLFYYGLPQV 82 Query: 153 LSILPQ 158 LS+L Q Sbjct: 83 LSVLTQ 88 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: 211 Number of extensions: 6 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: 224 Length adjustment: 26 Effective length of query: 371 Effective length of database: 198 Effective search space: 73458 Effective search space used: 73458 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