Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate SMc02119 SMc02119 general L-amino acid transport permease ABC transporter protein
Query= reanno::Smeli:SMc02119 (397 letters) >FitnessBrowser__Smeli:SMc02119 Length = 397 Score = 761 bits (1966), Expect = 0.0 Identities = 397/397 (100%), Positives = 397/397 (100%) Query: 1 MAIGVTNAPERSRSSGSIINDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASG 60 MAIGVTNAPERSRSSGSIINDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASG Sbjct: 1 MAIGVTNAPERSRSSGSIINDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASG 60 Query: 61 YDFVRSRAGFDVGQSLISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLS 120 YDFVRSRAGFDVGQSLISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLS Sbjct: 61 YDFVRSRAGFDVGQSLISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLS 120 Query: 121 HNWIIAKLSLAYVEVFRNIPPLLVIFFWYSGVLSILPQARDALALPFDIFLSNRGVAFPR 180 HNWIIAKLSLAYVEVFRNIPPLLVIFFWYSGVLSILPQARDALALPFDIFLSNRGVAFPR Sbjct: 121 HNWIIAKLSLAYVEVFRNIPPLLVIFFWYSGVLSILPQARDALALPFDIFLSNRGVAFPR 180 Query: 181 PIAEEGAEYTLLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVT 240 PIAEEGAEYTLLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVT Sbjct: 181 PIAEEGAEYTLLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVT 240 Query: 241 GAPITFDIPVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAA 300 GAPITFDIPVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAA Sbjct: 241 GAPITFDIPVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAA 300 Query: 301 HALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQT 360 HALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQT Sbjct: 301 HALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQT 360 Query: 361 GQSIEIVSIWLIVYLSLSLATSLFMNWYNARMALVER 397 GQSIEIVSIWLIVYLSLSLATSLFMNWYNARMALVER Sbjct: 361 GQSIEIVSIWLIVYLSLSLATSLFMNWYNARMALVER 397 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: 675 Number of extensions: 18 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: 397 Length of database: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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: 50 (23.9 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