Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate SMc02119 SMc02119 general L-amino acid transport permease ABC transporter protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__Smeli:SMc02119 Length = 397 Score = 371 bits (952), Expect = e-107 Identities = 188/375 (50%), Positives = 258/375 (68%), Gaps = 1/375 (0%) Query: 1 VRAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEAD 60 VR +Q +T++ + AL +++ DNT NL+ I SG+ F+ AGF + Q LI +T Sbjct: 24 VRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASGYDFVRSRAGFDVGQSLISFTSDS 83 Query: 61 SYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLL 120 +Y R L+G +NTLLV G+I ATI+GFI+G+ RLS NWII+KL+ YVEVFRNIPPLL Sbjct: 84 TYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIPPLL 143 Query: 121 QILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVL 180 I FWY V +P R A F+S+RG+ P + EG +++ V+A+ A V Sbjct: 144 VIFFWYSGVLSILPQARDALALPFDIFLSNRGVAFPRPIAEEGAEYTLLAFVIAVAASVF 203 Query: 181 MTRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVLI 240 R+A KR ATGE W L L + +P ++ L+ GAP+ +++P FN GG V+ Sbjct: 204 FARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVTGAPITFDIPVAGKFNLTGGSVVG 263 Query: 241 PELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVI 300 PE ++L LAL+ YTAAFIAEIVR+GI+ VS GQTEAA +LG+R T R V++PQA+R+I Sbjct: 264 PEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPALTTRLVVVPQAMRII 323 Query: 301 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS 360 IPPLTSQYLNL KNSSLA IGY ++V++ GT+LNQTGQ+IE+++I + VYL++S++ S Sbjct: 324 IPPLTSQYLNLTKNSSLAVAIGYADLVAV-GGTILNQTGQSIEIVSIWLIVYLSLSLATS 382 Query: 361 LLMNWYNKRIALIER 375 L MNWYN R+AL+ER Sbjct: 383 LFMNWYNARMALVER 397 Lambda K H 0.328 0.141 0.430 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: 442 Number of extensions: 20 Number of successful extensions: 2 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: 375 Length of database: 397 Length adjustment: 30 Effective length of query: 345 Effective length of database: 367 Effective search space: 126615 Effective search space used: 126615 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 (21.8 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