Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate GFF195 PGA1_c01990 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB
Query= reanno::Smeli:SMc02119 (397 letters) >FitnessBrowser__Phaeo:GFF195 Length = 410 Score = 304 bits (778), Expect = 3e-87 Identities = 173/410 (42%), Positives = 255/410 (62%), Gaps = 20/410 (4%) Query: 5 VTNAPERSRSSGSIINDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASGYDFV 64 +T+ P+ ++ND + R + +QAI ++LA I+++ +N + NLR A + Y F+ Sbjct: 4 LTDPPKAQFQLSMLVNDTRYRSLTFQAIAALVLALAIWYLGNNLIQNLRAAGLNISYGFL 63 Query: 65 RSRAGFDVGQSLISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWI 124 +G+D+ Q LI + S S++ RA +VG +NTLLVA+ ITATI G + G+ RLS+NW+ Sbjct: 64 GDPSGYDINQRLIEYDSQSSHARAAVVGVLNTLLVAVLACITATIFGVVAGVLRLSNNWL 123 Query: 125 IAKLSLAYVEVFRNIPPLLVIFFWYSGVLSILPQARD------ALALPFDIF-LSNRGVA 177 ++KL YVE+FRNIP L+ I ++ + +++P R+ ++ FD+F +NRGV Sbjct: 124 VSKLMAVYVEIFRNIPVLIWIIIIFTIMTAVMPGPREFRGDNATSSMLFDLFAFTNRGVY 183 Query: 178 FPRPIAEEG----AEYTLLAFVIAVAASVFFAR----YARKRQLATGERLPVLWTVLGL- 228 P P E G L + A+ S R A K Q TG R LG+ Sbjct: 184 IPMPWFESGFFASGALNWLVVIAALVGSFLVMRRIEANATKTQEKTGVRPKTKLIALGVW 243 Query: 229 IIGLPLVTFLVTGAPITFDIPVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAG 288 ++ L LV F++ +++++P FN GG +G ++L+ ALS YT AFIAE VRAG Sbjct: 244 LVPLALVLFVM---GLSWEVPELKGFNFKGGIKIGGPLIALWFALSIYTGAFIAENVRAG 300 Query: 289 IRGVSKGQTEAAHALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYAD 348 I+ ++KGQTEAA ALG+RP LVV+PQA+R+IIPPL S +LN+TKNSSLA+A+GYAD Sbjct: 301 IQAINKGQTEAAAALGLRPGRIMNLVVLPQALRVIIPPLISNFLNITKNSSLAIAVGYAD 360 Query: 349 LVA-VGGTILNQTGQSIEIVSIWLIVYLSLSLATSLFMNWYNARMALVER 397 + A +GG LNQTG++IE V + ++ YL+ SL S+ MN YNA + L ER Sbjct: 361 ITATLGGITLNQTGRAIECVLLLMLFYLTASLLISMVMNVYNASVKLKER 410 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: 418 Number of extensions: 15 Number of successful extensions: 3 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: 410 Length adjustment: 31 Effective length of query: 366 Effective length of database: 379 Effective search space: 138714 Effective search space used: 138714 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