Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate WP_086509148.1 BZY95_RS06445 amino acid ABC transporter permease
Query= reanno::Smeli:SMc02119 (397 letters) >NCBI__GCF_002151265.1:WP_086509148.1 Length = 396 Score = 412 bits (1058), Expect = e-119 Identities = 209/378 (55%), Positives = 272/378 (71%), Gaps = 1/378 (0%) Query: 21 DPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASGYDFVRSRAGFDVGQSLISFT 80 D R + +Q + I +AA + +I+ NT DNL I +G+ F+ AGF +GQSLI ++ Sbjct: 19 DRAKRALLFQVLLIAAVAAFLLYIIGNTQDNLAARGITTGFGFLDRTAGFGIGQSLIEYS 78 Query: 81 SDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIP 140 S STYGR +VG +NTLLV+ G+I ATIIGFIVGI RLS NW+IA+L+ Y+E+FRNIP Sbjct: 79 SQSTYGRTFVVGLLNTLLVSALGVIAATIIGFIVGIARLSPNWLIARLASGYIEIFRNIP 138 Query: 141 PLLVIFFWYSGVLSILPQARDALALPFDIFLSNRGVAFPRPIAEEGAEYTLLAFVIAVAA 200 LL IFFWY VL +P ARD+ +L IFL+ RG+ P P+ E G L FV+A+ A Sbjct: 139 LLLQIFFWYFAVLRAMPAARDSYSLGEVIFLNVRGLYLPEPLFESGFGLIPLTFVVAIVA 198 Query: 201 SVFFARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVTGAPITFDIPVAGKFNLTGGS 260 S+ + ++R ATG+RLP W L LI+GLP++ + TG P+T+D+P FN GG Sbjct: 199 SIALVIWNKRRHEATGKRLPAGWISLALILGLPMLVLVATGVPVTWDVPELRGFNFRGGI 258 Query: 261 VVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPALTTRLVVVPQAM 320 + PEF++L+LALS YTA+FIAEIVR+GI+ + GQTEAA AL + L RLVVVPQA+ Sbjct: 259 TIIPEFLALWLALSIYTASFIAEIVRSGIQAIPHGQTEAAQALSLPQKLVLRLVVVPQAL 318 Query: 321 RIIIPPLTSQYLNLTKNSSLAVAIGYADLVAV-GGTILNQTGQSIEIVSIWLIVYLSLSL 379 R+IIPPLTSQYLNL KNSSLA AIGY DLV+V GT LNQTGQ+IE++S+ + VYL +SL Sbjct: 319 RVIIPPLTSQYLNLIKNSSLATAIGYPDLVSVFAGTTLNQTGQAIEVISMTMAVYLIISL 378 Query: 380 ATSLFMNWYNARMALVER 397 S+FMNW+NAR+ALVER Sbjct: 379 LVSMFMNWFNARVALVER 396 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: 482 Number of extensions: 19 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: 397 Length of database: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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 24 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