Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate GFF2975 HP15_2919 amino acid ABC transporter, permease protein
Query= reanno::Smeli:SMc02119 (397 letters) >FitnessBrowser__Marino:GFF2975 Length = 223 Score = 84.3 bits (207), Expect = 3e-21 Identities = 67/225 (29%), Positives = 104/225 (46%), Gaps = 37/225 (16%) Query: 181 PIAEEGAEYTLL----AFVIAVAASVFFA----------RYARKRQLATGERLPVLWTVL 226 P +G YTLL +I A +FF R+ + P+L VL Sbjct: 17 PFLIKGIPYTLLISFGGLLIGFALGIFFGLLSINKKWFLRWPATAYIEIFRGTPILVQVL 76 Query: 227 GLIIGLPLVTFLVTGAPITFDIPVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVR 286 + GLP + G PI LT G A++ + A+I+E+VR Sbjct: 77 FIFYGLPDLI----GGPID---------PLTAG----------IAAIALNSGAYISEVVR 113 Query: 287 AGIRGVSKGQTEAAHALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGY 346 G++ + KGQTEA +LG+ T VV PQA R +IPPL +Q + K++SL IG Sbjct: 114 GGVQSIDKGQTEAGLSLGLSRTQTFWSVVWPQAFRRMIPPLGNQAIVSIKDTSLFSVIGV 173 Query: 347 ADLVAVGGTILNQTGQSIEIVSIWLIVYLSLSLATSLFMNWYNAR 391 +LV G + T + E+ + I+YL+++L+ S+ + + R Sbjct: 174 GELVRQGQIYIANTFTAFEVYFVVAILYLAITLSLSIILRFVERR 218 Score = 43.5 bits (101), Expect = 6e-09 Identities = 22/87 (25%), Positives = 41/87 (47%) Query: 89 LLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIPPLLVIFFW 148 L+ G TLL++ G++ +G G+ ++ W + + AY+E+FR P L+ + F Sbjct: 19 LIKGIPYTLLISFGGLLIGFALGIFFGLLSINKKWFLRWPATAYIEIFRGTPILVQVLFI 78 Query: 149 YSGVLSILPQARDALALPFDIFLSNRG 175 + G+ ++ D L N G Sbjct: 79 FYGLPDLIGGPIDPLTAGIAAIALNSG 105 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: 239 Number of extensions: 15 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: 223 Length adjustment: 26 Effective length of query: 371 Effective length of database: 197 Effective search space: 73087 Effective search space used: 73087 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