Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate GFF2245 HP15_2195 amino acid ABC transporter, permease protein
Query= reanno::Smeli:SMc02119 (397 letters) >FitnessBrowser__Marino:GFF2245 Length = 395 Score = 381 bits (979), Expect = e-110 Identities = 195/382 (51%), Positives = 270/382 (70%), Gaps = 9/382 (2%) Query: 21 DPQVRGIFYQAITIIILAALIYW----IVDNTVDNLRRANIASGYDFVRSRAGFDVGQSL 76 DP+VR +F+QA+ I AL++W +VDNT+ N+ I++G+ F+ AGF + +L Sbjct: 18 DPRVRSLFFQAVAI----ALVFWGGWILVDNTLSNMESRGISTGFGFLGETAGFGIIMNL 73 Query: 77 ISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVF 136 + + + +YGR VG NTLLV+ G++ ATI+GFI+G+ RLS NW++AK++L Y+EV Sbjct: 74 VPYDATMSYGRTFWVGLTNTLLVSAMGVVAATILGFIIGVARLSSNWLVAKMALVYIEVI 133 Query: 137 RNIPPLLVIFFWYSGVLSILPQARDALALPFDIFLSNRGVAFPRPIAEEGAEYTLLAFVI 196 RNIP LL IFFWY VLS LP R ++ + +FL+NRG+ P P+ +EG ++ Sbjct: 134 RNIPLLLQIFFWYFAVLSNLPSPRQSVDVGGALFLNNRGLYLPDPVTQEGFGIVWGGILL 193 Query: 197 AVAASVFFARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVTGAPITFDIPVAGKFNL 256 A+AA V +A+KRQLATG+ P + +++ +P++++LV G P+ +D+P FN Sbjct: 194 AIAAVVGIRIWAKKRQLATGQIFPTFKVGVAILVLVPIISYLVAGRPLEWDLPALRGFNF 253 Query: 257 TGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPALTTRLVVV 316 GG + PE +L++ALS YTA+FIAEIVR+GI VSKGQTEA+ ALG+ LT RLVV+ Sbjct: 254 GGGITIIPELAALWIALSLYTASFIAEIVRSGILSVSKGQTEASKALGLPNGLTLRLVVI 313 Query: 317 PQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAV-GGTILNQTGQSIEIVSIWLIVYL 375 PQAMR+IIPPLTSQYLNL KNSSLA AIGY DLVAV GT LNQTGQ++E+V+I + VYL Sbjct: 314 PQAMRVIIPPLTSQYLNLVKNSSLATAIGYPDLVAVFMGTTLNQTGQAVEVVAITMAVYL 373 Query: 376 SLSLATSLFMNWYNARMALVER 397 ++SL SLFMN YN +A+ ER Sbjct: 374 TISLLISLFMNIYNRAVAIKER 395 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: 480 Number of extensions: 22 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: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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