Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit
Query= reanno::Smeli:SMc02119 (397 letters) >NCBI__GCF_900156495.1:WP_083710231.1 Length = 589 Score = 85.9 bits (211), Expect = 3e-21 Identities = 74/208 (35%), Positives = 111/208 (53%), Gaps = 26/208 (12%) Query: 190 TLLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLGLIIGLP-LVTFLVTGAPITFDI 248 T+L V+AVA +R R L R+ + GLP +V LV G I Sbjct: 378 TILGMVLAVAG------ISRSRWLRWPARI-----YTDIFRGLPAVVVILVVGLGIG--- 423 Query: 249 PVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPA 308 PV NLTG + P ++ +AL+ AA+I EI R+GI+ V GQ EA+ A+G Sbjct: 424 PVVK--NLTGNN---PYWLGA-VALALLAAAYIGEIFRSGIQSVDDGQLEASRAIGFSYR 477 Query: 309 LTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIG----YADLVAVGGTILNQTGQSI 364 + RLVVVPQ +R ++P L +Q+++L K+SSL +G +L AVG + QTG Sbjct: 478 QSMRLVVVPQGVRRVLPALMNQFISLIKDSSLVYFLGLLASQRELFAVGRDLNAQTGNLS 537 Query: 365 EIVSIWLIVYLSLSLATSLFMNWYNARM 392 +V+ LI YL L++ + +N+ + R+ Sbjct: 538 PLVAAGLI-YLVLTIPLTHLVNYIDHRL 564 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: 488 Number of extensions: 27 Number of successful extensions: 1 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: 589 Length adjustment: 34 Effective length of query: 363 Effective length of database: 555 Effective search space: 201465 Effective search space used: 201465 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: 52 (24.6 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