Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine
Query= reanno::Smeli:SMc02119 (397 letters) >FitnessBrowser__SynE:Synpcc7942_0247 Length = 377 Score = 232 bits (591), Expect = 2e-65 Identities = 136/384 (35%), Positives = 209/384 (54%), Gaps = 14/384 (3%) Query: 9 PERSRSSGSIINDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASGYDFVRSRA 68 P R + G D ++ +Q + ++++ W+VDN V NL + ++ +D++ A Sbjct: 2 PFRLKLQGPFWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSA 61 Query: 69 GFDVGQSLISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKL 128 GF++G+S I++ + +Y RAL+VG +N+L V G+I T+IG + G+ S NW++ +L Sbjct: 62 GFNIGESAIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQL 121 Query: 129 SLAYVEVFRNIPPLLVIFFWYSGVLSILPQARDALALPFDIFLSNRGVAFPRPIAEEGAE 188 S YV V RN P LL + WY +L LP A+ ++LS +G+ P P Sbjct: 122 SRGYVAVVRNTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQTPGW-- 179 Query: 189 YTLLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVTGAPITFDI 248 L ++A+A +F + A++ +R P W L I + V L+T + Sbjct: 180 ---LVVILAIALVLFVSWLAQR------QRSPRDWRWLYGAIAVVTVLMLLTQLSWPQQL 230 Query: 249 PVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPA 308 + GG + EF +L L L YT AFI EI+R GI V GQ EAA ALG+ + Sbjct: 231 QPG---QIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRS 287 Query: 309 LTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQTGQSIEIVS 368 T +VVPQA+R+I+P L SQY+ KNSSLA+A+GY DL A T LNQTG+ +E+ Sbjct: 288 QTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFL 347 Query: 369 IWLIVYLSLSLATSLFMNWYNARM 392 I ++ YL+++ S MN R+ Sbjct: 348 ILMLTYLAINAVISAGMNGLQQRL 371 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: 416 Number of extensions: 15 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: 377 Length adjustment: 30 Effective length of query: 367 Effective length of database: 347 Effective search space: 127349 Effective search space used: 127349 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