Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate AO353_10020 AO353_10020 amino acid ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10020 Length = 278 Score = 82.8 bits (203), Expect = 1e-20 Identities = 64/201 (31%), Positives = 106/201 (52%), Gaps = 22/201 (10%) Query: 180 LVVILAIALVLFVSWLAQRQRSPRDW--RWLYGAIAVVTVLM---LLTQLSWPQQ-LQPG 233 L I+A +L+ F++ LA+ +S + Y + T L+ LL L PQ + PG Sbjct: 83 LCSIVASSLLGFITALARLSKSAVAFGIASFYASFFRGTPLLIQILLIYLGLPQLGIVPG 142 Query: 234 QIRGGL-RLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQ 292 I G+ LSL + GA+++EI R GI+ VP GQ EA+ ALG+ S W+ Sbjct: 143 AIAAGIIALSLNY-----------GAYLSEIFRAGIVGVPHGQREASLALGMRESVIFWR 191 Query: 293 IVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLT 352 + +PQA+R I+P +Q++ K+SSL +G ++ AQ+ GR ++ ++ T Sbjct: 192 VTLPQAMRTIIPPTTNQFISMLKDSSLISVMGVWEVMFLAQS----YGRSSYRYIEMLST 247 Query: 353 YLAINAVISAGMNGLQQRLQR 373 I ++S G+ +Q R++R Sbjct: 248 AAIIYWLLSIGLELIQARMER 268 Score = 30.0 bits (66), Expect = 8e-05 Identities = 17/70 (24%), Positives = 38/70 (54%), Gaps = 2/70 (2%) Query: 85 GLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVWY-- 142 G +L + ++ ++++G + +A S++ + ++ Y + R TPLL+Q+++ Y Sbjct: 74 GAALTLFLCLCSIVASSLLGFITALARLSKSAVAFGIASFYASFFRGTPLLIQILLIYLG 133 Query: 143 FPILLSLPAA 152 P L +P A Sbjct: 134 LPQLGIVPGA 143 Lambda K H 0.326 0.140 0.445 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: 271 Number of extensions: 14 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: 377 Length of database: 278 Length adjustment: 28 Effective length of query: 349 Effective length of database: 250 Effective search space: 87250 Effective search space used: 87250 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