Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate AO356_12035 AO356_12035 amino acid ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_12035 Length = 277 Score = 81.3 bits (199), Expect = 3e-20 Identities = 53/159 (33%), Positives = 87/159 (54%), Gaps = 17/159 (10%) Query: 217 VLMLLTQLSWPQQ-LQPGQIRGGL-RLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAG 274 + +LL L PQ + PG I G+ LSL + GA+++EI R GIL VP G Sbjct: 124 IQILLIYLGLPQLGVVPGAIAAGIIALSLNY-----------GAYLSEIFRAGILGVPNG 172 Query: 275 QWEAAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQT 334 Q EA+ ALGL+ + W++ +PQA+R I+P +Q++ K+SSL +G ++ AQ+ Sbjct: 173 QREASLALGLSETVIFWRVTLPQAMRTIIPPTTNQFISMLKDSSLISVMGVWEVMFLAQS 232 Query: 335 TLNQTGRPVEVFLILMLTYLAINAVISAGMNGLQQRLQR 373 GR ++ ++ T I ++S + +Q R++R Sbjct: 233 ----YGRSSYRYIEMLTTAAIIYWLMSIALELIQARMER 267 Score = 31.2 bits (69), Expect = 4e-05 Identities = 18/70 (25%), Positives = 38/70 (54%), Gaps = 2/70 (2%) Query: 85 GLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVWY-- 142 G V +L + ++ ++++G + +A S + + ++ Y + R TPLL+Q+++ Y Sbjct: 73 GAVLTLFLCLCSIVASSLLGFITALARLSSSAVAFGIASFYASFFRGTPLLIQILLIYLG 132 Query: 143 FPILLSLPAA 152 P L +P A Sbjct: 133 LPQLGVVPGA 142 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: 255 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 277 Length adjustment: 28 Effective length of query: 349 Effective length of database: 249 Effective search space: 86901 Effective search space used: 86901 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