Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate YP_004140220.1 Mesci_1006 polar amino acid ABC transporter inner membrane subunit
Query= reanno::Smeli:SMc02119 (397 letters) >NCBI__GCF_000185905.1:YP_004140220.1 Length = 269 Score = 90.5 bits (223), Expect = 5e-23 Identities = 73/223 (32%), Positives = 113/223 (50%), Gaps = 32/223 (14%) Query: 190 TLLAFVIAVAASVFFARYARK-----RQLATGERLPVLWTVLGLIIGLPLVTFLV----T 240 T++AFV+A A + A RQ+A + +I G+P++ L Sbjct: 53 TVVAFVLASAIGLGIALMGMSGSRWLRQIAR--------FYVEIIRGVPILVLLFWIAFA 104 Query: 241 GAP--------ITFDIPVAGKFNLTGGSVVGPEFMSLF---LALSFYTAAFIAEIVRAGI 289 GAP +T + AG F G ++ + L+ +AL+ +AFI+E+ RAGI Sbjct: 105 GAPAFVAAWNALTAPLQSAGLF----GELLVRDVSLLWRAIMALTIGYSAFISEVFRAGI 160 Query: 290 RGVSKGQTEAAHALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADL 349 + V KGQ EAA ALG+ A RL+V PQA+R I+PPL + ++ L K+SSL +G AD+ Sbjct: 161 QAVEKGQIEAAKALGLTRAQRFRLIVFPQAIRTILPPLGNDFVALVKDSSLVSVLGVADI 220 Query: 350 VAVGGTILNQTGQSIEIVSIWLIVYLSLSLATSLFMNWYNARM 392 +G + + E SI +YL L++ SL + R+ Sbjct: 221 TQMGKVYAAGSFRFFETYSITAYIYLILTVGLSLALRALERRL 263 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: 243 Number of extensions: 9 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: 269 Length adjustment: 28 Effective length of query: 369 Effective length of database: 241 Effective search space: 88929 Effective search space used: 88929 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 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