Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate WP_011842475.1 RSPH17029_RS18135 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_16280 (223 letters) >NCBI__GCF_000015985.1:WP_011842475.1 Length = 370 Score = 89.7 bits (221), Expect = 7e-23 Identities = 70/226 (30%), Positives = 108/226 (47%), Gaps = 10/226 (4%) Query: 3 LDFSGVV--QAVP-GMWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYV 59 L F GV+ + VP W G+ +T+ L V+ G+ + LLAL R + + ++ ++ Sbjct: 145 LMFGGVLGLRYVPTSEWGGLPLTMLLFTGTVLIGMPVAVLLALGRRAPLPVARGVSVVFI 204 Query: 60 NYFRSIPLLLVITWFYLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQ 119 R +PL+ ++ F F L G + + V +F A Y E++R G+Q Sbjct: 205 EALRGVPLITIL--FVAVNVFPLFLPAGVE--VNKLLRITVGIAIFFACYQAEVIRGGLQ 260 Query: 120 SIPKGQMGAAKALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFL 179 +IP GQ AA +L + Y Q R IILPQA R P + I ++TS V +GL D L Sbjct: 261 AIPTGQYEAAASLSLSYWQTTRRIILPQALRISLPAITNHIIAAMKNTSFVIIIGLFDIL 320 Query: 180 NATRA-SGDIIGRA--NEFLIIAGLVYFTISFAASRLVKRLQKRFA 222 AT A D + R E + VY +A S ++++K A Sbjct: 321 TATTAVMQDPLWRKFYIEAYLFVAAVYLFFGYALSLYARQVEKWIA 366 Lambda K H 0.331 0.143 0.425 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: 155 Number of extensions: 3 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: 223 Length of database: 370 Length adjustment: 26 Effective length of query: 197 Effective length of database: 344 Effective search space: 67768 Effective search space used: 67768 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. 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