Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= reanno::pseudo5_N2C3_1:AO356_00470 (220 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 121 bits (304), Expect = 2e-32 Identities = 70/209 (33%), Positives = 120/209 (57%), Gaps = 14/209 (6%) Query: 19 WAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRF----YVDLIRGTPVFVLV 74 W+G L ++ +L+++V L G++L GR R+ Y++L RG P+ ++ Sbjct: 188 WSGLLLTLATALISMVCS----LPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTIL 243 Query: 75 LACFYMAPAL---GWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIGLT 131 M P + W+I ++GLT+F +++AE VRG LQA+P+GQ EA+ A+GL Sbjct: 244 FFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLN 303 Query: 132 FYQSLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMT--- 188 +Q+ +++LPQALR +P V +++ +TLLS++G+ ELL ++ I+A Sbjct: 304 LFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRY 363 Query: 189 LEFYLFAGFLFFIINYAIELLGRHIEKRV 217 E YLF G L+++ Y + L R +E+R+ Sbjct: 364 AEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392 Lambda K H 0.330 0.142 0.443 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: 364 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 220 Length of database: 396 Length adjustment: 26 Effective length of query: 194 Effective length of database: 370 Effective search space: 71780 Effective search space used: 71780 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 (21.8 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