Align lysine-specific permease (characterized)
to candidate WP_033100257.1 JG50_RS0106285 amino acid permease
Query= CharProtDB::CH_003129 (489 letters) >NCBI__GCF_000763315.1:WP_033100257.1 Length = 446 Score = 280 bits (716), Expect = 7e-80 Identities = 159/410 (38%), Positives = 237/410 (57%), Gaps = 25/410 (6%) Query: 13 LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTSLGEL 72 L+++L RH+ M+A+GG+IG G+F S TIS AGPG + SY L G+++Y +M+++ E+ Sbjct: 5 LQKQLLPRHVQMMALGGAIGAGIFQGSAETISAAGPG-VIFSYALAGILLYIVMSAMAEM 63 Query: 73 AAYMPVSGSFATYGQNYVEEGFG----FALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDT 128 A G T + V + FG F LGW Y+ W + +AV++V A + +WF Sbjct: 64 AL-----GFAGTDLRGLVHKAFGTRVSFILGWLYFIQWVLVMAVEIVTAGTFLQYWF-SV 117 Query: 129 PGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQPA 188 P W+ S + VI +N SVR FGE EYW + +K+ T+IVF+I+G L++ GI AQ Sbjct: 118 PVWLLSLIVTLVIIAINLFSVRLFGEIEYWLTSVKIVTLIVFVILGALLLFGIIPSAQAP 177 Query: 189 GWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFWR 248 G +N+ + F G+ ++ +IV FS+ GTE+IG+ E +D K +PR ++ V R Sbjct: 178 GLTNYRVHGGFFPLGWQGVLSSLLIVIFSYGGTEMIGLTITEMKDAKKTLPRVIKGVILR 237 Query: 249 ILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAV 308 I LFYV +LII+ +IP+ D S SPF V GL A +MN ++LTAV Sbjct: 238 ICLFYVLPLLIITGLIPW--------DQVKSSGSPFVEVLSAVGLKGVANIMNFILLTAV 289 Query: 309 LSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGNQ 368 +SA NSGMYA+TRMLY+LA + +AP F +L + GVP AL A++V L L + + Sbjct: 290 ISAANSGMYATTRMLYSLAGEKEAPAFFTRLGKRGVPIYALAASSVCLFLGSLVAFIAPE 349 Query: 369 TVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFP 418 +V+ +L+ G T + W+ I +SH + R Y +R FFP Sbjct: 350 SVFQYLMGIPGYTVILTWILICLSHLKLRGKYE------RTPDFRLSFFP 393 Lambda K H 0.327 0.142 0.451 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: 660 Number of extensions: 47 Number of successful extensions: 5 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: 489 Length of database: 446 Length adjustment: 33 Effective length of query: 456 Effective length of database: 413 Effective search space: 188328 Effective search space used: 188328 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: 51 (24.3 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