Align lysine-specific permease (characterized)
to candidate WP_058929813.1 AU252_RS05225 amino acid permease
Query= CharProtDB::CH_003129 (489 letters) >NCBI__GCF_001484605.1:WP_058929813.1 Length = 470 Score = 263 bits (672), Expect = 1e-74 Identities = 152/428 (35%), Positives = 234/428 (54%), Gaps = 15/428 (3%) Query: 8 TEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMT 67 T L LK R LTM+ +G +IG GLF+ SGA I AGP L+SY++ G ++ +M Sbjct: 7 TSGRALGAALKPRQLTMMGLGSAIGAGLFIGSGAGIQAAGPA-VLISYLVAGTLIILVMW 65 Query: 68 SLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPD 127 +LGE+AA P SG+F+ Y G +GW +W V IA + + A ++S FP Sbjct: 66 ALGEMAAANPDSGAFSVYTAKAYGPVAGATVGWLWWLQLVVVIAAEALGAAGLLSTIFPA 125 Query: 128 TPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQP 187 P W+ + +F+ V+ +N SV+ FGE E+WF+L+KV ++ F++VG ++ G G Q Sbjct: 126 LPVWLMAFVFIVVLTAVNLTSVKNFGEFEFWFALLKVAAIVGFLLVGAALLFGWLPGVQS 185 Query: 188 AGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFW 247 G +N+T G+ GFA + +V F+F GTE++ +AA E+ +PA+++ AVR V W Sbjct: 186 PGLANFT-GDGFAPDGFAGIATALFVVAFAFGGTEIVSVAAAETAEPARSVRTAVRTVLW 244 Query: 248 RILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTA 307 RIL+FY+ AI +I+ ++P L SPF V + AG+ AA + V + A Sbjct: 245 RILVFYIGAIFVIAAVVPVGSAGL---------KSPFAAVLEAAGMPGAATAITLVAVAA 295 Query: 308 VLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGN 367 +LSA N+ +Y ++RM Y+LA G+APR+ A +S+ VP A+ A+ + + + Sbjct: 296 LLSALNANLYGASRMAYSLADRGEAPRLLASVSKARVPVVAVLASVAFGVVTVVLELAFP 355 Query: 368 QTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIFA-FI 426 + V LLN G T + W ++ R +G +LP R FP F I Sbjct: 356 EKVLPVLLNIVGSTCLLVWTSALLAQLALRLRANREG---TELPLRMPGFPWLTCFGLLI 412 Query: 427 LCLIITLG 434 L I T+G Sbjct: 413 LAAIFTVG 420 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: 663 Number of extensions: 46 Number of successful extensions: 4 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: 470 Length adjustment: 34 Effective length of query: 455 Effective length of database: 436 Effective search space: 198380 Effective search space used: 198380 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 Apr 09 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