Align lysine-specific permease (characterized)
to candidate WP_057509355.1 ABB28_RS14795 amino acid permease
Query= CharProtDB::CH_003129 (489 letters) >NCBI__GCF_001431535.1:WP_057509355.1 Length = 460 Score = 228 bits (581), Expect = 3e-64 Identities = 142/425 (33%), Positives = 225/425 (52%), Gaps = 16/425 (3%) Query: 11 PGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTSLG 70 P L LK R L M+ +G +IG GLF+ SG + AGP LLSY++ G +V +M +LG Sbjct: 14 PRLGHALKPRQLIMMGLGSAIGAGLFLGSGVGVQLAGPA-VLLSYLVAGALVIIVMNALG 72 Query: 71 ELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDTPG 130 E+AA P SG+F+ Y + + G +GW +W + IA + V A +++ + Sbjct: 73 EMAANKPTSGAFSVYAADALGPTAGATVGWLWWVQLVIVIAAEAVGAAGLLATVWTGLSV 132 Query: 131 WIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQPAGW 190 + + F+ +N + V+ FGE E+WF+++KV ++ FI +G +++G A G Sbjct: 133 PMAALAFMLFFTAINLLGVKNFGEFEFWFAILKVAAILGFIAIGAALLLGWLPDATSPGL 192 Query: 191 SNWTIGEAPFAGGFAAMIGVAMIVG-FSFQGTELIGIAAGESEDPAKNIPRAVRQVFWRI 249 SN+T G FA A +G A++V F+F GTE++ +AA E+EDP ++I RA+R V WRI Sbjct: 193 SNFT-GNGGFAPTGLAGVGAALLVVIFAFGGTEIVAVAAAETEDPERSIARAIRTVAWRI 251 Query: 250 LLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAVL 309 L+FY+ ++ +I ++P+T +L SPF V + A + A + V + A+L Sbjct: 252 LVFYIGSLSVIIAVVPWTSEAL---------KSPFAAVLEAANIPGAGTAITLVAVIALL 302 Query: 310 SAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGNQT 369 SA N+ +Y ++RM+++LA +AP + R VP A+ A+ + + + Sbjct: 303 SALNANLYGASRMIFSLAQRREAPAVLGWADRRQVPVLAVLASVLFGFAATVMELVFPDR 362 Query: 370 VYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFP-LGPIFAFILC 428 V LLN G T + W +S RR G LP+R FP L + IL Sbjct: 363 VLPVLLNIVGSTCLLVWTLSLLSQLVLRRRADRAG---VALPFRMAAFPWLTALALAILA 419 Query: 429 LIITL 433 LI L Sbjct: 420 LIFAL 424 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: 649 Number of extensions: 41 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: 460 Length adjustment: 33 Effective length of query: 456 Effective length of database: 427 Effective search space: 194712 Effective search space used: 194712 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