Align lysine-specific permease (characterized)
to candidate N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__Dyella79:N515DRAFT_3653 Length = 453 Score = 270 bits (689), Expect = 1e-76 Identities = 158/460 (34%), Positives = 241/460 (52%), Gaps = 27/460 (5%) Query: 13 LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTSLGEL 72 L+R L RH+T +A+G +IG GLF+ S I+ AGP L +Y+ G M++ +M +LGE+ Sbjct: 5 LQRRLTPRHITFMALGMAIGAGLFLGSANAINLAGPS-VLFAYLFGGAMIFIIMRALGEM 63 Query: 73 AAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDTPGWI 132 A + PV+GSF+TY Y+ G+ GWNYW + A + M WFP+ P WI Sbjct: 64 AVHDPVAGSFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQWFPELPQWI 123 Query: 133 WSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMI-IGIFKGAQPAGWS 191 W + +I LN ++V+ +GE E+WF+LIKV TV++ I+ G MI +G G QP G + Sbjct: 124 WVFGSVAMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGNGGQPVGLA 183 Query: 192 N-WTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFWRIL 250 N W+ G F GF M+ +V F+F G E IG+AAGE+ P + IPRAV V WRIL Sbjct: 184 NLWSHG-GWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWRIL 242 Query: 251 LFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAVLS 310 +FYV A+ +I I P+ D SPF F G+ AA ++N V++TA LS Sbjct: 243 IFYVGALFVIMAIYPW--------DQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALS 294 Query: 311 AGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGNQTV 370 NS ++ +RMLY+L+ +AP ++S GVP A+ T + + + + Sbjct: 295 GFNSTTFSGSRMLYSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERI 354 Query: 371 YLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIFAFILCLI 430 + +++ W+ + I+HY FRR H P R+ +PL + + Sbjct: 355 FAMMMSILAFNTVWTWMMVLIAHYSFRR-----RHGATAFPLRA--WPLTSVVCLLFLAF 407 Query: 431 ITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGYKLI 470 + Y A + A Y+G +++ Y+L+ Sbjct: 408 VLFMLGYSADTR--------VALYVGAGWVVLLSLAYRLL 439 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: 790 Number of extensions: 54 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: 453 Length adjustment: 33 Effective length of query: 456 Effective length of database: 420 Effective search space: 191520 Effective search space used: 191520 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 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