Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate GFF1065 PS417_05405 D-alanine/D-serine/glycine permease
Query= TCDB::K7VV21 (488 letters) >FitnessBrowser__WCS417:GFF1065 Length = 472 Score = 303 bits (777), Expect = 7e-87 Identities = 180/463 (38%), Positives = 267/463 (57%), Gaps = 27/463 (5%) Query: 13 VKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFLMTSLGEM 72 +KR L RH+ ++ALG IG GLFL S I AGP + +Y++ G + +M +LGEM Sbjct: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGP-AIMLSYIIGGLAILVIMRALGEM 76 Query: 73 ATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFWLPDVPSWI 132 A + P +GSFS Y Y+ P GF GWNYW W +T ++TAVA+ + W PD P WI Sbjct: 77 AVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWI 136 Query: 133 FSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSIFGIMGGHIDVAKNL 192 ++L ALI + SIN ++VK FGE E+W + IKI V ++ ++IG + I G+ VA L Sbjct: 137 WALAALISMGSINLIAVKAFGEFEFWFALIKI-VTIIAMVIGGVGIIAFGFGNDGVA--L 193 Query: 193 SVGNHGFVGGLGSFTTGG--GILGVLLVAGFSFQGTELLGITAGEAENPEKSIPKAMNSI 250 + N + G F G G+L L + F++ G E++G+TAGEA+NP+K+IP A+ S+ Sbjct: 194 GISN---LWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSV 250 Query: 251 FWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASIMNAVVLTS 310 FWRIL+FY+ ++FV+ +I P+ + G SPF + FER+G AA I+N VV+T+ Sbjct: 251 FWRILLFYVGALFVILSIYPWNEIGTQG------SPFVMTFERLGIKTAAGIINFVVITA 304 Query: 311 VVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIALLATTAVALL-TFLTSIYG 369 +S+ N G++++ RMLYSLA++G AP F+KTS NG+P ALL + LL L + Sbjct: 305 ALSSCNGGIFSTGRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVP 364 Query: 370 VSFFTFLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFPFGPILALIM 429 F ++ S + W+ I ++ +FR++ + L Y L+P LAL Sbjct: 365 EKVFVWVTSIATFGAIWTWLMILLAQLKFRKS--LSPAEQAGLKYRMWLYPVSSYLALAF 422 Query: 430 TVLVTLGQDPMLLFGKTWVQGVVMYAAIPLFFIL--YLGYKFK 470 +LV M F T + +Y P+F +L L Y FK Sbjct: 423 LLLVV---GLMAYFPDT---RIALYVG-PVFLVLLTVLFYVFK 458 Lambda K H 0.326 0.141 0.425 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: 587 Number of extensions: 30 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: 488 Length of database: 472 Length adjustment: 34 Effective length of query: 454 Effective length of database: 438 Effective search space: 198852 Effective search space used: 198852 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 (21.6 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