Align Lysine permease LysP (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family
Query= SwissProt::A2RNZ6 (508 letters) >FitnessBrowser__Burk376:H281DRAFT_04042 Length = 506 Score = 299 bits (766), Expect = 1e-85 Identities = 172/481 (35%), Positives = 270/481 (56%), Gaps = 43/481 (8%) Query: 23 NSSNSTTETQVKRALKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMV 82 N N+ + +KR LK+RH+ +IALGG IGTGLFL S V+ AGP + Y + G + Sbjct: 45 NLDNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGP-SMILGYAIGGVIA 103 Query: 83 YFLMTSLGEMATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIK 142 + +M LGEM P +GSFS + +Y GF GWNYW+ + + +LTAV + Sbjct: 104 FMIMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVH 163 Query: 143 FWLPDVPSWIFSLIALIIVFSINALSVKTFGETEYWLSAIKITVVV-LFLIIGFLSIFGI 201 +W P VP+W+ +L+ + +IN +VK +GETE+W + IK+ V+ + L G+L + G Sbjct: 164 YWWPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGH 223 Query: 202 MGGHIDVAKNLSVGN---HGFVGGLGSFTTGGGILGVLLVAGFSFQGTELLGITAGEAEN 258 G ++ S G HGF G+ +L V FSF G EL+GITA EA+ Sbjct: 224 GGPQASISNLWSHGGFFPHGF----------HGLFTMLAVIMFSFGGLELIGITAAEADE 273 Query: 259 PEKSIPKAMNSIFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSI 318 P+KSIPKA+N + +RIL+FYI S+ V+ ++ P+ + +A SPF ++F ++G ++ Sbjct: 274 PQKSIPKAVNQVIYRILIFYICSLAVLLSLYPWNEV------AAGGSPFVMIFSQIGSTL 327 Query: 319 AASIMNAVVLTSVVSAANSGMYASTRMLYSLAKDGGAPKIFSKTSKNGIPFIAL----LA 374 A+++N VVLT+ +S NSG+YA++RMLY LA+ G AP+ K + G+P++A+ LA Sbjct: 328 TANVLNVVVLTAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALA 387 Query: 375 TTAVALLTFLTSIYGVSFFTLLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPY 434 T ++ +L + LV A+ + + W I+++H + RRA VA G + L + Sbjct: 388 TFTCVIVNYLIPAEALGLLMALVVAALV---LNWALISLTHLKSRRAMVAAG---ETLVF 441 Query: 435 HAKLFPFGP--ILALIMTVLVTLGQDPMLLFGKTWVQGVVMYAAIPLFF-ILYLGYKFKN 491 + FP LA + +LV L P L V +P++ +++ GY FK Sbjct: 442 KSFWFPVSNWICLAFMALILVILAMTPGL---------SVSVLLVPVWLVVMWAGYAFKR 492 Query: 492 K 492 + Sbjct: 493 R 493 Lambda K H 0.326 0.141 0.422 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: 594 Number of extensions: 33 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: 508 Length of database: 506 Length adjustment: 34 Effective length of query: 474 Effective length of database: 472 Effective search space: 223728 Effective search space used: 223728 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: 52 (24.6 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