Align Lysine permease LysP (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family
Query= SwissProt::A2RNZ6 (508 letters) >lcl|FitnessBrowser__Burk376:H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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