Align Lysine permease LysP (characterized)
to candidate Pf1N1B4_1580 Histidine transport protein (permease)
Query= SwissProt::A2RNZ6 (508 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580 Length = 469 Score = 281 bits (720), Expect = 3e-80 Identities = 160/451 (35%), Positives = 261/451 (57%), Gaps = 24/451 (5%) Query: 33 VKRALKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFLMTSLGEM 92 +KR L +RH+ +ALG IGTGLF S I AGP L AY++ GA V+ +M +LGEM Sbjct: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGP-AVLLAYLIGGAAVFMVMRALGEM 66 Query: 93 ATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFWLPDVPSWI 152 A + P +GSF Y + Y+ P GF LGW Y I D+TA + + FW P+V WI Sbjct: 67 AVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVDRWI 126 Query: 153 FSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGF-LSIFGIMGGHIDVAKN 211 + L + +V +N +VK FGE E+WLS +K+ +V ++ GF + +FGI A + Sbjct: 127 WVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGAQATD 186 Query: 212 LS-VGNHGFVGGLGSFTTG-GGILGVLLVAGFSFQGTELLGITAGEAENPEKSIPKAMNS 269 +S + +HG G G GG++ V F+F G E++G+TAGEA++P++ +P+A+N+ Sbjct: 187 ISNLWSHG-----GFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINA 241 Query: 270 IFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASIMNAVVLT 329 + RIL+FY+L++ V+ +I P+ +G SPF +F+ +G S AA+I+N VV++ Sbjct: 242 VPLRILLFYVLTMLVLMSIFPWQQ---IGSQG---SPFVQIFDNLGISSAATILNIVVIS 295 Query: 330 SVVSAANSGMYASTRMLYSLAKDGGAPKIFSKTSKNGIPFIALLATTAVALL-TFLTSIY 388 + VSA NS ++ + RM+Y LA+ G APK F++ S+NG+P++ ++ ++ LL L + Sbjct: 296 AAVSAINSDIFGAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLI 355 Query: 389 GVSFFTLLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFPFGPI--LA 446 + F L+ S + W+ I + RR+ A+ V +L + +P+ P+ +A Sbjct: 356 PENVFLLIASVATFATVWVWLMILFTQVAMRRSMSAE--QVAQLKFPVPFWPYAPMAAIA 413 Query: 447 LIMTVLVTLGQDP----MLLFGKTWVQGVVM 473 ++ + LG P L+ G W+ +V+ Sbjct: 414 FMLFIFGVLGYFPDTQAALIVGVVWIVLLVL 444 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: 601 Number of extensions: 35 Number of successful extensions: 6 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: 469 Length adjustment: 34 Effective length of query: 474 Effective length of database: 435 Effective search space: 206190 Effective search space used: 206190 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