Align Lysine permease LysP (characterized)
to candidate 14258 b0112 aromatic amino acid transporter (NCBI)
Query= SwissProt::A2RNZ6 (508 letters) >FitnessBrowser__Keio:14258 Length = 457 Score = 305 bits (782), Expect = 2e-87 Identities = 175/467 (37%), Positives = 263/467 (56%), Gaps = 31/467 (6%) Query: 32 QVKRALKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFLMTSLGE 91 Q+KR LK+RH+ +IALGG IGTGLFL S VI +AGP G + Y + G + + +M LGE Sbjct: 10 QLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGP-GIILGYAIAGFIAFLIMRQLGE 68 Query: 92 MATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFWLPDVPSW 151 M P +GSFS + +Y GFA GWNYW+ + + +LTAV I+FW P++P+W Sbjct: 69 MVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTW 128 Query: 152 IFSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSIFGIMGGHIDVAKN 211 + + + +++ +IN +VK FGE E+W + IK+ VV +I G +F GG N Sbjct: 129 VSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGGPQATVSN 188 Query: 212 L----SVGNHGFVGGLGSFTTGGGILGVLLVAGFSFQGTELLGITAGEAENPEKSIPKAM 267 L HGF G++ ++ + FSF G EL+GITA EA+NPE+SIPKA Sbjct: 189 LWDQGGFLPHGFT----------GLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKAT 238 Query: 268 NSIFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASIMNAVV 327 N + +RIL+FYI S+ V+ +++P+T +A SPF ++F +G + A+ +N VV Sbjct: 239 NQVIYRILIFYIGSLAVLLSLMPWTRV------TADTSPFVLIFHELGDTFVANALNIVV 292 Query: 328 LTSVVSAANSGMYASTRMLYSLAKDGGAPKIFSKTSKNGIPFIALLATTAV-ALLTFLTS 386 LT+ +S NS +Y ++RML+ LA+ G APK + K G+P +L + V AL + Sbjct: 293 LTAALSVYNSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINY 352 Query: 387 IYGVSFFTLLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFPFGPILA 446 + S F LL++ I W I+++H +FRRA QG V + P A L+P G + Sbjct: 353 LAPESAFGLLMALVVSALVINWAMISLAHMKFRRAKQEQGV-VTRFP--ALLYPLGNWIC 409 Query: 447 LIMTVLVTLGQDPMLLFGKTWVQGVVMYAAIPLFFILYLGYKFKNKT 493 L+ V +++ T + +Y +L +GY FK KT Sbjct: 410 LLFMAAV------LVIMLMTPGMAISVYLIPVWLIVLGIGYLFKEKT 450 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: 562 Number of extensions: 28 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: 457 Length adjustment: 34 Effective length of query: 474 Effective length of database: 423 Effective search space: 200502 Effective search space used: 200502 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