Align Lysine permease LysP (characterized)
to candidate RR42_RS33495 RR42_RS33495 aromatic amino acid transporter
Query= SwissProt::A2RNZ6 (508 letters) >FitnessBrowser__Cup4G11:RR42_RS33495 Length = 465 Score = 285 bits (728), Expect = 3e-81 Identities = 173/480 (36%), Positives = 264/480 (55%), Gaps = 32/480 (6%) Query: 20 ILENSSNSTTETQVKRALKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIG 79 ++ N+S++T T +KR LK+RH+ +IALGG IGTGLFL I AGP L Y + G Sbjct: 1 MVPNASDNTDAT-LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGP-SVLLGYAVAG 58 Query: 80 AMVYFLMTSLGEMATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVAL 139 + +F+M LGEM P +GSFS + +Y GF GWNYW+ + + +L+AV + Sbjct: 59 IIAFFIMRQLGEMVVDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGI 118 Query: 140 CIKFWLPDVPSWIFSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLII-GFLSI 198 +++W P +P+W +L +++ +IN SVK+FGE E+W S +K+ +V ++ G+L Sbjct: 119 YVQYWWPHIPTWASALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLA 178 Query: 199 FGIMGGHIDVAKNLSVGNHGFVGGLGSFTTG-GGILGVLLVAGFSFQGTELLGITAGEAE 257 G G V+ ++ HG G F G G++ + V FSF G EL+GITA EA+ Sbjct: 179 SGTAGPQASVS---NLWQHG-----GFFPNGISGLVMAMAVIMFSFGGLELVGITAAEAD 230 Query: 258 NPEKSIPKAMNSIFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFS 317 PEK+IPKA N + +RIL+FY+ ++ V+ ++ P+ + + GG SPF ++F + Sbjct: 231 EPEKTIPKATNQVIYRILIFYVGALGVLLSLYPW-EKVVTGG-----SPFVLIFHAMNSD 284 Query: 318 IAASIMNAVVLTSVVSAANSGMYASTRMLYSLAKDGGAPKIFSKTSKNGIPFIAL-LATT 376 I A+++NAVVLT+ +S NSG+Y ++RML+ LAK G APK K +K GIP AL ++ Sbjct: 285 IVATVLNAVVLTAALSVYNSGVYCNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSAL 344 Query: 377 AVALLTFLTSIYGVSFFTLLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDV--KKLPY 434 A A + F LL+ I W I+I H +FRR A G++ K L Y Sbjct: 345 ATAACVVINYFMPGEAFELLMGLVVSALIINWAMISIIHLKFRRDKRAAGQETRFKSLGY 404 Query: 435 HAKLFPFGPILALIMTVLVTLGQDPMLLFGKTWVQGVVMYAAIPLFFILYLGYKFKNKTK 494 + LA + +L + P L + +Y +L L Y+ + K K Sbjct: 405 PLTNY---VCLAFLAGILYVMYLTPGL--------RISVYLIPAWLAVLGLSYRLRQKQK 453 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: 563 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: 508 Length of database: 465 Length adjustment: 34 Effective length of query: 474 Effective length of database: 431 Effective search space: 204294 Effective search space used: 204294 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