Align Probable lysine/arginine permease CAN2; Basic amino acids permease CAN2 (characterized)
to candidate RR42_RS33495 RR42_RS33495 aromatic amino acid transporter
Query= SwissProt::Q59WU0 (568 letters) >FitnessBrowser__Cup4G11:RR42_RS33495 Length = 465 Score = 230 bits (587), Expect = 8e-65 Identities = 147/447 (32%), Positives = 231/447 (51%), Gaps = 45/447 (10%) Query: 57 VKRDLKARHVSMIAIGGTIGTGLFISTGSLLHTTGPVMSLISFLFVTTLAYSVTQSLGEM 116 +KR LK RH+ +IA+GG IGTGLF+ + GP + L+ + +A+ + + LGEM Sbjct: 13 LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSV-LLGYAVAGIIAFFIMRQLGEM 71 Query: 117 TTYIPVSGSFAQFITRWVSKSCGAANGWLYWFSWAITFALELSVVGQVIQYWTDAVPLAG 176 PV+GSF+ F ++ G +GW YW + + ELS VG +QYW +P Sbjct: 72 VVDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWA 131 Query: 177 WISIFFVLLTTFNLFPVKYYGEVEFWIASTKVIAIVGWLIYAFCMVCGAGKTGPVG--FR 234 FF+L+ NL VK +GE+EFW + KV+AIVG +++ ++ +G GP Sbjct: 132 SALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLL-ASGTAGPQASVSN 190 Query: 235 YWRNGYAWGDGMIVSNNGKYAISFINGLINA----VFTFQGTELVAVTAGEAS--PRAIR 288 W++G + +G I+GL+ A +F+F G ELV +TA EA + I Sbjct: 191 LWQHGGFFPNG-------------ISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIP 237 Query: 289 SAIKKVMFRILVFYVLCMLFIGLLVPYNDPKLTQDGGFTRNSPFLIAMENSGTKVLPHIF 348 A +V++RIL+FYV + + L P+ + T SPF++ + ++ + Sbjct: 238 KATNQVIYRILIFYVGALGVLLSLYPW-------EKVVTGGSPFVLIFHAMNSDIVATVL 290 Query: 349 NAVIVTTIISAGNSNVYSGSRILYGLAQAGVAPKFFLKTNKGGVPYFAV----LFTAAFG 404 NAV++T +S NS VY SR+L+GLA+ G APK LK NK G+P A+ L TAA Sbjct: 291 NAVVLTAALSVYNSGVYCNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACV 350 Query: 405 ALGYLACSEDGNKAFTWLLNIIATAGLIAWGFISVSHVRFMNVLRKRGLSRDILPYKAFF 464 + Y E AF L+ ++ +A +I W IS+ H++F R G +K+ Sbjct: 351 VINYFMPGE----AFELLMGLVVSALIINWAMISIIHLKFRRDKRAAGQE---TRFKSLG 403 Query: 465 MPYSAYYAII----IIFIVVLIQGFTV 487 P + Y + I++++ L G + Sbjct: 404 YPLTNYVCLAFLAGILYVMYLTPGLRI 430 Lambda K H 0.326 0.141 0.448 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: 726 Number of extensions: 33 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: 568 Length of database: 465 Length adjustment: 35 Effective length of query: 533 Effective length of database: 430 Effective search space: 229190 Effective search space used: 229190 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