Align lysine-specific permease (characterized)
to candidate RR42_RS11100 RR42_RS11100 gamma-aminobutyrate permease
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__Cup4G11:RR42_RS11100 Length = 509 Score = 668 bits (1724), Expect = 0.0 Identities = 321/475 (67%), Positives = 384/475 (80%) Query: 9 EAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTS 68 E L+R+LKARHLTMIAIGG++GTGLFVASGA+ISQAGPGGALL Y LIGLMVY LMTS Sbjct: 14 EHDDLQRKLKARHLTMIAIGGAVGTGLFVASGASISQAGPGGALLMYCLIGLMVYCLMTS 73 Query: 69 LGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDT 128 LGELA +MPV+GSF TY YVEEGFGFALGW+YW++ AVTIAV+L AAQLVM +WFP Sbjct: 74 LGELAVHMPVAGSFVTYSALYVEEGFGFALGWSYWFSLAVTIAVELAAAQLVMQYWFPHV 133 Query: 129 PGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQPA 188 G +WSA FL ++F LN SVRGFGEAEYWF+LIKV T+++F+ G++MI GI +G + Sbjct: 134 SGVVWSAGFLLLMFGLNAFSVRGFGEAEYWFALIKVATILIFLAAGLMMIFGIMQGGPQS 193 Query: 189 GWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFWR 248 GW N+T+G+APF GG AM GVAMI GFSFQGTE +G+AAGE+ DPA+ IPRA+RQ FWR Sbjct: 194 GWHNFTLGDAPFVGGIPAMFGVAMIAGFSFQGTETVGVAAGEAADPARTIPRAIRQTFWR 253 Query: 249 ILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAV 308 ILLFYV AILII ++IPYTDPSLLRNDV DI VSPF LVF+HAGL AA +MNAV+LTA+ Sbjct: 254 ILLFYVLAILIIGVLIPYTDPSLLRNDVTDIGVSPFALVFRHAGLAFAAGLMNAVVLTAL 313 Query: 309 LSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGNQ 368 LSAG S MYASTR+LY LA G+APR A+LS GVP AL+ATT + LCFL+S+FG++ Sbjct: 314 LSAGTSSMYASTRILYGLAVSGRAPRALARLSANGVPYVALFATTAVGALCFLSSLFGDK 373 Query: 369 TVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIFAFILC 428 VYLWLLNTSGMTGFIAWLGIAISHYRFRRG V QG+ +DL YRS +P GP+FA +LC Sbjct: 374 AVYLWLLNTSGMTGFIAWLGIAISHYRFRRGLVHQGYKPSDLAYRSPLYPFGPLFAIVLC 433 Query: 429 LIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGYKLIKGTHFVRYSEMKF 483 ++I LGQNY+AF W + TYIG+PLFL++W GY+L+K T + Y +M F Sbjct: 434 VVIVLGQNYQAFSDVRGRWLEIVGTYIGVPLFLVLWLGYRLVKKTRLIDYEDMPF 488 Lambda K H 0.327 0.142 0.451 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: 916 Number of extensions: 33 Number of successful extensions: 1 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: 489 Length of database: 509 Length adjustment: 34 Effective length of query: 455 Effective length of database: 475 Effective search space: 216125 Effective search space used: 216125 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