Align lysine-specific permease (characterized)
to candidate RR42_RS33780 RR42_RS33780 GABA permease
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__Cup4G11:RR42_RS33780 Length = 474 Score = 273 bits (699), Expect = 7e-78 Identities = 151/409 (36%), Positives = 228/409 (55%), Gaps = 29/409 (7%) Query: 1 MVSETKTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGL 60 M+ + ++ GL+ LK RH+TMIA+GG IG GLFV SG I AGP A++S+++ GL Sbjct: 1 MIHHQQQQQSSGLKHGLKQRHMTMIALGGVIGAGLFVGSGVVIKSAGPA-AVISFLITGL 59 Query: 61 MVYFLMTSLGELAAYMPVSGSFATYGQNY------VEEGFGFALGWNYWYNWAVTIAVDL 114 +V +M LGE+A +P GSF Y + + E GF GW YWY W + +A++ Sbjct: 60 LVVLVMRMLGEMACALPTVGSFYEYAREAWSDRPAMGELAGFLTGWMYWYFWVIVVALEA 119 Query: 115 VAAQLVMSWWFPDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVG 174 VA ++ +W P P W S + L ++ L N ISV+ FGE E+WF+ IKV ++VF+ + Sbjct: 120 VAGASLVQFWLPGVPAWSISLVLLVMLTLTNLISVKSFGEFEFWFASIKVAAIVVFLFLA 179 Query: 175 VLMIIGIFKGAQPAGWSNWTIGEAPFAGGFA------AMIGVAMIVGFSFQGTELIGIAA 228 L ++G++ GA ++ GGFA + G GF F G E++ IAA Sbjct: 180 GLFVLGMWPGATA------SVAHLTVHGGFAPNGIMPVLTGAVAATGFYF-GAEIVTIAA 232 Query: 229 GESEDPAKNIPRAVRQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVF 288 E+ +P K + RA V R+L+FYV ++L++ ++P+ + +P+ Sbjct: 233 AETAEPQKAVARATSSVITRVLVFYVGSVLLVVCLVPWNSAGI---------ATPYVSAL 283 Query: 289 QHAGLLSAAAVMNAVILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNA 348 + +AA +MNAV+LTAVLSA NSG+YAS+RML+ L G AP+ A+LSR GVP A Sbjct: 284 NAMRIPAAAQIMNAVVLTAVLSALNSGLYASSRMLFALTKRGDAPKALARLSRNGVPVRA 343 Query: 349 LYATTVIAGLCFLTSMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFR 397 + T+ + S V+ +L+N+ G ++ IAIS R R Sbjct: 344 ILFATLFGYGAVVMSYVSPDKVFAFLVNSYGTVAIFVYILIAISQLRLR 392 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: 679 Number of extensions: 36 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: 489 Length of database: 474 Length adjustment: 34 Effective length of query: 455 Effective length of database: 440 Effective search space: 200200 Effective search space used: 200200 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