Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate SMc00138 SMc00138 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >FitnessBrowser__Smeli:SMc00138 Length = 276 Score = 148 bits (373), Expect = 1e-40 Identities = 79/216 (36%), Positives = 126/216 (58%), Gaps = 2/216 (0%) Query: 13 PLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPMLVQLF 72 P + GL TL L+ S+L G + +LP+ L R+SK + A+ Y Y RGTP++ QLF Sbjct: 60 PSFLSGLGVTLTLVISSILMGAVLSLPVALGRMSKNRLWGWLAYAYVYFFRGTPLITQLF 119 Query: 73 LIYYGLAQFEAVRESF-LWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAA 131 LIYYGL F E+ LW + A CA F +NT+AY AEI+ G++ + P G+ E A Sbjct: 120 LIYYGLGSFRPQLETVGLWWFFRDAWNCALFTFTLNTAAYQAEILRGAIESVPRGQREGA 179 Query: 132 KAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQY 191 A+G+ + +++LP A+ AL Y NE+I+M++ +++ +IVT+ D+ G R ++ Sbjct: 180 AALGLPERVAFFKVILPQAMIVALRPYGNEIILMIKGSAIVAIVTVFDLMGETRRAFSRT 239 Query: 192 YLPFEAYITAGVFYLCMTFILVRLFKMAEHRWLGYL 227 + ++ YI A + YL M +L ++ E R +L Sbjct: 240 F-DYQMYIWAAILYLLMVELLRNIWGWLEARLTRHL 274 Lambda K H 0.329 0.139 0.427 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: 167 Number of extensions: 11 Number of successful extensions: 2 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: 232 Length of database: 276 Length adjustment: 24 Effective length of query: 208 Effective length of database: 252 Effective search space: 52416 Effective search space used: 52416 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 (21.8 bits) S2: 46 (22.3 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