Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_085638697.1 MGEO_RS13240 ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >NCBI__GCF_002115805.1:WP_085638697.1 Length = 240 Score = 223 bits (567), Expect = 3e-63 Identities = 111/229 (48%), Positives = 155/229 (67%), Gaps = 1/229 (0%) Query: 4 DYNVIWEALPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIR 63 D+ +I++ L + G TL+L L+LL G L A+PL + R ++P++N W YTY R Sbjct: 2 DFMLIFDNLDRFVEGAWVTLQLTFLALLLGGLIAIPLAIARAYRKPVLNPIIWGYTYAFR 61 Query: 64 GTPMLVQLFLIYYGLAQFEAVRESFLW-PWLSSATFCACLAFAINTSAYTAEIIAGSLRA 122 GTP+LVQ +L Y+GL QFEAVR SFLW P LS +C +AF +NT+AYT E + G++ Sbjct: 62 GTPLLVQTYLFYFGLGQFEAVRNSFLWSPILSDPWWCVLIAFTLNTAAYTTEFLRGAIET 121 Query: 123 TPNGEIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITG 182 TP GEIEAAKA GMS + + ++LPSA RRALP YSNEVI L + +AS VTL D+ G Sbjct: 122 TPRGEIEAAKAAGMSPWTRMRLVVLPSAFRRALPAYSNEVIFTLHGSVIASTVTLQDLLG 181 Query: 183 AARTVNAQYYLPFEAYITAGVFYLCMTFILVRLFKMAEHRWLGYLAPRK 231 R +N +YYL +E ++TA +FY+ + F++ F+ AE R+L +L PR+ Sbjct: 182 VGRWLNGRYYLAYEGFVTAMLFYMAIVFMISLAFRYAEKRYLKHLRPRE 230 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: 165 Number of extensions: 5 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: 240 Length adjustment: 23 Effective length of query: 209 Effective length of database: 217 Effective search space: 45353 Effective search space used: 45353 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 24 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