Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate RR42_RS16450 RR42_RS16450 hypothetical protein
Query= reanno::pseudo5_N2C3_1:AO356_00475 (220 letters) >FitnessBrowser__Cup4G11:RR42_RS16450 Length = 211 Score = 148 bits (373), Expect = 9e-41 Identities = 79/209 (37%), Positives = 122/209 (58%) Query: 5 LNFAAVWRDFDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVI 64 ++F V LL L + LA+V+ G V GL +A S+H VLR A +Y+ + Sbjct: 3 IDFVQVLPYLPILLKAALLTILLAVVTQVCGTVFGLLLALGRDSRHAVLRGAAFIYIWIF 62 Query: 65 RNTPILVLILLIYFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQREAG 124 R TP+L+ + +Y+A P G+RL+ LP+ +I LS+ + AY E+ R G+ ++H+GQREA Sbjct: 63 RGTPVLLHLFFVYYAAPMFGLRLEALPAAIIALSMSSAAYNAEIIRAGIRAVHRGQREAA 122 Query: 125 LAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVES 184 A+G+ ++ +V +P R VLP NFIS K TSLA+ I VPEL A+ I + Sbjct: 123 QAVGMTNPRILRHVILPQATRIVLPPYMGNFISHTKSTSLASVITVPELMLSAQTIYSST 182 Query: 185 YRVIETWLVTTALYVAACYLIAMVLRYFE 213 YR +E + A+Y+A ++ +V +FE Sbjct: 183 YRAVEVLTIAGAIYLALTTVLTLVQLHFE 211 Lambda K H 0.329 0.142 0.414 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: 131 Number of extensions: 3 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: 220 Length of database: 211 Length adjustment: 22 Effective length of query: 198 Effective length of database: 189 Effective search space: 37422 Effective search space used: 37422 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: 45 (21.9 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