Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate BPHYT_RS08555 BPHYT_RS08555 ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_00475 (220 letters) >FitnessBrowser__BFirm:BPHYT_RS08555 Length = 219 Score = 155 bits (392), Expect = 6e-43 Identities = 84/202 (41%), Positives = 122/202 (60%) Query: 17 LLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVIRNTPILVLILLI 76 L G L + A++S+ G + G +A +S +RVL +A +YV+V+R TP+LV I +I Sbjct: 14 LAQGAVLTVKFAVLSMIFGLIAGAVLALMGVSHNRVLNWIARIYVSVMRGTPLLVQIFVI 73 Query: 77 YFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQREAGLAIGLGEWQVKA 136 Y+ LPS GI LD P+ VI LS AYL+E RG +L IH GQ A ++GL Q Sbjct: 74 YYGLPSFGISLDPTPAGVIALSANVAAYLSESMRGAILGIHNGQWLAAYSLGLSRRQTLR 133 Query: 137 YVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYRVIETWLVTTA 196 YV P LR +P++SN+ ISL KDTSL + I V EL A++I +Y+ + +L A Sbjct: 134 YVIAPQALRIAVPSMSNSLISLIKDTSLVSVITVTELLRSAQEIIASTYQPLPLYLAAAA 193 Query: 197 LYVAACYLIAMVLRYFEQRLAI 218 +Y C ++ V R++E+RLA+ Sbjct: 194 VYWVLCQVLESVQRWYERRLAL 215 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: 147 Number of extensions: 8 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: 219 Length adjustment: 22 Effective length of query: 198 Effective length of database: 197 Effective search space: 39006 Effective search space used: 39006 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