Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate SMa0079 SMa0079 ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_00475 (220 letters) >FitnessBrowser__Smeli:SMa0079 Length = 222 Score = 139 bits (349), Expect = 6e-38 Identities = 75/198 (37%), Positives = 114/198 (57%) Query: 3 YQLNFAAVWRDFDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVT 62 Y+ NFA V FD LL G L + L+ ++ IG V+ + A+ + +LR + Y+ Sbjct: 2 YEFNFAPVLASFDQLLVGAWLTVRLSCAAMLIGLVVSVFCAWGKTAGPAILRHVIDGYIE 61 Query: 63 VIRNTPILVLILLIYFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQRE 122 +IRNTP LV I I+F +PSLG+RL + ++ L + GAY TE+ R G+ SIHKGQ E Sbjct: 62 IIRNTPFLVQIFFIFFGMPSLGLRLSPNSAALLALVVNFGAYGTEIIRAGIESIHKGQVE 121 Query: 123 AGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINV 182 AG A+GL Q+ YV + LR V PAL++ FI L +TS+ + I+ +L + Sbjct: 122 AGWALGLSRPQIFRYVVMKPALRTVYPALTSQFIYLMLNTSVVSVISADDLAAAGNDLQS 181 Query: 183 ESYRVIETWLVTTALYVA 200 ++ E ++ T +Y+A Sbjct: 182 ATFASFEVYIAVTLIYLA 199 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: 135 Number of extensions: 6 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: 222 Length adjustment: 22 Effective length of query: 198 Effective length of database: 200 Effective search space: 39600 Effective search space used: 39600 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