Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized)
to candidate GFF773 PGA1_c07870 alpha-glucoside transport system permease protein AglF
Query= reanno::Smeli:SMc02872 (315 letters) >FitnessBrowser__Phaeo:GFF773 Length = 335 Score = 126 bits (316), Expect = 8e-34 Identities = 94/309 (30%), Positives = 153/309 (49%), Gaps = 28/309 (9%) Query: 13 IKRPRRWHILVFLLPALVVYTAVMILPLFETLRQSFYNTVDGQLT-FVGLGNFKVLFGDP 71 I+R +FL PAL+ + P+ ETLR S V G + FVGL N++ + + Sbjct: 45 IRRANMIRPWLFLFPALLALGLYLAYPVVETLRLSVTERVPGGGSEFVGLANYQQMLAE- 103 Query: 72 RWAADFWNALKNNFVFFLIHMAVQNPIGIALAAMLSVPKLRFGAFYRTAIFLPTLLSFVI 131 A FW AL+NNF++ L+ A G+ LAA L+ +L +G ++ IF+P +SFV Sbjct: 104 ---AKFWEALQNNFLWLLVVPAASTAFGL-LAAQLT-DRLAWGNIAKSLIFMPMAISFVG 158 Query: 132 VGFIWKLILSPIWGVAPYLLDTVG-LRSLF------GP--WLGKPDTALIAVSLISVWQY 182 IWKL+ + P D +G L +L+ GP WL P + ++ +W Sbjct: 159 AAVIWKLV----YDARPEGTDQIGVLNALYIYFGGDGPMQWLTIPFWNSFFLMMVLIWIQ 214 Query: 183 IGIPMMLIYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGIVSILTFVGNFNA 242 G M+++ AAL IP+E EAA +DG + F+KIK+P I+ I +V + Sbjct: 215 TGFAMVILSAALRGIPEETVEAAIVDGAGPFQIFFKIKVPQIMDTIVVVWTTITIVVLKV 274 Query: 243 FDLIYTVQGALAGPDKSTDILGTLLYRTFFGFQLQLGDRSMGATIAAIMFLIILAGVALY 302 FD+++ A+ T +L +Y F + D +G+ A ++ L++L + Sbjct: 275 FDIVF----AMTNGQWETQVLANYMYDKLF----RANDWGVGSASAMVIMLLVLPILVWN 326 Query: 303 LFGIQRRMR 311 ++ +R MR Sbjct: 327 VYNARREMR 335 Lambda K H 0.331 0.146 0.461 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: 340 Number of extensions: 18 Number of successful extensions: 4 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: 315 Length of database: 335 Length adjustment: 28 Effective length of query: 287 Effective length of database: 307 Effective search space: 88109 Effective search space used: 88109 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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