Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized)
to candidate SM_b20327 SM_b20327 trehalosemaltose transporter permease
Query= reanno::Smeli:SMc02871 (279 letters) >FitnessBrowser__Smeli:SM_b20327 Length = 276 Score = 150 bits (378), Expect = 4e-41 Identities = 89/273 (32%), Positives = 141/273 (51%), Gaps = 13/273 (4%) Query: 13 AVHAALIAYTLIALFPVFLTIVNSFKSRNAIFREPLAVPTPETFSLIGYETVLKQGDFIG 72 A +A + L+A+FP + I+ S KS A+FR P SL Y + G F+ Sbjct: 10 AFYALVAVIILVAVFPFYYAILTSLKSGTALFRIDY---WPTDISLANYAGIFSHGTFVR 66 Query: 73 YFQNSIIVTVVSIALVLLFGAMAAFALSEYRFRGNTLMGLYLALGIMIPIRLGTVAILQG 132 NS++V + +A+ LL AA+AL+ RFRG L+ L + M P +A+L G Sbjct: 67 NLGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFP----QIAVLAG 122 Query: 133 MVA----TGLVNTLTALILVYTAQGLPLAVFILSEFMRTVSDDLKNAGRIDGLSEYAIFL 188 + G+ NT ALI Y LP V++L+ FMR + +++ A +DG S + + Sbjct: 123 LFELIRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVIT 182 Query: 189 RLVLPLIRPAMATVAVFTMIPIWNDLWFPLILAPAEATKTVTLGSQIFIG--QFVTNWNA 246 R+ +PL+ PA+ T + I WN+ F L + +TV + + G QF W Sbjct: 183 RVFMPLMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWGN 242 Query: 247 VLSALSLAIFPVLVLYVIFSRQLIRGITAGAVK 279 +++A + P++VL +IF R++I G+TAG VK Sbjct: 243 IMAASVIVTVPLVVLVLIFQRRIISGLTAGGVK 275 Lambda K H 0.330 0.142 0.409 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: 240 Number of extensions: 13 Number of successful extensions: 5 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: 279 Length of database: 276 Length adjustment: 25 Effective length of query: 254 Effective length of database: 251 Effective search space: 63754 Effective search space used: 63754 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: 47 (22.7 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