Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized)
to candidate PfGW456L13_1896 Glucose ABC transport system, inner membrane component 2
Query= reanno::Smeli:SMc02871 (279 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1896 Length = 281 Score = 135 bits (340), Expect = 1e-36 Identities = 85/281 (30%), Positives = 141/281 (50%), Gaps = 7/281 (2%) Query: 1 MSKARASFMRTGAVHAALIAYTLIALFPVFLTIVNSFKSRNAIFREPLAVPTPETFSLIG 60 + K+ SF R A++A L+ + L P+ + ++ SFKS I R + P IG Sbjct: 5 LGKSGISFSRI-AIYATLLLAAAVYLIPLVVMLLTSFKSPEDI-RTGNLLSWPTVIDGIG 62 Query: 61 YETVLKQGDFIG-YFQNSIIVTVVSIALVLLFGAMAAFALSEYRFRGNTLMGLYLALGIM 119 + +K D +G YF NS+ +TV ++ + GAM + LS +RFRG+ L L G Sbjct: 63 W---IKAWDVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCF 119 Query: 120 IPIRLGTVAILQGMVATGLVNTLTALILVYTAQGLPLAVFILSEFMRTVSDDLKNAGRID 179 +P + + + GL NT T L+LV+ GL + ++ D L A R+D Sbjct: 120 LPFQTVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLD 179 Query: 180 GLSEYAIFLRLVLPLIRPAMATVAVFTMIPIWNDLWFPLILAPAEATK-TVTLGSQIFIG 238 G + IFL+++LP+ P + ++ IWND F ++ A +A TV L + + Sbjct: 180 GAGFFTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTS 239 Query: 239 QFVTNWNAVLSALSLAIFPVLVLYVIFSRQLIRGITAGAVK 279 +N ++A +A P L++Y+ + +RG+T+GAVK Sbjct: 240 TGAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVK 280 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: 255 Number of extensions: 17 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: 279 Length of database: 281 Length adjustment: 26 Effective length of query: 253 Effective length of database: 255 Effective search space: 64515 Effective search space used: 64515 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