Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized)
to candidate SM_b21459 SM_b21459 sugar uptake ABC transporter permease
Query= reanno::Smeli:SMc02872 (315 letters) >FitnessBrowser__Smeli:SM_b21459 Length = 297 Score = 135 bits (339), Expect = 2e-36 Identities = 96/299 (32%), Positives = 146/299 (48%), Gaps = 17/299 (5%) Query: 13 IKRPRRWHILVFLLPALVVYTAVMILPLFETLRQSF---YNTVDGQLTFVGLGNFKVLFG 69 ++R +R +FLLP L+ AV I PL ++ SF Y FVG+ NF + Sbjct: 7 MERQQRRTAWIFLLPLLLTLMAVAIWPLARSIFFSFTDAYLDAPSDYGFVGIENFVEVAE 66 Query: 70 DPRWAADFWNALKNNFVFFLIHMAVQNPIGIALAAMLSVPKLRFGAFYRTAIFLPTLLSF 129 DP FW A++N VF L+ + ++ +G+A+A +L L G R AI +P + Sbjct: 67 DPV----FWGAVRNTLVFTLVSVGLETLLGLAIALLLHRAFLGRG-IVRAAILIPWAMPM 121 Query: 130 VIVGFIWKLILSPIWGVAPYLLDTVGLRSLFGPWLGKPDTALIAVSLISVWQYIGIPMML 189 V+ IW+ +L+ +G+ LL +GL W P L V I VW ++L Sbjct: 122 VVSARIWEWMLNDQFGLINKLLVALGLVEKGVAWTADPSLILGTVIFIDVWVTTPFMVLL 181 Query: 190 IYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGIVSILTFVGNFNAFDLIYTV 249 I A L IP+E+ EAA++ GV W +FW I LPL PAIG+ + + FDL Y Sbjct: 182 ILAGLQLIPEEIYEAADVSGVPQWKRFWSITLPLATPAIGVAILFRTLDALRMFDLSY-- 239 Query: 250 QGALAGPDKSTDILGTLLYRTFFGFQLQLGDRSMGATIAAIMFLIILAGVALYLFGIQR 308 LA +++T + FQ D +GA + +F+II +A+ + G+ R Sbjct: 240 --VLAANNENTMTMSIYARDQLISFQ----DLGLGAAASTWVFMII-GLIAIVIVGLLR 291 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: 330 Number of extensions: 22 Number of successful extensions: 2 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: 297 Length adjustment: 27 Effective length of query: 288 Effective length of database: 270 Effective search space: 77760 Effective search space used: 77760 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