Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__Dyella79:N515DRAFT_3133 Length = 273 Score = 115 bits (288), Expect = 1e-30 Identities = 82/263 (31%), Positives = 133/263 (50%), Gaps = 10/263 (3%) Query: 21 VVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAFIASLLNS 80 +V + P+ W+L +S + SA P P+ L+ Y L A LLNS Sbjct: 19 LVAVFPLLWMLSVSFMRPGEASALPPPLLPTHATLANYHELFER------AGMGRYLLNS 72 Query: 81 IKVAGMATLAAVVVAVPAAWAVSRTPAVAWS-LYAVIATYMLPPVALAV-PLYMGLAYFG 138 + V+ TL ++ + A +A ++ L+ V+ ++ P +A+ PL++ L Y G Sbjct: 73 LGVSSAITLLSLAFNLMAGYAFAKLRFSGRERLFQVLLGGLVIPAQVAMLPLFLLLKYLG 132 Query: 139 LLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARLDQILRILTLPLAAP 198 L+NS A+V + F +L++ IP ++ AA IDGA +I + LPL P Sbjct: 133 LVNSY--AAVVVPAMATIFGIFLVRQYARGIPDDLMEAARIDGAGELRIFVQIVLPLLKP 190 Query: 199 VMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGRVSDYGLIATAGVLAALP 258 +M T A+F FL AW++F + L+ + Q TL +A+A L+ V D L+ V+ LP Sbjct: 191 IMVTLAIFTFLTAWNDFMWPLIALTGQEHYTLPIALASLSREHVQDSELMMAGSVVTVLP 250 Query: 259 PVLIGLIMQRALISGLTSGGVKG 281 +++ L +QR + GL G VKG Sbjct: 251 VLVLFLALQRYYLQGLLLGSVKG 273 Lambda K H 0.325 0.136 0.402 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: 181 Number of extensions: 3 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: 281 Length of database: 273 Length adjustment: 25 Effective length of query: 256 Effective length of database: 248 Effective search space: 63488 Effective search space used: 63488 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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