Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >MicrobesOnline__882:209225 Length = 354 Score = 158 bits (400), Expect = 2e-43 Identities = 90/226 (39%), Positives = 125/226 (55%), Gaps = 14/226 (6%) Query: 17 EVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVNDLPPRARN 76 EV+H ++L E + LVGPSG GK+T LR IAGL+ G I + PP+ Sbjct: 16 EVLHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTIRV-------TPPQGHG 68 Query: 77 --ISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAIL-----DLAHLLER 129 + +VFQ Y L+PH++V EN+ F + G +K RV DLAH+ R Sbjct: 69 GGVVLVFQDYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRAFRLDTDDLAHMASR 128 Query: 130 RPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIY 189 P+QLS GQRQRVA+ RA+V P V L DEP +NLD LR ++ ++ + R + Sbjct: 129 YPAQLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFVRDVVRRFGVATVT 188 Query: 190 VTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIG 235 VTHD EA + DR+ +M G + Q+ P DV+R PA + A F+G Sbjct: 189 VTHDLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARFLG 234 Lambda K H 0.320 0.137 0.397 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: 323 Number of extensions: 21 Number of successful extensions: 3 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: 365 Length of database: 354 Length adjustment: 29 Effective length of query: 336 Effective length of database: 325 Effective search space: 109200 Effective search space used: 109200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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