Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 214 bits (545), Expect = 3e-60 Identities = 125/307 (40%), Positives = 178/307 (57%), Gaps = 13/307 (4%) Query: 14 GALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVNDLPPR 73 G ++ G+ L+V E +AL+GPSG GK+T LR IAGLE S G+I IG + V + + Sbjct: 16 GKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRIGEQMVFESAKK 75 Query: 74 A------RNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDLAHLL 127 R + VFQSYAL+PH TV EN+ + LK+ P EI+ RV E A L L L Sbjct: 76 IEVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQRVQEVLANLGLGDLS 135 Query: 128 ERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATM 187 ER P QLSGGQ+QRVA+ R++V P V L DEPLSNLDAKLR + R +++L + + Sbjct: 136 ERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARIWLRQLIIDLNLSA 195 Query: 188 IYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEEAVLT 247 + VTHDQ EAM ++D++V+++DG IEQ GTP++++ P + FVA F+G+ Sbjct: 196 VCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFMGANNTISGLVTDV 255 Query: 248 DGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAVHEIELPVT 307 DG A G L R R+ ++ G + T +R + + + + LP+T Sbjct: 256 DGDSARIEGNGWALRGRLRTPLKAGDRATAVVRLEKI-------KLAQTPKENSLRLPLT 308 Query: 308 ITEPLGN 314 + LGN Sbjct: 309 ASVYLGN 315 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: 310 Number of extensions: 11 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: 365 Length of database: 353 Length adjustment: 29 Effective length of query: 336 Effective length of database: 324 Effective search space: 108864 Effective search space used: 108864 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 Apr 09 2024. 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