Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 203 bits (517), Expect = 5e-57 Identities = 105/235 (44%), Positives = 155/235 (65%), Gaps = 10/235 (4%) Query: 6 LKKLVKRYG--ALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63 L ++ K++ +L V + E++ E + LVGPSGCGK+T LRMIAG E + G+I++ Sbjct: 9 LDRVCKQFSGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLA 68 Query: 64 GRKV----NDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119 G V LPP R++ MVFQ YAL+PH+TV +N+ F L+ A + +A A Sbjct: 69 GETVATAQRSLPPETRSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSAAVAR----QALA 124 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 ++ L L R P +LSGGQ+QRVA+ RA+ QP + L DEPLSNLD ++R ++R E++ + Sbjct: 125 LVGLEGLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDI 184 Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFI 234 + QAT I VTHDQ EA+++ DR+ +MR G EQ+G PE++F+ PA++FVA F+ Sbjct: 185 LRQAQATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFL 239 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: 333 Number of extensions: 14 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: 368 Length adjustment: 30 Effective length of query: 335 Effective length of database: 338 Effective search space: 113230 Effective search space used: 113230 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