Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 155 bits (391), Expect = 2e-42 Identities = 90/219 (41%), Positives = 132/219 (60%), Gaps = 8/219 (3%) Query: 23 DLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVND------LPPRARN 76 D + EF+A+VGPSG GK+T LRMIAGL + G+I G R D P+ R+ Sbjct: 22 DFSCRAGEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQNRH 81 Query: 77 ISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDLAHLLERRPSQLSG 136 I V Q + L+P ++ N+ +L P++E + R A ++L L +R PSQLSG Sbjct: 82 IGFVPQHFGLFPKLSALGNIMAALDHL--PSQERRPRALAALEKVNLHGLTDRLPSQLSG 139 Query: 137 GQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVTHDQVE 196 GQ+QRVA+ RA+ R+P V L DEP S +D + R ++ E+ +L A + +I VTHD E Sbjct: 140 GQKQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDLNE 199 Query: 197 AMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIG 235 A+ L+D ++++ GH+ Q GTP+DVF RP + VA +G Sbjct: 200 ALLLADSMLLISQGHMLQHGTPQDVFSRPRNEAVARQMG 238 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: 295 Number of extensions: 10 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: 370 Length adjustment: 30 Effective length of query: 335 Effective length of database: 340 Effective search space: 113900 Effective search space used: 113900 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