Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__ANA3:7026373 Length = 349 Score = 182 bits (461), Expect = 2e-50 Identities = 103/275 (37%), Positives = 161/275 (58%), Gaps = 9/275 (3%) Query: 4 VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63 + L ++ Y +V+ G+DL + E +AL+GPSGCGK+T LR +AGL+ +S G I+I Sbjct: 5 LNLHQVHSDYQGQQVLKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQIN 64 Query: 64 GRKVND----LPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119 G+ V+ +P R I M+FQ YAL+PH+TVAEN+ F +A + K R+ + A Sbjct: 65 GKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFG--VAKLTPAQRKARLDDMLA 122 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 ++ L L +R P +LSGGQ+QRV++ RA+ +P + L DEP SN+DA++R + EI+ + Sbjct: 123 LVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIRSI 182 Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPM 239 + + ++VTH + EA +D + I G I Q G E+++ P +++VA F+GS Sbjct: 183 LKQRNVSAVFVTHSKDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADFLGSG-- 240 Query: 240 NMEEAVLTDG-KLAFASGATLPLPPRFRSLVREGQ 273 N A + DG + G L P +S GQ Sbjct: 241 NYLPAEVIDGHSVVTPIGELRSLTPLSQSHAFNGQ 275 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: 268 Number of extensions: 8 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: 349 Length adjustment: 29 Effective length of query: 336 Effective length of database: 320 Effective search space: 107520 Effective search space used: 107520 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