Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Marino:GFF1380 Length = 362 Score = 210 bits (535), Expect = 4e-59 Identities = 107/250 (42%), Positives = 159/250 (63%), Gaps = 6/250 (2%) Query: 4 VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63 + ++ + K + + +H I+L + D + AL+GPSG GK+T LR+IAGLE G I Sbjct: 3 IEIQGINKFFDKFQALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRFS 62 Query: 64 GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAE----EIKTRVAEAAA 119 G+ V DL R R + VFQ YAL+ HMTVAEN+ F L + R EI+ RV + Sbjct: 63 GKDVTDLHVRDRRVGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDLLE 122 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 ++ L HL +R P+QLSGGQ+QR+A+ RA+ +P++ L DEP LDAK+R +R ++ L Sbjct: 123 MVQLEHLADRYPAQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLRSL 182 Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPM 239 H + T ++VTHDQ EA+ LSD++V+M +G IEQV TP +++ RP ++FV F+G + Sbjct: 183 HDELHFTSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLGQ--V 240 Query: 240 NMEEAVLTDG 249 N+ + DG Sbjct: 241 NVLSGKIRDG 250 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: 363 Number of extensions: 18 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: 362 Length adjustment: 29 Effective length of query: 336 Effective length of database: 333 Effective search space: 111888 Effective search space used: 111888 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