Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 313 bits (801), Expect = 6e-90 Identities = 163/373 (43%), Positives = 241/373 (64%), Gaps = 12/373 (3%) Query: 1 MAPVTLKKLVKRYGAL--EVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGG 58 M+ + L+ + K Y + E + GID+++ EF+ LVGPSGCGKST + IAGLE ++ G Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 59 AIEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAA 118 +I + G+ ++ + P+ R+I+MVFQSYALYP M+V EN+ F LKI G P EI V A Sbjct: 61 SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120 Query: 119 AILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKK 178 +L ++ L+ ++P+ LSGGQ+QRVAMGRA+ R+P ++LFDEPLSNLDAKLR ++RTEIKK Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180 Query: 179 LHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPP 238 LH R++ T++YVTHDQ+EAMTL+DRI +++DG ++Q+GTP++V+ RP FVAGF+GSP Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240 Query: 239 MNMEEAVLTDGKLAFAS------GATLPLP-PRFRSLVREGQKVTFGLRPDDVYPSGHGL 291 M+ + G+ + G ++ LP P F + R G+KV G+RP+ + Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLA-DRVGKKVILGIRPEHITQPQD-- 297 Query: 292 HAGDADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLAR 351 D V + E + +TEP G + + Q N + R+ P+ GE + FD+ + Sbjct: 298 QKNDQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDMKK 357 Query: 352 AHLFDGETGRALA 364 FD ET + +A Sbjct: 358 VVFFDPETEKRIA 370 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: 408 Number of extensions: 13 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: 372 Length adjustment: 30 Effective length of query: 335 Effective length of database: 342 Effective search space: 114570 Effective search space used: 114570 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