Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate BPHYT_RS05040 BPHYT_RS05040 sugar ABC transporter ATPase
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__BFirm:BPHYT_RS05040 Length = 371 Score = 319 bits (817), Expect = 9e-92 Identities = 180/378 (47%), Positives = 245/378 (64%), Gaps = 21/378 (5%) Query: 1 MAPVTLKKLVKRY-GALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGA 59 MA ++++ + K Y + V+ G++++++D +F+ LVG SGCGKST L MIAGLE V+ G Sbjct: 1 MASLSIRDVYKTYPNGVPVLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKGE 60 Query: 60 IEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119 I+I G+ VN+L P+ R+I+MVFQSYALYP MTV EN+ F L I P E V + Sbjct: 61 IQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKNEQTQIVDRVSN 120 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 L + HLL+R+P QLSGGQRQRVAMGRA+ R P +FLFDEPLSNLDAKLR ++R+EIK L Sbjct: 121 TLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKLL 180 Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPM 239 H R+ T++YVTHDQ+EAMTL DRI +M+DG ++Q G P++++ P+ FVAGFIG+PPM Sbjct: 181 HQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFIGAPPM 240 Query: 240 NMEEAVLTDGKLAFA-------SGATLPLP---PRFRSLVREGQKVTFGLRPDDVYPSGH 289 N + L + A + L LP + RS V G++V GLRP+ + Sbjct: 241 NFIQGKLVEQGAGVALELDTGVARTALNLPFDSAKVRSHV--GREVILGLRPERI-TDAR 297 Query: 290 GLHAGDADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRM---LNPRPLRPGEAVPMS 346 G H GD + IE+ V + EP G +TLVF Q NG+ VSR+ NP+PL + Sbjct: 298 GAH-GDNAKLQPIEVKVDVIEPTGPDTLVFAQVNGKRIVSRVHPASNPQPL---ANTTLL 353 Query: 347 FDLARAHLFDGETGRALA 364 FD ++A LFD +A Sbjct: 354 FDTSKAVLFDPSNEERIA 371 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: 396 Number of extensions: 19 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: 371 Length adjustment: 30 Effective length of query: 335 Effective length of database: 341 Effective search space: 114235 Effective search space used: 114235 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