Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Phaeo:GFF1645 Length = 355 Score = 327 bits (838), Expect = 3e-94 Identities = 182/359 (50%), Positives = 238/359 (66%), Gaps = 17/359 (4%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 MA + L+ + KRYGA+EV+ I+L+++D EFI LVGPSGCGKST LRMIAGLE ++ G Sbjct: 1 MARIELRDVAKRYGAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDF 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 EI G+++ND+ PR R+I+MVFQSYALYPHM VA NMGFS++I PAEE ++RVA AA Sbjct: 61 EIDGQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAET 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 L L+ L++R P LSGGQRQRVAMGRAI+R P FLFDEPLSNLDA LR ++R EI +LH Sbjct: 121 LGLSSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLH 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240 ++ ATMIYVTHDQVEA+TL+DRIV++ G I+QVG+P +++ RPA KFVA FIGSP MN Sbjct: 181 KQLGATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTMN 240 Query: 241 MEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPD--DVYPSGHGLHAGDADA 298 + + +G L L + V G+RP+ DV G G AD Sbjct: 241 ILPVSGAASGVMATNGMMLTLD----HMHDTAAAVELGIRPEHLDVVEPGEGHLIAVADV 296 Query: 299 VHEIELPVTITEPLGNETLVFTQFNG-RDWVSRMLNPRPLRPGEAVPMSFDLARAHLFD 356 V E LG++T ++ + +G + R P+R GE + + AH+FD Sbjct: 297 V----------ERLGSDTNIYAKVDGLGPLMVRKHGNVPVRSGERLGLRVQAQNAHIFD 345 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: 9 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: 355 Length adjustment: 29 Effective length of query: 336 Effective length of database: 326 Effective search space: 109536 Effective search space used: 109536 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