Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 323 bits (828), Expect = 4e-93 Identities = 177/363 (48%), Positives = 238/363 (65%), Gaps = 19/363 (5%) Query: 1 MAPVTLKKLVKRY-GALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGA 59 MA VTL + K Y +E V +++D EF+ LVGPSGCGKST LRMIAGLE+++ G Sbjct: 1 MAQVTLNSVRKVYPNGVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEGT 60 Query: 60 IEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119 +EIG R VN++ P R+I+MVFQ+YALYPHMTV +N+ + LK P EIK +VAEAA Sbjct: 61 LEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAAK 120 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 +L+L L+R+PSQLSGGQRQRVAMGRAIVR P +FLFDEPLSNLDAKLR Q+R EIK L Sbjct: 121 MLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKAL 180 Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPM 239 R+ T IYVTHDQVEAMT++DRI+++ G IEQ+GTP +++ PA+ FVA F+G+PPM Sbjct: 181 QRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPPM 240 Query: 240 NMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQ-KVTFGLRPDDVYPSGHGLHAGDADA 298 N+ +A + +G++ G ++ +L Q V G+RP+DV G Sbjct: 241 NLLDATIANGQVTLPDGVSM------GALDTSAQGAVKLGIRPEDVQLVAEG-------- 286 Query: 299 VHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLFDGE 358 + + V + E LG L+ + G+ + +L P+ PG +S D A LFD E Sbjct: 287 --GLAIDVELIEELGAHRLLHGKLGGQPFTIHVLKDIPVDPG-THQISVDPAAICLFDAE 343 Query: 359 TGR 361 +G+ Sbjct: 344 SGQ 346 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: 355 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: 348 Length adjustment: 29 Effective length of query: 336 Effective length of database: 319 Effective search space: 107184 Effective search space used: 107184 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