Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 350 bits (898), Expect = e-101 Identities = 193/371 (52%), Positives = 252/371 (67%), Gaps = 14/371 (3%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 MA + L ++ KR+ VV L V D+EF+ LVGPSGCGKSTTLRMIAGLEEV+ G I Sbjct: 1 MAEIKLDQVNKRFKKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEI 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 IGGR VN +PP+ R+I+MVFQSYALYPHM V +NM F L G P +EI RV +AA I Sbjct: 61 SIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEI 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 L ++ LL+RRP+QLSGGQRQRVAMGRAIVR P FLFDEPLSNLDAKLR Q+R E+ KLH Sbjct: 121 LGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLH 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240 R+Q+T++YVTHDQ+EAMTL+DRIV+M+DG I QVG P +V+ RPA +FVAGFIGSP MN Sbjct: 181 ERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMN 240 Query: 241 MEEAVLTD--GKLAFASGATLPLP-PRFRSLVREG---QKVTFGLRPDDVYPSGHGLHAG 294 + L + G L + G + L PR R+ G + V FG+RP+DV G Sbjct: 241 FLDVRLVEEAGDL-WVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVKE-----RPG 294 Query: 295 DA--DAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARA 352 DA + V + V + EP+G+E ++ + +R+ +R + + ++ ++ + Sbjct: 295 DALPEGVEPLRAEVDVREPIGSEVIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKM 354 Query: 353 HLFDGETGRAL 363 HLFD E+ +AL Sbjct: 355 HLFDPESEQAL 365 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: 425 Number of extensions: 15 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: 368 Length adjustment: 30 Effective length of query: 335 Effective length of database: 338 Effective search space: 113230 Effective search space used: 113230 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 Apr 09 2024. 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