Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein Length = 364 Score = 318 bits (816), Expect = 1e-91 Identities = 187/365 (51%), Positives = 235/365 (64%), Gaps = 15/365 (4%) Query: 1 MAPVTLKKLVKRYGALEV-VHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGA 59 MA V L KL K Y V V E+ D E + LVGPSGCGK+T LRMIAGLE +SGG Sbjct: 1 MAKVRLDKLRKVYPNGHVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGGT 60 Query: 60 IEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119 + IG R VND+ P+ R+I+MVFQ+YALYPHMTVAEN+GF LK+ G+P EI+ RVAEAA Sbjct: 61 LSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAAR 120 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 +L+L L+ RP+ LSGGQRQRVA+GRA+VR P VFL DEPLSNLDAKLR +R EI ++ Sbjct: 121 MLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIARI 180 Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPM 239 H R++ATM+YVTHDQ+EAMTL RIV++ G I+Q+ TP +++ PA FVAGF+GSP M Sbjct: 181 HQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPAM 240 Query: 240 NMEEAVL-TDG--KLAFASGATL--PLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAG 294 N+ +L DG KLA G + LP + + GLRP+D+ L A Sbjct: 241 NLLRGILYRDGGWKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDLL-----LCAD 295 Query: 295 DADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPL-RPGEAVPMSFDLARAH 353 A A +L V EP+GNE + + VSRM PR L PG + F R H Sbjct: 296 AAGAALAAQLEV--VEPVGNEVFLNLRHGELALVSRM-PPRELPAPGSTLHFGFAPERLH 352 Query: 354 LFDGE 358 FD + Sbjct: 353 FFDAK 357 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: 394 Number of extensions: 16 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: 364 Length adjustment: 29 Effective length of query: 336 Effective length of database: 335 Effective search space: 112560 Effective search space used: 112560 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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