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) >FitnessBrowser__Dyella79:N515DRAFT_4212 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:
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