Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate AO353_25895 AO353_25895 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25895 Length = 367 Score = 317 bits (813), Expect = 2e-91 Identities = 171/362 (47%), Positives = 238/362 (65%), Gaps = 15/362 (4%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 MA + +K L K + ++ GIDLEV DREF+ VGPSGCGKST LR+IAGLEEV+ G I Sbjct: 1 MAHLKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTI 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 E+ GR + ++ P R+++MVFQ+YALYPHM+V +NM F+L +AG E++ +V EAA I Sbjct: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARI 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 L+L +LER+P QLSGGQRQRVA+GRAIVR P +FLFDEPLSNLDA LR Q+R E+ +LH Sbjct: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240 +QATMIYVTHDQVEAMTL+D++V++ G IEQVG+P +++ +PA FVAGF+G+P M Sbjct: 181 KELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240 Query: 241 MEEAVLT-----DGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGD 295 + +T + ++ +G + LP +L G VT G+RP+ + + GD Sbjct: 241 FLKGKVTRVERQNCEVLLDAGTRITLPLSGANL-SIGGAVTLGIRPEHL----NLALPGD 295 Query: 296 ADAVHEIELPVTITEPLGNETLVFT-QFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHL 354 +++ ++E LG++T +G R+ R GE + + D HL Sbjct: 296 C----TLQVTADVSERLGSDTFCHVLTASGEALTMRIRGDLASRYGEQLSLHLDAEHCHL 351 Query: 355 FD 356 FD Sbjct: 352 FD 353 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: 381 Number of extensions: 10 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: 367 Length adjustment: 30 Effective length of query: 335 Effective length of database: 337 Effective search space: 112895 Effective search space used: 112895 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