Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate RR42_RS22875 RR42_RS22875 ABC transporter
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Cup4G11:RR42_RS22875 Length = 351 Score = 278 bits (712), Expect = 1e-79 Identities = 160/369 (43%), Positives = 214/369 (57%), Gaps = 37/369 (10%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 MA V + L KR+ V GIDL V + EF+ L+GPSG GK+T LR+IAGLE + G I Sbjct: 1 MATVETRSLTKRFDGTNAVDGIDLAVHEAEFLVLLGPSGSGKTTLLRLIAGLEAPTSGDI 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 +GGR V LPPRA N++MVFQSYALYPH++VA N+ F L+ P E I +V+ AAA+ Sbjct: 61 LVGGRVVTGLPPRAHNMAMVFQSYALYPHLSVAGNIAFPLEAQRMPREAIARKVSWAAAL 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 + HLL R+P QLSGG+RQRVA+ RA+VR+P FL DEPLSNLDAKLRT R E+++L Sbjct: 121 FGIGHLLSRKPRQLSGGERQRVALARAVVREPVAFLLDEPLSNLDAKLRTSAREELQQLQ 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240 R+ T IYVTHDQ+EA+ L DR+ I+ G + Q+GTP+ V+ +PA FVA FIGSPPMN Sbjct: 181 RRLATTTIYVTHDQIEALALGDRVAILDHGRVHQLGTPQQVYEQPADTFVATFIGSPPMN 240 Query: 241 MEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAVH 300 + V TD + G RP+ P G +A+ Sbjct: 241 L---VDTDA-------------------------LVTGFRPEHFLPRE---VYGSDEALE 269 Query: 301 EIELPVTITEPLGNETLVFTQFNGRDWVSRMLN------PRPLRPGEAVPMSFDLARAHL 354 +T E LG++ LV+ +++++ PL G P + A Sbjct: 270 PFPFHITRIENLGSDRLVYGLLEPPLPPAKVISRIPCTVTFPLETGARYPFAVRRADLRR 329 Query: 355 FDGETGRAL 363 FD +G +L Sbjct: 330 FDPRSGASL 338 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: 397 Number of extensions: 14 Number of successful extensions: 1 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: 351 Length adjustment: 29 Effective length of query: 336 Effective length of database: 322 Effective search space: 108192 Effective search space used: 108192 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