Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 3607124 Dshi_0546 ABC transporter related (RefSeq)
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Dino:3607124 Length = 338 Score = 312 bits (800), Expect = 7e-90 Identities = 176/366 (48%), Positives = 233/366 (63%), Gaps = 31/366 (8%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 MA + + K+ K YG + + I+L+++D EF+ VGPSGCGKST LR +AGLE VS G I Sbjct: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 EIGGR V + P R+++MVFQSYALYPHMTV ENM F +K+ G + K R+AEAA + Sbjct: 61 EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 L L L+R+P QLSGGQRQRVA+GRAIV+ P VFLFDEPLSNLDAKLR Q+R E++ LH Sbjct: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240 ++ ATMIYVTHDQVEAMT++D+IV++ G IEQVG+P D++ +P ++FVA FIGSP MN Sbjct: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240 Query: 241 MEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPD--DVYPSGHGLHAGDADA 298 + F+S L + + + G RP+ ++ P G G Sbjct: 241 V-----------FSSDVGL------QDISLDASAAFVGCRPEHIEIVPDGDG-------- 275 Query: 299 VHEIELPVTITEPLGNETLVFTQF-NGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLFDG 357 I V + E LG E+L++ G V+R+ + G AV + F R H FD Sbjct: 276 --HIAATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFD- 332 Query: 358 ETGRAL 363 E GRA+ Sbjct: 333 EAGRAI 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: 348 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: 338 Length adjustment: 29 Effective length of query: 336 Effective length of database: 309 Effective search space: 103824 Effective search space used: 103824 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