Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Putida:PP_1018 Length = 384 Score = 320 bits (821), Expect = 3e-92 Identities = 173/370 (46%), Positives = 236/370 (63%), Gaps = 12/370 (3%) Query: 1 MAPVTLKKLVKRYGA--LEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGG 58 MA + L+ + K YG+ + + I L +KD EF+ LVGPSGCGKST + IAGLE+++GG Sbjct: 1 MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60 Query: 59 AIEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAA 118 AI I + V+ + P+ R+I+MVFQSYALYP M+V EN+ F LKI P I VA A Sbjct: 61 AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120 Query: 119 AILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKK 178 +L + HLL R+P+QLSGGQ+QRVAMGRA+ R+P ++LFDEPLSNLDAKLR ++RTE+K Sbjct: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 179 LHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPP 238 +H R++ T +YVTHDQ+EAMTL D++ +M+DG I+Q GTP+ ++ PA +FVA FIGSPP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240 Query: 239 MNMEEAVLT--DGKLAF---ASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHA 293 MN L DG+L + A LP + EG+++ G+RP+ + L A Sbjct: 241 MNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQI-----ALGA 295 Query: 294 GDADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAH 353 D + + I V +TEP G + LVF N R+ R G+ + + FD AR Sbjct: 296 ADGNGLPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGDTLNLQFDPARVL 355 Query: 354 LFDGETGRAL 363 LFD G L Sbjct: 356 LFDAANGERL 365 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: 405 Number of extensions: 15 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: 384 Length adjustment: 30 Effective length of query: 335 Effective length of database: 354 Effective search space: 118590 Effective search space used: 118590 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: 50 (23.9 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