Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 306 bits (785), Expect = 5e-88 Identities = 171/373 (45%), Positives = 238/373 (63%), Gaps = 18/373 (4%) Query: 1 MAPVTLKKLVKRYGALEV--VHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGG 58 MA + L+ + K YG ++ + I L++ EF+ LVGPSGCGKST + IAGLE ++GG Sbjct: 1 MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60 Query: 59 AIEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAA 118 I + G ++ P+ R+I+MVFQSYALYP M+V +N+ F LK+ PA +I+ VA A Sbjct: 61 EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120 Query: 119 AILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKK 178 +L + LLER+PSQLSGGQ+QRVAMGRA+ R+P ++LFDEPLSNLDAKLR ++RTEIK Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180 Query: 179 LHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPP 238 +H R++ T +YVTHDQ+EAMTL D++ +M+DG I+Q GTP +++ PA FVA FIGSPP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSPP 240 Query: 239 MNMEEAVLTD------GKLAFASGA-TLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGL 291 MN + G L G+ LPLP +R+ +++ G+RP+ + GL Sbjct: 241 MNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRD-RELILGIRPEQI-----GL 294 Query: 292 -HAGDADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLA 350 AG AD + + + + EP G +TLV N R+ + R GE + + FD Sbjct: 295 APAGSAD--FSLAVDIEVVEPTGPDTLVVFTLNQVKACCRLAPDQAPRVGETLNLQFDPR 352 Query: 351 RAHLFDGETGRAL 363 RA LFD +TG L Sbjct: 353 RALLFDAQTGERL 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: 396 Number of extensions: 11 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: 390 Length adjustment: 30 Effective length of query: 335 Effective length of database: 360 Effective search space: 120600 Effective search space used: 120600 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