Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 292 bits (748), Expect = 8e-84 Identities = 159/361 (44%), Positives = 228/361 (63%), Gaps = 32/361 (8%) Query: 1 MAGIKIDKINKFYGTTQ--ALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSG 58 MA +++ + K YG +Q L DI L I+ GEF++ VGPSGCGKSTL+ +AGLE ++ G Sbjct: 1 MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60 Query: 59 RIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAA 118 I + G D++ P DRD+AMVFQSYALYP M+VR+N+ FG+K+ +E +A A Sbjct: 61 EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120 Query: 119 RVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEG 178 ++LQ+E L+RKP QLSGGQ+QRVA+GRA+ + P ++LFDEPLSNLDAKLRV+MR E++ Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180 Query: 179 LHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPA 238 +H++L T +YVTHDQ+EAMT+ DK+ V+ G I+Q G+P ++Y+ P + FVA FIGSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSPP 240 Query: 239 MN---------------VFSSDVGLQDISLDASA--------AFVGCRPEHIEIVPDG-- 273 MN V +S+ G ++ L ++ +G RPE I + P G Sbjct: 241 MNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPEQIGLAPAGSA 300 Query: 274 DGHIAATVHVKERLGGESLLYLGLKGGGQIVA--RVGGDDETKVGAAVSLRFSRHRLHQF 331 D +A + V E G ++L+ L Q+ A R+ D +VG ++L+F R F Sbjct: 301 DFSLAVDIEVVEPTGPDTLVVFTL---NQVKACCRLAPDQAPRVGETLNLQFDPRRALLF 357 Query: 332 D 332 D Sbjct: 358 D 358 Lambda K H 0.320 0.139 0.396 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: 385 Number of extensions: 16 Number of successful extensions: 3 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: 338 Length of database: 390 Length adjustment: 29 Effective length of query: 309 Effective length of database: 361 Effective search space: 111549 Effective search space used: 111549 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