Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__WCS417:GFF4321 Length = 386 Score = 293 bits (749), Expect = 6e-84 Identities = 158/359 (44%), Positives = 230/359 (64%), Gaps = 28/359 (7%) Query: 1 MAGIKIDKINKFYGT--TQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSG 58 MA +++ +NK YG L +I L I++GEF++ VGPSGCGKSTL+ +AGLE ++ G Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 59 RIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAA 118 I IG +DV+ + P DRD+AMVFQSYALYP M+VREN+EFG+K+ +A A Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 Query: 119 RVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEG 178 ++LQ+E L+RKPGQLSGGQ+QRVA+GRA+ + P ++LFDEPLSNLDAKLRV+MR E++ Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 179 LHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPA 238 +H++L T +YVTHDQ+EAMT+ DK+ V+ G I+Q G+P ++Y+ P ++FVA FIGSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 Query: 239 MN---------------VFSSDVGLQDISLDASAA-------FVGCRPEHIEIVP---DG 273 MN + S +++L+ + A +G RPE I + D Sbjct: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 Query: 274 DGHIAATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFD 332 I A V V E G ++L+++ L ++ R+ D +VG ++L+F ++ FD Sbjct: 301 ASSIRAEVQVTEPTGPDTLVFVQL-NDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFD 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: 386 Number of extensions: 13 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: 338 Length of database: 386 Length adjustment: 29 Effective length of query: 309 Effective length of database: 357 Effective search space: 110313 Effective search space used: 110313 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