Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 3607124 Dshi_0546 ABC transporter related (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Dino:3607124 Length = 338 Score = 294 bits (753), Expect = 2e-84 Identities = 158/360 (43%), Positives = 227/360 (63%), Gaps = 30/360 (8%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA +++ +NK YG L +I L I+DGEF++ VGPSGCGKSTL+ +AGLE +S G Sbjct: 1 MAGIKIDKINKFYGT--TQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 I + D++ + P DRD+AMVFQSYALYP M+VR+N+ FG+K+ E +A + Sbjct: 59 RIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++LQ+E L RKPGQLSGGQ+QRVA+GRA+ + P ++LFDEPLSNLDAKLRV+MR E++ Sbjct: 119 RVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEG 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +H++L T +YVTHDQ+EAMT+ DK+ V+ G I+Q G+P D+Y+ P + FVA FIGSP Sbjct: 179 LHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPA 238 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQI-ILANGEAN 299 MN +G+QD L+ +G RPE I I+ +G+ + Sbjct: 239 MNVF----------------------SSDVGLQDISLDASAAFVGCRPEHIEIVPDGDGH 276 Query: 300 GLPTIRAEVQVTEPTGPDTLVFVNL-NDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFD 358 I A V V E G ++L+++ L ++ R+ D VG ++L+F ++ FD Sbjct: 277 ----IAATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFD 332 Lambda K H 0.319 0.138 0.393 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: 393 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: 386 Length of database: 338 Length adjustment: 29 Effective length of query: 357 Effective length of database: 309 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 (21.7 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