Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 3607949 Dshi_1357 ABC transporter related (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Dino:3607949 Length = 349 Score = 295 bits (754), Expect = 2e-84 Identities = 167/360 (46%), Positives = 221/360 (61%), Gaps = 20/360 (5%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 M + L V K +G +K ++L+I DGEF++ VGPSGCGKSTL+ I GLE S G Sbjct: 1 MGAITLSKVEKWFGD--VQVIKGVDLEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 A+L+D D++ P R + MVFQSYALYP MSVR+N+ F LK P AEI E+V + Sbjct: 59 AMLIDGVDVTDHPPAKRGLTMVFQSYALYPHMSVRENMGFSLKTAGAPAAEIAEKVEAAA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +L++E L R+P LSGGQ+QRVA+GR++ R P +LFDEPLSNLDA LRVEMR E+ Sbjct: 119 AVLKLEPYLDRRPKDLSGGQRQRVAIGRSIVRAPTAFLFDEPLSNLDAALRVEMRYEIAK 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +HQ L TT +YVTHDQ+EAMTL D++ V++ G I Q GTP+++Y PANLFVA FIGSP Sbjct: 179 LHQSLDTTMIYVTHDQVEAMTLADRIVVLEFGKIAQVGTPRELYETPANLFVAQFIGSPK 238 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVI-LGIRPEQIILANGEAN 299 MN +P D+G+ R G +G DR + LGIRPE I A Sbjct: 239 MNVMP-----------CTTDAGRYRLSAGRGGVFSG--DRPAVQLGIRPEHI---TPGAP 282 Query: 300 GLPTIRAEVQVTEPTGPDTLVFVNLN-DTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFD 358 G V V E G DTL+ ++ + +V R+ D G+ + L F+P ++ FD Sbjct: 283 GTGACDGRVDVVEYLGADTLLVLDCGPEGRVTVRVIGDTDLTPGDAVGLSFNPDRLSFFD 342 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: 368 Number of extensions: 12 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: 349 Length adjustment: 30 Effective length of query: 356 Effective length of database: 319 Effective search space: 113564 Effective search space used: 113564 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