Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 136 bits (342), Expect = 7e-37 Identities = 82/222 (36%), Positives = 122/222 (54%), Gaps = 9/222 (4%) Query: 21 LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMSPKD--RD 78 L ++ L I+ G F+ LVG SG GK+TL+ I L I G I ++ D++ + R Sbjct: 17 LDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVAAQPVAELRRR 76 Query: 79 IAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHL----LSRKPG 134 I VFQ L+P MSV +N+A +++ +P +E ARV++LL + L R+P Sbjct: 77 IGYVFQGIGLFPHMSVAENVALVPRLQGVPR---EERAARVAELLDLVALPADFAERRPA 133 Query: 135 QLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTH 194 QLSGGQ QRV RALA RP I L DEP LD R E+ + +H+ + T++ VTH Sbjct: 134 QLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEAMGLTSLIVTH 193 Query: 195 DQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFI 236 D EA+ L D+V V+ +G I P+ + + + + + I Sbjct: 194 DMAEALLLADRVIVIGEGRILADQPPRALIHGAGDPRIEAMI 235 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: 189 Number of extensions: 6 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: 386 Length of database: 252 Length adjustment: 27 Effective length of query: 359 Effective length of database: 225 Effective search space: 80775 Effective search space used: 80775 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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