Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 130 bits (327), Expect = 4e-35 Identities = 80/238 (33%), Positives = 129/238 (54%), Gaps = 8/238 (3%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 + + V K YG L+N+ L + GE +++ GPSG GKSTL+ CI GLET G I Sbjct: 2 IHMAGVGKWYGGY--HALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIR 59 Query: 64 VDDADISG----MSPKDRDIAMVFQSYALYPTMSVRDNIAFG-LKIRKMPTAEIDEEVAR 118 + + ++ + + MVFQ + L+P +++ +N A +K+R + + Sbjct: 60 IGEDEVRPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARE 119 Query: 119 VSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178 + + ++I + P QLSGGQQQR A+ RALA +P+I LFDEP S LDA++ E+ M Sbjct: 120 LLERVRIADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIM 179 Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFI 236 K + T + VTH+ A + D++ M G I + G+P+D + P + +F+ Sbjct: 180 KALATE-GITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFL 236 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: 234 Number of extensions: 8 Number of successful extensions: 4 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: 241 Length adjustment: 27 Effective length of query: 359 Effective length of database: 214 Effective search space: 76826 Effective search space used: 76826 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