Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_000526715.1:WP_024851725.1 Length = 282 Score = 143 bits (360), Expect = 7e-39 Identities = 91/213 (42%), Positives = 127/213 (59%), Gaps = 12/213 (5%) Query: 6 LRNVNKTY--GPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 + +NKT+ G + L++I+L + + EF+ LVG SGCGKSTL+ I GLE ++ G +L Sbjct: 7 ISGLNKTFITKKGAVEVLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKGQVL 66 Query: 64 VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFG--LKIRKMPTA--EIDEEVARV 119 VD+ +I KDR AMVFQ Y+LYP ++V++NI F LKI +I V R Sbjct: 67 VDE-EIVNKPGKDR--AMVFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMVDRS 123 Query: 120 SKLLQI---EHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176 LL + E + P QLSGG +QRVA+ RAL +P + L DEP LDA+ R M Sbjct: 124 YALLDLMGLEKVQDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREVMHD 183 Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVM 209 + + + K+T V+VTHD EA+ L D+V VM Sbjct: 184 LILHLFEIEKSTIVFVTHDVEEAIYLADRVVVM 216 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: 282 Number of extensions: 10 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: 282 Length adjustment: 28 Effective length of query: 358 Effective length of database: 254 Effective search space: 90932 Effective search space used: 90932 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 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