Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000526715.1:WP_024851725.1 Length = 282 Score = 148 bits (373), Expect = 2e-40 Identities = 93/215 (43%), Positives = 131/215 (60%), Gaps = 15/215 (6%) Query: 6 LTGVEKAY----GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLE 61 ++G+ K + G V+VL +I+L +++ E + VG SGCGKSTLLR+I GLEK+T G + Sbjct: 7 ISGLNKTFITKKGAVEVLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKGQVL 66 Query: 62 IDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQ----AEIDAAVE-- 115 +D +VN P R AMVFQ Y+LYP +TV+EN+ F+ + Q +I + V+ Sbjct: 67 VDEEIVNK-PGKDR--AMVFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMVDRS 123 Query: 116 -AAAEKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRL 174 A + + L + D P LSGG RQRVAI R+++ P V L DEP LDA R Sbjct: 124 YALLDLMGLEKVQDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREVMHD 183 Query: 175 EIAQLKEAMPESTMVYVTHDQVEAMTLATRIVVLA 209 I L E + +ST+V+VTHD EA+ LA R+VV+A Sbjct: 184 LILHLFE-IEKSTIVFVTHDVEEAIYLADRVVVMA 217 Lambda K H 0.316 0.135 0.379 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: 266 Number of extensions: 16 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: 373 Length of database: 282 Length adjustment: 28 Effective length of query: 345 Effective length of database: 254 Effective search space: 87630 Effective search space used: 87630 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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