Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000526715.1:WP_024851725.1 Length = 282 Score = 151 bits (381), Expect = 2e-41 Identities = 90/227 (39%), Positives = 134/227 (59%), Gaps = 15/227 (6%) Query: 21 VENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMNDASPKDRDIA 80 +E+ +L + + EF+ VG SGCGKST LR+I GLE +T+G + +D++++N +D A Sbjct: 24 LESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKGQVLVDEEIVNKPG---KDRA 80 Query: 81 MVFQNYALYPHMSVYENMAFGLKLRKYKKD----DINKRVHEA---AEILGLTEFLERKP 133 MVFQ+Y+LYP ++V EN+ F L+ + DI V + +++GL + + P Sbjct: 81 MVFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMVDRSYALLDLMGLEKVQDSHP 140 Query: 134 ADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVT 193 LSGG RQRVA+ RA++ V LMDEP LDA+ R M I + +T ++VT Sbjct: 141 NQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREVMHDLILHLFEIEKSTIVFVT 200 Query: 194 HDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIG---TPQELYNEP 237 HD EA+ LADR+V+M+ PNP + SI I G Q++ N P Sbjct: 201 HDVEEAIYLADRVVVMA--PNPGRIDSIYDISLPGGSERSQDVKNHP 245 Lambda K H 0.318 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: 272 Number of extensions: 12 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: 377 Length of database: 282 Length adjustment: 28 Effective length of query: 349 Effective length of database: 254 Effective search space: 88646 Effective search space used: 88646 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 (21.7 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