Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000007345.1:WP_011020381.1 Length = 353 Score = 168 bits (425), Expect = 2e-46 Identities = 98/275 (35%), Positives = 159/275 (57%), Gaps = 11/275 (4%) Query: 19 LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVPPAQRGIA 78 L I+L ++G+ + +GPSG GKS LL I G G++ ++G + P +R I+ Sbjct: 18 LKGIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQGSVFLEGRDITFFSPDKRQIS 77 Query: 79 MVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALSGGQ 138 +V+Q L+PHM + EN+++AL+ K + +I+ V A L + + L R P LSGG+ Sbjct: 78 IVYQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIAGVLGIRELLHRKPDTLSGGE 137 Query: 139 RQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPE--STMVYVTHDQV 196 +QR ++ RS+V PK+ L DEP S LDA R R LK+A+ + +T+++VTHD Sbjct: 138 KQRASLARSLVARPKLLLLDEPFSALDARTREKLR---EMLKKAIADYSTTVLHVTHDFE 194 Query: 197 EAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGKIIGTGAQTTV 256 + LA R+VV+ G + QVG P ++ +P +FVA+F+G+ N+L G + + TV Sbjct: 195 DVWALANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGT---NVLKGTVKALEGKLTV 251 Query: 257 EMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEA 291 +G + Y +D + G V V +RPE+++ A Sbjct: 252 IDAEG---MEIYSADPAEPGENVTVSIRPEEIILA 283 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: 316 Number of extensions: 20 Number of successful extensions: 2 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: 353 Length adjustment: 29 Effective length of query: 344 Effective length of database: 324 Effective search space: 111456 Effective search space used: 111456 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: 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