Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_055436456.1 ASC41_RS09735 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_001418085.1:WP_055436456.1 Length = 303 Score = 109 bits (272), Expect = 1e-28 Identities = 79/263 (30%), Positives = 132/263 (50%), Gaps = 13/263 (4%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL--- 60 L + + +Y VL +++ +++ GE + +G SGCGKSTLL+++ G + GT+ Sbjct: 2 LNVKNLSFSYKKTPVLKDLSFNVKPGEYLAVIGESGCGKSTLLKVLRGEYDLNNGTVFWK 61 Query: 61 --EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAA 118 EI G N V + V Q + L P+++V EN+ L K + + A Sbjct: 62 KEEILGPKHNLVI-GYDFMKYVAQEFELEPYISVAENIGQHLSNFYKEEKKERTA--ELL 118 Query: 119 EKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQ 178 E ++L K LSGGQ+QRVA+ R++ PK+ L DEP S++D + + R I + Sbjct: 119 EVVELTNLASTKVKLLSGGQKQRVALARALANAPKILLLDEPFSHIDNFKKQSLRRNIFK 178 Query: 179 -LKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGS 237 LK+ T + +HD+ + + A +++VL I +P +LY PE +A F G Sbjct: 179 YLKD--KNITCIVASHDKEDVLGFADQMMVLNDNKIEAYNTPEQLYNTPETPLIASFFG- 235 Query: 238 PKMNLLPGKIIGTGAQTTVEMTD 260 + N++ I+ VE +D Sbjct: 236 -EFNVINDTIVYAHQLKIVEKSD 257 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: 229 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: 373 Length of database: 303 Length adjustment: 28 Effective length of query: 345 Effective length of database: 275 Effective search space: 94875 Effective search space used: 94875 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 Sep 24 2021. 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