Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_091518158.1 BM253_RS01840 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_900115115.1:WP_091518158.1 Length = 249 Score = 112 bits (280), Expect = 1e-29 Identities = 70/227 (30%), Positives = 119/227 (52%), Gaps = 4/227 (1%) Query: 4 LKLTGVEKAY--GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLE 61 +K+ + K Y D + L+N+ L+I Q + +GP+G GK+TL+ ++ G+ + T G+ E Sbjct: 5 IKIQNISKQYKGADFQSLNNVVLNIPQQSVFGLLGPNGAGKTTLISILCGIIQPTLGSYE 64 Query: 62 IDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKL 121 I+G + + I +V Q YALYP +T EN+ + + S+A++ A + L Sbjct: 65 INGISNKNTSSIKNIIGVVPQEYALYPTLTAYENLMYFGSLYNVSKADLKAKIPEFLIHL 124 Query: 122 QLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKE 181 L ++ + + SGG ++RV + I+ +PKV DEP +D R AT ++ +L Sbjct: 125 GLENFMHKKIQTFSGGMKRRVNLIAGILHNPKVLFLDEPTVGVDVQSR-ATIIDYLKLLN 183 Query: 182 AMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPEN 228 +T+VY +H EA T I ++ G + G+P EL E N Sbjct: 184 -QQGTTIVYTSHLMAEAQDFCTDIAIIDQGSVFVQGTPKELIENVPN 229 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: 186 Number of extensions: 14 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: 249 Length adjustment: 27 Effective length of query: 346 Effective length of database: 222 Effective search space: 76812 Effective search space used: 76812 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 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