Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_047006469.1 AAW01_RS01810 phosphate ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_001010925.1:WP_047006469.1 Length = 280 Score = 104 bits (259), Expect = 3e-27 Identities = 74/247 (29%), Positives = 125/247 (50%), Gaps = 19/247 (7%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKI-----TGG 58 ++ GV+ YGD + + ++++DI + F+GPSGCGKST LR + + G Sbjct: 33 MRAQGVDVYYGDKRAIDDVSIDIYTEYVTAFIGPSGCGKSTFLRALNRMNDTIPSASVKG 92 Query: 59 TLEIDGTVV----NDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKI--AKKSQAEIDA 112 +E+DG + DV + + MVFQ +P ++ EN+++ +I +++ ++D Sbjct: 93 RIELDGDDIYASGMDVVQLRARVGMVFQKPNPFP-KSIYENIAYGPRIHGLAENRNDVDE 151 Query: 113 AVEAAAEKLQLGQYL-DRLP---KALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAAL 168 VE + + L + + DRL ALSGGQ+QR+ I R+I DP+V L DEP S LD Sbjct: 152 IVEKSLRRAGLWEEVKDRLQDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDP-- 209 Query: 169 RVATRLEIAQLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPEN 228 +AT + E +V VTH +A ++ R G + + G +++ P Sbjct: 210 -IATAKIEELIDELRGRYGIVIVTHSMQQAARVSQRTAFFHLGKMVEYGHTSDIFTNPRE 268 Query: 229 EFVAQFI 235 + +I Sbjct: 269 KRTQDYI 275 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: 205 Number of extensions: 11 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: 280 Length adjustment: 28 Effective length of query: 345 Effective length of database: 252 Effective search space: 86940 Effective search space used: 86940 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