Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_084058302.1 B9A12_RS12460 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_900176285.1:WP_084058302.1 Length = 361 Score = 174 bits (442), Expect = 3e-48 Identities = 106/284 (37%), Positives = 161/284 (56%), Gaps = 10/284 (3%) Query: 19 LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVPPAQRGIA 78 L NI+ + G +GPSGCGK+T+L +I+GL T G + D V ++PP QR IA Sbjct: 25 LKNIDTVWEDGGAYALLGPSGCGKTTMLNIISGLLTPTRGRVLYDDRDVTELPPEQRNIA 84 Query: 79 MVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALSGGQ 138 VFQ LY M+V +N++F L+ I V+ AE L L L + LS Sbjct: 85 QVFQFPVLYDTMSVFDNLAFPLRNRGLDPQTIHRRVQEVAEVLDLTADLKKKAAGLSADA 144 Query: 139 RQRVAIGRSIVR-DPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHDQVE 197 +Q++++GR +VR D LFDEPL+ +D L+ R ++ ++ E + + T++YVTHDQVE Sbjct: 145 KQKISLGRGLVREDVAAILFDEPLTVIDPHLKWHLRRKLKEIHEKL-QLTLIYVTHDQVE 203 Query: 198 AMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGKIIGTGAQTTVE 257 A+T A +++V+ G + Q+G+P EL+E+P ++FV FIGSP MN +P ++ G A Sbjct: 204 ALTFADKVLVMYEGEMVQMGTPAELFEEPRHKFVGYFIGSPGMNFIPCRLEGNRA----- 258 Query: 258 MTDGGRAVSDYPSDDSLMG--AAVNVGVRPEDM-VEAAPGGDYV 298 + DG V D + G +G+RP + V PG D + Sbjct: 259 VCDGASVVLDEETVRRAQGKEGPFELGIRPMYLEVHDEPGDDRI 302 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: 344 Number of extensions: 17 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: 361 Length adjustment: 30 Effective length of query: 343 Effective length of database: 331 Effective search space: 113533 Effective search space used: 113533 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