Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 210 bits (535), Expect = 5e-59 Identities = 125/327 (38%), Positives = 183/327 (55%), Gaps = 11/327 (3%) Query: 3 DLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEI 62 DL+LTG+ K +G + ++L I QG +G SGCGK+T LRMI+GLE T G + + Sbjct: 18 DLRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHL 77 Query: 63 DGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQ 122 V D P +R + VFQ+YAL+PH+ + EN++F L+ ++ + VE + ++ Sbjct: 78 GDQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLR--RRGIRSVKKPVEDMLDLVE 135 Query: 123 LGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEA 182 LG R P LSGGQ+QR+A+ R+++ P+V L DEPL LD LR ++E+ +++ Sbjct: 136 LGHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLE 195 Query: 183 MPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNL 242 + T V+VTHDQ EAMT+A I V+ G I Q+GSP ELYE P FVA F+G + NL Sbjct: 196 V-GLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLG--QSNL 252 Query: 243 LPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEA-----APGGDY 297 + G + V++ GR+++ + V +GVRPE + A P G Sbjct: 253 IAGTVESVSGD-VVQVAAHGRSLALPAARCRTTSGPVILGVRPEKVRIAKTEAEVPSGAN 311 Query: 298 VFEGKVAITEALGEVTLLYFEAPSGED 324 GKV +G T E PSGE+ Sbjct: 312 HLTGKVTDASFIGVSTQYLVELPSGEE 338 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: 353 Number of extensions: 19 Number of successful extensions: 4 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: 386 Length adjustment: 30 Effective length of query: 343 Effective length of database: 356 Effective search space: 122108 Effective search space used: 122108 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: 50 (23.9 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