Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_068221987.1 AWW68_RS13720 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_001592965.1:WP_068221987.1 Length = 288 Score = 141 bits (355), Expect = 3e-38 Identities = 86/222 (38%), Positives = 130/222 (58%), Gaps = 12/222 (5%) Query: 21 NINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID-----GTVVNDVPPAQR 75 +++ Q GE +V G SG GK++LLRMIAGL G + + G N + P QR Sbjct: 20 DLDFKCQAGEFLVISGESGAGKTSLLRMIAGLMNPDSGNIISNQEPWFGHKTN-IKPQQR 78 Query: 76 GIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALS 135 +VFQ YAL+P+MTV N+ +ALK KSQA D+ +E + +++ ++ P LS Sbjct: 79 NCGLVFQQYALFPNMTVEGNLRYALK---KSQA--DSIIEELLDIMEIKGLRNQKPNQLS 133 Query: 136 GGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHDQ 195 GGQ+QRVA+ R++V+ PK+ L DEPLS LD ++R+ + + ++ + E T + VTHD Sbjct: 134 GGQQQRVALARTLVQKPKLLLLDEPLSALDRSMRIRLQEYLKKVHQQF-ELTTIMVTHDP 192 Query: 196 VEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGS 237 EA+ LA RI+ + G I + G P E++ QF G+ Sbjct: 193 SEALRLADRIIEIEKGNITKDGKPTEVFGNKSLSGKFQFTGA 234 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: 226 Number of extensions: 13 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: 288 Length adjustment: 28 Effective length of query: 345 Effective length of database: 260 Effective search space: 89700 Effective search space used: 89700 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