Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_109737982.1 C1634_RS05005 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_002899945.2:WP_109737982.1 Length = 306 Score = 140 bits (353), Expect = 5e-38 Identities = 82/242 (33%), Positives = 124/242 (51%), Gaps = 4/242 (1%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 +K+ + K++ K + +I+ E++V +G SGCGK+T L+MI L + G + ID Sbjct: 2 IKVESISKSFNGKKAVDHISFQAFDQEILVLLGTSGCGKTTTLKMINRLIEADAGNIFID 61 Query: 64 GTVVND--VPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKL 121 G + D + GI V Q L+PH T+++N++ ++ K + + + KL Sbjct: 62 GKNIRDQKAEELRMGIGFVMQHSGLFPHYTIQQNIAVVPELLKWDKKKTERRTHELLAKL 121 Query: 122 QLG-QYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180 L + L R P LSGGQ+QRV I R+++ D V L DEP LD + E L Sbjct: 122 HLSEEVLSRFPHELSGGQQQRVGIARALIADSPVLLMDEPFGALDNITKADIHSEFKSL- 180 Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240 E + T+V VTHD EA L RI ++ G I Q G+P E+ P N FV F ++ Sbjct: 181 EDLKNKTIVLVTHDVQEAFDLGHRICLMDQGKIVQTGTPKEILYHPSNHFVRDFFAENRL 240 Query: 241 NL 242 L Sbjct: 241 LL 242 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: 201 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: 306 Length adjustment: 28 Effective length of query: 345 Effective length of database: 278 Effective search space: 95910 Effective search space used: 95910 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 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