Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 152 bits (385), Expect = 1e-41 Identities = 82/215 (38%), Positives = 130/215 (60%), Gaps = 6/215 (2%) Query: 25 DIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKI---ND---IEPQNRDIA 78 +I GE V++G SG GKST++R L L SG + IDG+ I ND ++ + ++ Sbjct: 52 EIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKVRRAKLS 111 Query: 79 MVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIKHLLDRKPKELSGGQ 138 MVFQS+AL PHMTV +N FGL++ + +R + E + ++ + P ELSGG Sbjct: 112 MVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPDELSGGM 171 Query: 139 RQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYVTHDQMEAT 198 +QRV L R L+ ++L DE S LD +R++M+ E+ +L +K T+++++HD EA Sbjct: 172 QQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHDLDEAM 231 Query: 199 TLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATF 233 +GDRIA+++ G + Q+GTP EI P + ++ F Sbjct: 232 RIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAF 266 Lambda K H 0.318 0.136 0.383 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: 315 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: 347 Length of database: 415 Length adjustment: 30 Effective length of query: 317 Effective length of database: 385 Effective search space: 122045 Effective search space used: 122045 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 (21.7 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