Align ABC transporter (characterized, see rationale)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= uniprot:A0A166QFW2 (381 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 174 bits (441), Expect = 4e-48 Identities = 95/233 (40%), Positives = 144/233 (61%), Gaps = 7/233 (3%) Query: 19 LRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRV---ND---LEP 72 ++D S EI GE V +G SG GKST++R++ L G +LIDG + ND ++ Sbjct: 46 VQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKV 105 Query: 73 RERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLLQRKPK 132 R + MVFQS+AL PHM+V N +FGL++ DK + +R L+ + + L+ + P Sbjct: 106 RRAKLSMVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPD 165 Query: 133 ELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTMIYVTH 192 ELSGG +QRV + R +A +PDILL DE S LD +R +M++E+ +L + T+++++H Sbjct: 166 ELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISH 225 Query: 193 DQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFV-AGFLGSPRMNFLSA 244 D EAM + D+I ++ GGRV QVG+P E+ + PA +V A F G N L+A Sbjct: 226 DLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRGVDPTNILTA 278 Lambda K H 0.320 0.137 0.394 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: 303 Number of extensions: 12 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: 381 Length of database: 415 Length adjustment: 31 Effective length of query: 350 Effective length of database: 384 Effective search space: 134400 Effective search space used: 134400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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