Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= reanno::Dino:3607124 (338 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 157 bits (396), Expect = 6e-43 Identities = 88/243 (36%), Positives = 141/243 (58%), Gaps = 8/243 (3%) Query: 15 TTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVTT----- 69 TT + D + +I GE V +G SG GKST++R L L +SG++ I G D+ Sbjct: 42 TTVGVQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQ 101 Query: 70 -VEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQLEDYLD 128 V+ L+MVFQS+AL PHMTV +N FG++++G + R++R +A + LE + + Sbjct: 102 LVKVRRAKLSMVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAE 161 Query: 129 RKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMI 188 P +LSGG +QRV + R + +P + L DE S LD +R +M+ EL L + T++ Sbjct: 162 SMPDELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIV 221 Query: 189 YVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFV-AEFIGSPAMNVFSS-DV 246 +++HD EAM + D+I ++ GR+ QVG+P ++ P +V A F G N+ ++ D+ Sbjct: 222 FISHDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRGVDPTNILTAGDI 281 Query: 247 GLQ 249 Q Sbjct: 282 ATQ 284 Lambda K H 0.320 0.139 0.396 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: 330 Number of extensions: 21 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: 338 Length of database: 415 Length adjustment: 30 Effective length of query: 308 Effective length of database: 385 Effective search space: 118580 Effective search space used: 118580 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