Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_011384270.1 AMB_RS09430 ABC transporter ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >NCBI__GCF_000009985.1:WP_011384270.1 Length = 262 Score = 128 bits (321), Expect = 2e-34 Identities = 72/189 (38%), Positives = 108/189 (57%), Gaps = 4/189 (2%) Query: 19 LFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVTTVEPADRDLA 78 L D++L++ G+F+ VG SG GKSTLLR +AGL G++ + EP R + Sbjct: 31 LQDLDLEVRHGDFIALVGQSGAGKSTLLRVIAGLVPAVLGQVYVE----PPKEPDSRQIG 86 Query: 79 MVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQLEDYLDRKPGQLSGGQ 138 MVFQ L P V N+E+G++ R+ R A ++ L ++ DR P LSGGQ Sbjct: 87 MVFQDARLLPWRRVLANVEYGLEGLVKSRHERRRRALAALDLVGLTEFADRWPHHLSGGQ 146 Query: 139 RQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYVTHDQVEAM 198 RQRV + RA+ P++ L DEP LD R ++ +L + + G ++I+VTHD EA Sbjct: 147 RQRVGLARALAVRPALLLMDEPFGALDPATRHGLQDQLLSIWQATGTSIIFVTHDIDEAT 206 Query: 199 TMADKIVVL 207 +AD+++VL Sbjct: 207 YLADRVIVL 215 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: 246 Number of extensions: 7 Number of successful extensions: 3 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: 262 Length adjustment: 26 Effective length of query: 312 Effective length of database: 236 Effective search space: 73632 Effective search space used: 73632 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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