Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >NCBI__GCF_000526715.1:WP_024852149.1 Length = 263 Score = 147 bits (372), Expect = 2e-40 Identities = 90/217 (41%), Positives = 131/217 (60%), Gaps = 4/217 (1%) Query: 18 VMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTIDGMRVNDVAPAKRGI 77 V+ +INL+I G+ +G SGCGKSTL++MIAGL S G + I+G V V P+ + Sbjct: 24 VLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVRINGKTV--VKPSAKW- 80 Query: 78 AMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKILHIDHLLDRKPKQLSGG 137 M+FQ +LYP M++ +N A GL AGT K + D V ++ + D+ ++LSGG Sbjct: 81 NMMFQKPSLYPWMSVRENAALGLVFAGTYKQKQDR-VEELLDMVGLSEHKDKNVQELSGG 139 Query: 138 QRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLHDELKTTMIYVTHDQVEA 197 Q+QRVA+ R++ +P++ L DEP S LDA R ++ E A++ E TMI VTHD EA Sbjct: 140 QQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQICHEQGITMIMVTHDIEEA 199 Query: 198 MTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFI 234 + +ADK+V++S E VG + P +R A FI Sbjct: 200 IAMADKVVIMSHNPGEIVGDLDVPLTYPRDRSAADFI 236 Lambda K H 0.320 0.135 0.384 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: 194 Number of extensions: 9 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: 369 Length of database: 263 Length adjustment: 27 Effective length of query: 342 Effective length of database: 236 Effective search space: 80712 Effective search space used: 80712 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 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