Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_018371978.1 BN415_RS05890 amino acid ABC transporter ATP-binding protein
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >NCBI__GCF_000341525.1:WP_018371978.1 Length = 246 Score = 130 bits (327), Expect = 4e-35 Identities = 81/238 (34%), Positives = 131/238 (55%), Gaps = 13/238 (5%) Query: 6 LRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTIDGM 65 +++++K++ +NEV++DI+L I +GE + +G SG GKSTL+R I LE SGG++ G Sbjct: 8 IKHLKKSFGKNEVLKDISLTIHEGEVISIIGSSGSGKSTLLRSINLLEQPSGGEIHYKGT 67 Query: 66 RV----NDVAPAKRGIAMVFQSYALYPHMTLYDN--MAFGLKLAGTKKPEIDAAVRNAAK 119 V D+ + + MVFQS+ L+ ++ + +N +A L + A N K Sbjct: 68 NVLAEGYDLTHYREKLGMVFQSFNLFENLNVLENTIVAQTTVLKRDRSEAEKIAKENLEK 127 Query: 120 ILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARL 179 + + KPKQLSGGQ+QRVAI RA++ P LFDEP S LD +M E ++ Sbjct: 128 VGMGERFWQAKPKQLSGGQKQRVAIARALSMNPDAILFDEPTSALDP----EMVGEVLKI 183 Query: 180 HDELK---TTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFI 234 +L TMI VTH+ A ++D+++ + G + + G+P ++ P F+ Sbjct: 184 MQDLAKEGLTMIVVTHEMEFARDVSDRVIFMDKGVIAEEGNPKDIFTNPKEERTKEFL 241 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: 215 Number of extensions: 7 Number of successful extensions: 4 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: 246 Length adjustment: 27 Effective length of query: 342 Effective length of database: 219 Effective search space: 74898 Effective search space used: 74898 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 24 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