Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_092482139.1 BM299_RS03860 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_900115975.1:WP_092482139.1 Length = 390 Score = 152 bits (385), Expect = 1e-41 Identities = 81/218 (37%), Positives = 125/218 (57%), Gaps = 6/218 (2%) Query: 23 NLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEPKD------RG 76 + ++ GE V++G SG GKSTL+ C+ L + G+I++ N+ + K Sbjct: 48 SFQVEEGEVFVIMGLSGSGKSTLIRCLNLLNKPTAGEIYVDGDNILEYDKKQLKKFRQEK 107 Query: 77 IGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPSELSG 136 + MVFQ + L TV N+ +GL+V KIP E + K+A + + P+ELSG Sbjct: 108 VAMVFQHFGLLSHRTVIGNVEYGLEVKKIPKNERCEIAKKAIANAGLAGWENKMPNELSG 167 Query: 137 GQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVTHDQIE 196 G +QRV + RAL D D+ L DEP S LD +R +++ E+ L LK T+I++THD E Sbjct: 168 GMQQRVGLARALANDPDILLMDEPFSALDPLIRRDMQYELMELQSRLKKTIIFITHDINE 227 Query: 197 ALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFI 234 A + DR+AVMK GVI+Q+ P + +PE+ ++ F+ Sbjct: 228 AFKIGDRVAVMKDGVIEQIGTPEELLASPESEYIENFV 265 Lambda K H 0.320 0.137 0.392 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: 304 Number of extensions: 16 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: 361 Length of database: 390 Length adjustment: 30 Effective length of query: 331 Effective length of database: 360 Effective search space: 119160 Effective search space used: 119160 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