Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_092482139.1 BM299_RS03860 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_900115975.1:WP_092482139.1 Length = 390 Score = 159 bits (403), Expect = 1e-43 Identities = 83/222 (37%), Positives = 132/222 (59%), Gaps = 6/222 (2%) Query: 21 LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMSPKD---- 76 ++N ++++GE +++G SG GKSTL+ C+ L + G I VD +I K Sbjct: 44 IRNASFQVEEGEVFVIMGLSGSGKSTLIRCLNLLNKPTAGEIYVDGDNILEYDKKQLKKF 103 Query: 77 --RDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLLSRKPG 134 +AMVFQ + L +V N+ +GL+++K+P E E + + ++ P Sbjct: 104 RQEKVAMVFQHFGLLSHRTVIGNVEYGLEVKKIPKNERCEIAKKAIANAGLAGWENKMPN 163 Query: 135 QLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTH 194 +LSGG QQRV + RALA P I L DEP S LD +R +M+ E+ + RLK T +++TH Sbjct: 164 ELSGGMQQRVGLARALANDPDILLMDEPFSALDPLIRRDMQYELMELQSRLKKTIIFITH 223 Query: 195 DQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFI 236 D EA +GD+VAVMKDG+I+Q GTP+++ +P + ++ +F+ Sbjct: 224 DINEAFKIGDRVAVMKDGVIEQIGTPEELLASPESEYIENFV 265 Score = 24.3 bits (51), Expect = 0.006 Identities = 14/60 (23%), Positives = 25/60 (41%) Query: 200 MTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNFIPLRLQRKDGRLLALL 259 +T+ D + +K+ + D Y F+ I PL + +DG+LL L+ Sbjct: 321 VTIDDTIKAIKENKTLREILKHDYYTTDCEAFLQDLIPKATDTKYPLAVIDEDGKLLGLI 380 Lambda K H 0.319 0.138 0.393 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: 354 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 386 Length of database: 390 Length adjustment: 30 Effective length of query: 356 Effective length of database: 360 Effective search space: 128160 Effective search space used: 128160 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 (21.7 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