Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 197 bits (501), Expect = 4e-55 Identities = 121/297 (40%), Positives = 174/297 (58%), Gaps = 14/297 (4%) Query: 4 LLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD---- 59 L + D+ + G ++ G+ LD+ +GE V +GPSG GK+TLLR IAGLE + G Sbjct: 6 LSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRIG 65 Query: 60 --MFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGA 117 M + + +V KR + VFQSYAL+PH TVY+N+A+G+++ + EI +RV+ Sbjct: 66 EQMVFESAKKIEVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQRVQEV 125 Query: 118 ADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIA 177 L L +R P LSGGQ+QRVA+ R++ NP+V L DEPLSNLDA LR RI + Sbjct: 126 LANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARIWLR 185 Query: 178 KLSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGS 237 +L + + + + VTHDQ EAM +AD++V+L G IEQ G P E+Y P +LFVA F+G Sbjct: 186 QLIIDL-NLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFMG- 243 Query: 238 PAMNVIPATITATGQQTAVSLAGGKSV--TLDVPTNASENGKTASFGVRPEDLRVTE 292 A N I +T +A G ++ L P A G A+ VR E +++ + Sbjct: 244 -ANNTISGLVTDVDGDSARIEGNGWALRGRLRTPLKA---GDRATAVVRLEKIKLAQ 296 Lambda K H 0.320 0.137 0.387 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: 315 Number of extensions: 14 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: 362 Length of database: 353 Length adjustment: 29 Effective length of query: 333 Effective length of database: 324 Effective search space: 107892 Effective search space used: 107892 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: 49 (23.5 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