Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_057508140.1 ABB28_RS08055 lipoprotein-releasing system ATP-binding protein LolD
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_001431535.1:WP_057508140.1 Length = 237 Score = 110 bits (275), Expect = 4e-29 Identities = 66/202 (32%), Positives = 106/202 (52%), Gaps = 7/202 (3%) Query: 19 PTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAP---- 74 P +L+++ GE + ++G SG GKST L +L GL+ + G +F+ + ++ ++ Sbjct: 29 PVFDGLDLQVSAGETVAIIGASGAGKSTLLHLLGGLDTPSAGEVFVTGQQMSTLSDGARG 88 Query: 75 --RDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERK 132 R+R + V+Q + L P T EN+ + + G N R + ++GL L+ K Sbjct: 89 LLRNRALGFVYQFHHLLPEFTALENVMMPVLLGGGEVAAANDRARQLLESVGLGHRLQHK 148 Query: 133 PKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYV 192 P LSGG+RQR A+ RA+V P L DEP NLD + + L R + V V Sbjct: 149 PGELSGGERQRAAVARALVNQPACVLGDEPTGNLDDRTAGTVFELMLELNRARHTSLVLV 208 Query: 193 THDQTEALTMGDRIAVLKDGYL 214 THD++ A + DR+ L++G L Sbjct: 209 THDRSLARKL-DRVLELREGKL 229 Lambda K H 0.316 0.135 0.380 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: 197 Number of extensions: 11 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: 376 Length of database: 237 Length adjustment: 26 Effective length of query: 350 Effective length of database: 211 Effective search space: 73850 Effective search space used: 73850 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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