Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 135 bits (341), Expect = 9e-37 Identities = 80/202 (39%), Positives = 109/202 (53%), Gaps = 3/202 (1%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTH--VAPRDRDIAMV 82 +L I G F+ LVG SG GK+T L+ + L + G I I +DV VA R I V Sbjct: 21 SLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVAAQPVAELRRRIGYV 80 Query: 83 FQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGL-TEFLERKPKALSGGQR 141 FQ L+PHM+V EN+ ++ G ++E RV E + L +F ER+P LSGGQ Sbjct: 81 FQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLVALPADFAERRPAQLSGGQA 140 Query: 142 QRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALT 201 QRV RA+ P + LMDEP LD R + AL +G+T++ VTHD EAL Sbjct: 141 QRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEAMGLTSLIVTHDMAEALL 200 Query: 202 MGDRIAVLKDGYLQQVGAPREL 223 + DR+ V+ +G + PR L Sbjct: 201 LADRVIVIGEGRILADQPPRAL 222 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: 212 Number of extensions: 12 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: 1 Length of query: 376 Length of database: 252 Length adjustment: 27 Effective length of query: 349 Effective length of database: 225 Effective search space: 78525 Effective search space used: 78525 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 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