Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Ga0059261_2293 Ga0059261_2293 cell division ATP-binding protein FtsE
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Korea:Ga0059261_2293 Length = 235 Score = 107 bits (267), Expect = 3e-28 Identities = 65/198 (32%), Positives = 106/198 (53%), Gaps = 9/198 (4%) Query: 4 VTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIF 63 V F++ L Y G T+ + ++ G F + G SG GK++ LR+L + T G + Sbjct: 5 VQFENVGLRY-GTGAETLSDVSFTLSAGSFYFVTGASGAGKTSLLRLLYLAQRPTRGIVR 63 Query: 64 IGDKDVTHVAPRDR------DIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVD 117 + +D + PR R I +VFQ++ L PH++ +N+ L++AG + +I V Sbjct: 64 LFGEDAGAL-PRKRLPGFRRRIGVVFQDFRLLPHLSAYDNVALPLRVAGIPEADIEGPVR 122 Query: 118 EAAATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQ 177 E A +GL + KP LSGG++QR+A+ RA++ P++ + DEP N+D + + Sbjct: 123 EMIAWVGLKDRDSAKPPTLSGGEQQRIAIARAVITRPEILIADEPTGNVDPDMAERLLHL 182 Query: 178 IAALQRKLGVTTVYVTHD 195 +L R LG T V THD Sbjct: 183 FDSLNR-LGTTVVVATHD 199 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: 195 Number of extensions: 7 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: 235 Length adjustment: 26 Effective length of query: 350 Effective length of database: 209 Effective search space: 73150 Effective search space used: 73150 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 17 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