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::Q70HW1 (384 letters) >FitnessBrowser__Korea:Ga0059261_2293 Length = 235 Score = 104 bits (259), Expect = 3e-27 Identities = 59/186 (31%), Positives = 99/186 (53%), Gaps = 6/186 (3%) Query: 15 GQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPP 74 G T+ D + + F G SG GKT+ LR++ + T G + + +P Sbjct: 15 GTGAETLSDVSFTLSAGSFYFVTGASGAGKTSLLRLLYLAQRPTRGIVRLFGEDAGALPR 74 Query: 75 KD-----RDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLL 129 K R I +VFQ++ L PH++ Y N+A L++ +P+A+I+ V+E + + Sbjct: 75 KRLPGFRRRIGVVFQDFRLLPHLSAYDNVALPLRVAGIPEADIEGPVREMIAWVGLKDRD 134 Query: 130 DRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTV 189 KP LSGG++QR+A+ RA++ P++ + DEP N+D + ++ L+ RL TTV Sbjct: 135 SAKPPTLSGGEQQRIAIARAVITRPEILIADEPTGNVDPDMAERLLHLFDSLN-RLGTTV 193 Query: 190 IYVTHD 195 + THD Sbjct: 194 VVATHD 199 Lambda K H 0.321 0.138 0.395 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: 219 Number of extensions: 7 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: 384 Length of database: 235 Length adjustment: 27 Effective length of query: 357 Effective length of database: 208 Effective search space: 74256 Effective search space used: 74256 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: 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