Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Ga0059261_2293 Ga0059261_2293 cell division ATP-binding protein FtsE
Query= reanno::Phaeo:GFF1302 (334 letters) >FitnessBrowser__Korea:Ga0059261_2293 Length = 235 Score = 120 bits (300), Expect = 4e-32 Identities = 67/196 (34%), Positives = 108/196 (55%), Gaps = 7/196 (3%) Query: 4 IKLESVTKNFGP-VEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRI 62 ++ E+V +G E + + T+ G F G SG GK++LLRL+ + T G +R+ Sbjct: 5 VQFENVGLRYGTGAETLSDVSFTLSAGSFYFVTGASGAGKTSLLRLLYLAQRPTRGIVRL 64 Query: 63 DGEDA-----TNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNA 117 GEDA +P +R + +VFQ + L PH+S N+A P+++AGIP + + + Sbjct: 65 FGEDAGALPRKRLPGFRRRIGVVFQDFRLLPHLSAYDNVALPLRVAGIPEADIEGPVREM 124 Query: 118 AAALNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEIS 177 A + L D +P LSGG++QR+AI RA++ P + DEP N+D + + L + Sbjct: 125 IAWVGLKDRDSAKPPTLSGGEQQRIAIARAVITRPEILIADEPTGNVDPDMAERL-LHLF 183 Query: 178 ELHKRLATTMIYVTHD 193 + RL TT++ THD Sbjct: 184 DSLNRLGTTVVVATHD 199 Lambda K H 0.320 0.138 0.400 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: 204 Number of extensions: 5 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: 334 Length of database: 235 Length adjustment: 26 Effective length of query: 308 Effective length of database: 209 Effective search space: 64372 Effective search space used: 64372 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: 47 (22.7 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