Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 8500413 DvMF_1163 ABC transporter related (RefSeq)
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Miya:8500413 Length = 255 Score = 203 bits (516), Expect = 4e-57 Identities = 117/264 (44%), Positives = 168/264 (63%), Gaps = 15/264 (5%) Query: 10 PLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLT 69 PLL ++ +T RFGGL AV+D + S ++ A+IGPNGAGKTT+FN ++GFY PT G++ Sbjct: 2 PLLEMKGVTQRFGGLQAVSDFNISLEERKLIALIGPNGAGKTTVFNLVSGFYQPTEGQII 61 Query: 70 LRHADGKEFLLERMPGYRISQKAS--VARTFQNIRLFGGMSVLENLIVAQHNKLIRASGF 127 DGK G R Q + +ARTFQNIRL+ MSVL+N+ +AQH++L G+ Sbjct: 62 F---DGKP-----TAGLRPHQVTARGIARTFQNIRLWHEMSVLDNIRIAQHHRL----GY 109 Query: 128 SI-AGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTE 186 +I L +TR+E +A L+ + L + A NLPYG QRR+EIARAM Sbjct: 110 TIWDAFLRTGRFTRSEGNIDTIAWEMLEAMDLKDAAHELPRNLPYGLQRRVEIARAMSIR 169 Query: 187 PVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGR 246 P +L LDEPAAGLN + L L+ +I DE I + +IEH M VVM++ + + V+D+G Sbjct: 170 PKLLLLDEPAAGLNSADVDGLIKLIRWIHDEFDIAIWMIEHQMKVVMSLCEWIKVIDFGS 229 Query: 247 KISDGDPAFVKNDPAVIRAYLGEE 270 I++G P ++++P VI+AYLG++ Sbjct: 230 TIAEGTPEEIQSNPVVIKAYLGDD 253 Lambda K H 0.319 0.137 0.397 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: 205 Number of extensions: 10 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: 294 Length of database: 255 Length adjustment: 25 Effective length of query: 269 Effective length of database: 230 Effective search space: 61870 Effective search space used: 61870 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