Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate AO356_08485 AO356_08485 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_08485 Length = 290 Score = 263 bits (672), Expect = 3e-75 Identities = 141/287 (49%), Positives = 188/287 (65%), Gaps = 27/287 (9%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L VE+L M+FGG+ A++DVS I A+IGPNGAGKTT+FNC+TGFY T G++ L Sbjct: 5 VLKVENLMMQFGGIKALSDVSLQVKRNSIFALIGPNGAGKTTVFNCLTGFYKATGGKIEL 64 Query: 71 -----------------RHAD-------GKEFLLERMPGYRISQKASVARTFQNIRLFGG 106 R D + G + +A +ARTFQNIRLF Sbjct: 65 NVRGEQTNVIKLLGEAFRPTDFVSPKSFASRLYYKMFGGTHLVNRAGLARTFQNIRLFKE 124 Query: 107 MSVLENLIVAQHNKLIRASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEA 166 MSVLENL+VAQH + R+ +AG+L Y + E +A+D A YWL+ V L++ A+ A Sbjct: 125 MSVLENLLVAQHMWVNRS---MVAGILNTKGYRKAESDALDHAFYWLEVVDLVDCANRLA 181 Query: 167 GNLPYGAQRRLEIARAMCTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIE 226 G L YG QRRLEIARAMCT P ++CLDEPAAGLNP+E+ L+ ++ +RDEH + V+LIE Sbjct: 182 GELSYGQQRRLEIARAMCTRPQIICLDEPAAGLNPQETEALSAMIRLLRDEHDLTVVLIE 241 Query: 227 HDMSVVMTISDHVVVLDYGRKISDGDPAFVKNDPAVIRAYLGEEEDE 273 HDM +VM+ISDH+VVLD+G I++G P ++NDP VI AYLG +E+E Sbjct: 242 HDMGMVMSISDHIVVLDHGNVIAEGGPEAIRNDPKVIAAYLGADEEE 288 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: 230 Number of extensions: 4 Number of successful extensions: 3 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: 294 Length of database: 290 Length adjustment: 26 Effective length of query: 268 Effective length of database: 264 Effective search space: 70752 Effective search space used: 70752 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 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