Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Dsui_0842 Dsui_0842 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__PS:Dsui_0842 Length = 593 Score = 187 bits (475), Expect = 5e-52 Identities = 113/265 (42%), Positives = 162/265 (61%), Gaps = 16/265 (6%) Query: 9 TPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRL 68 T LL E +T RFGGLVA D++ + GE+ A+IGPNGAGK+T+FNCI+G P+ GR+ Sbjct: 343 TVLLQAEGVTKRFGGLVANKDMALTVQAGEVMALIGPNGAGKSTMFNCISGVNPPSEGRI 402 Query: 69 TLRHADGKEFLLERMPGY--RISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASG 126 + FL + + G R + ++RTFQ++RL GM+VLEN+ + H +R Sbjct: 403 S--------FLGQPVAGLEARDIARLGLSRTFQHVRLLSGMTVLENVAIGAH---LRGRH 451 Query: 127 FSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTE 186 +A GL E + A ++RV L E AG+L G QR +EIARA+ + Sbjct: 452 NYLAA--GLRLERAEEARLLAEAARQIERVGLAEHMFDAAGSLALGKQRIIEIARALAAD 509 Query: 187 PVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGR 246 P +L LDEPAAGL E LA+LL +R E +G+LL+EHDM VM ++D VVV+++G Sbjct: 510 PCLLLLDEPAAGLRYLEKQALAELLRKLRGE-GMGILLVEHDMDFVMGLADRVVVMEFGE 568 Query: 247 KISDGDPAFVKNDPAVIRAYLGEEE 271 K+++G P ++ +PAV+ AYLG E Sbjct: 569 KLAEGLPEEIQKNPAVLEAYLGGVE 593 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: 397 Number of extensions: 17 Number of successful extensions: 4 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: 593 Length adjustment: 31 Effective length of query: 263 Effective length of database: 562 Effective search space: 147806 Effective search space used: 147806 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: 50 (23.9 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