Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 8501895 DvMF_2610 ABC transporter related (RefSeq)
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Miya:8501895 Length = 270 Score = 246 bits (628), Expect = 4e-70 Identities = 130/268 (48%), Positives = 176/268 (65%), Gaps = 4/268 (1%) Query: 3 TQSMTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYT 62 T + +L V ++M FGGL A+N+V GEI A+IGPNGAGKTT FNCITG Y Sbjct: 4 TTANAAAAVLDVRSISMNFGGLRALNEVDLQVRQGEIVALIGPNGAGKTTFFNCITGIYV 63 Query: 63 PTVGRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLI 122 PT G + + DG+ + + +++ ++RTFQNIRLF MSVLEN+++ +H Sbjct: 64 PTEGTVHVTPRDGRTVTVNGLKASQVTA-LGMSRTFQNIRLFPTMSVLENVMIGRH---C 119 Query: 123 RASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARA 182 R + LL P E+ V+ + L V L + EA NLPYGAQRRLEIARA Sbjct: 120 RTRAGILGALLRDPKTRAEEQRIVEESYALLKSVNLHQHYKDEARNLPYGAQRRLEIARA 179 Query: 183 MCTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVL 242 + TEP +LCLDEPAAG+NP+E+ EL +L+ IR+ H++ VLLIEHDMS+VM++SD + V+ Sbjct: 180 LATEPFLLCLDEPAAGMNPQETHELKELVIEIRERHELSVLLIEHDMSMVMSLSDRIYVM 239 Query: 243 DYGRKISDGDPAFVKNDPAVIRAYLGEE 270 +YG KI++G P V +P VI+AYLGEE Sbjct: 240 EYGSKIAEGTPEEVSKNPRVIKAYLGEE 267 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: 201 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: 294 Length of database: 270 Length adjustment: 26 Effective length of query: 268 Effective length of database: 244 Effective search space: 65392 Effective search space used: 65392 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