Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 6938983 Sama_3081 ABC transporter, ATP-binding protein, putative (RefSeq)
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__SB2B:6938983 Length = 270 Score = 103 bits (258), Expect = 3e-27 Identities = 85/268 (31%), Positives = 131/268 (48%), Gaps = 24/268 (8%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 L+ V +L G V D+S S G++TAI+GP+G GKTTL I G P G + Sbjct: 8 LVEVRNLGFSRGERVIYEDISLSIPKGKVTAIMGPSGIGKTTLLKLIAGQLVPDHGEVLF 67 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 + + + R + + ++ S+ FQ+ LF M+V +N+ A L SG A Sbjct: 68 DGVNIHD--ISRSELFELRKRMSML--FQSGALFTDMNVFDNIAFA----LREHSGLDEA 119 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 + + L K L+ V L A L G QRR+ +ARA+ EP M+ Sbjct: 120 II-----------RRIVLMK--LEAVGLRGAAMLMPSELSGGMQRRVALARAIALEPEMV 166 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 DEP AG +P G L L+ + D + +++ HD+ V+ I+D+V V+ R I+ Sbjct: 167 MYDEPFAGQDPISMGVLVKLIRELSDALNLTSVVVSHDVGEVLGIADYVYVIAEKRIIAQ 226 Query: 251 GDPAFVK--NDPAVIRAYLGEEEDEELP 276 G PA +K +DP +R ++G E D +P Sbjct: 227 GTPAQLKSSHDPR-LRQFIGGEPDGPVP 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: 169 Number of extensions: 10 Number of successful extensions: 2 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