Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate GFF3209 PGA1_c32620 high-affinity branched-chain amino acid transport ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__Phaeo:GFF3209 Length = 269 Score = 216 bits (551), Expect = 3e-61 Identities = 112/252 (44%), Positives = 158/252 (62%), Gaps = 1/252 (0%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 ++++++++ RFGG+ A+ + I G+I +IGPNGAGK++ NVI+G Y P G Sbjct: 17 VMEMKNITLRFGGVVAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQEGEVLF 76 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124 GKP P+EVA+ GIARTFQNI LF M+VL+NVM G K N+F A Sbjct: 77 RGKPRPQMRPYEVARQGIARTFQNIALFDGMSVLDNVMTGRLNFMKTNIFQQAIWRGKAE 136 Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184 EE RE ++++DF+ I K L YG ++R+E+ARALA +P+LL LDEP AGM Sbjct: 137 AEETENREAVERIIDFLEIQAIRKTPVARLPYGLKKRVELARALAAEPKLLLLDEPMAGM 196 Query: 185 NATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKN 243 N EK + ++ + E G TI LIEHD+ ++M L +R+ V+DYGK I +G P +V+ N Sbjct: 197 NVEEKEDMSRFILDVNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGKKIGDGTPDEVRNN 256 Query: 244 PAVIEAYLGAGH 255 VI+AYLG H Sbjct: 257 QDVIDAYLGVSH 268 Lambda K H 0.320 0.138 0.394 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: 184 Number of extensions: 6 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: 255 Length of database: 269 Length adjustment: 25 Effective length of query: 230 Effective length of database: 244 Effective search space: 56120 Effective search space used: 56120 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