Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF3091 PGA1_c31420 branched-chain amino acid transport system ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Phaeo:GFF3091 Length = 258 Score = 158 bits (400), Expect = 1e-43 Identities = 100/261 (38%), Positives = 146/261 (55%), Gaps = 14/261 (5%) Query: 8 TTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGR 67 T PLLT + LT+RFGG VAV+ V+ + + GE+TAI+GPNGAGKTT FN I+G + GR Sbjct: 2 TAPLLTTDDLTVRFGGHVAVDAVTCAFHAGELTAIVGPNGAGKTTYFNLISGQIPASAGR 61 Query: 68 LTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGF 127 +TL D + KA + R FQ LF ++VLEN+ + K R GF Sbjct: 62 VTLNGQDISAASVSART------KAGIGRAFQMTNLFPDLTVLENVRLVVQAKARR--GF 113 Query: 128 SIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEP 187 + L S + +D A+ L RVRLL+ + L +G QR+LE+A + +P Sbjct: 114 N------LWSVVTGHTDLMDQAEEILARVRLLDERNQIVSELSHGNQRKLEVALLIALDP 167 Query: 188 VMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRK 247 ++ DEP AG++ E+ + DL+ ++ + VLL+EH M V+ T++D ++VL G Sbjct: 168 LIYMFDEPTAGMSVDEAPVVLDLIADLKAQTDRTVLLVEHKMDVIRTLADRIIVLHNGAL 227 Query: 248 ISDGDPAFVKNDPAVIRAYLG 268 +DG PA V V AY+G Sbjct: 228 AADGAPAEVMASDIVQEAYMG 248 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: 180 Number of extensions: 7 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: 258 Length adjustment: 25 Effective length of query: 269 Effective length of database: 233 Effective search space: 62677 Effective search space used: 62677 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