Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate GFF3909 PGA1_65p00120 putative amino-acid ABC transporter, permease protein
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__Phaeo:GFF3909 Length = 224 Score = 102 bits (255), Expect = 5e-27 Identities = 67/227 (29%), Positives = 115/227 (50%), Gaps = 10/227 (4%) Query: 4 DFDFLFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFR 63 D ++ + LL+ VP TL + +++L +L+ ++ RV + ++ +I FR Sbjct: 5 DIAYMLGLVPVLLSYVPLTLFMAVVAMVLALVLASLLAVERVLRIPVLDQLVVLFISFFR 64 Query: 64 GSPLLIQMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAV 123 G+PLL+Q+FL YYG+ Q + A++ L L A Y AE IR ++ V Sbjct: 65 GTPLLVQLFLFYYGLPQVLSVLTQI------NGVSAAIMGLTLHFAAYMAESIRAAILGV 118 Query: 124 PVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGV 183 Q EA SIG++ ++RR++ P A R P + ++K T+LA + V E+ G Sbjct: 119 DRSQWEAAQSIGMTRGQMMRRIVLPQAARIAAPTLVNYFIDMIKGTSLAFTLGVTEMMGA 178 Query: 184 AQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETRLSRHLRAA 230 Q+ ++ E F+ A+IY +++V L +++ RL HL A Sbjct: 179 TQKEAAGSFLYFEAFLVVAVIY----WILVEALSLVQRRLETHLNKA 221 Lambda K H 0.331 0.143 0.431 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: 121 Number of extensions: 5 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: 250 Length of database: 224 Length adjustment: 23 Effective length of query: 227 Effective length of database: 201 Effective search space: 45627 Effective search space used: 45627 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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