Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__SynE:Synpcc7942_0247 Length = 377 Score = 79.3 bits (194), Expect = 1e-19 Identities = 46/129 (35%), Positives = 73/129 (56%) Query: 97 YMCAVLSLALCTAGYTAEIIRGGLMAVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLP 156 + +L L T + EIIRGG+++VP GQ EA ++GL+ L +++ P ALR +P Sbjct: 245 FTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVP 304 Query: 157 AYSTEAVLLVKSTALASLVTVWEVTGVAQQIIQQTYRTTEVFICAALIYLFLNFVIVRLL 216 + +++ V K+++LA V ++ AQ + QT R EVF+ L YL +N VI + Sbjct: 305 SLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGM 364 Query: 217 GMLETRLSR 225 L+ RL R Sbjct: 365 NGLQQRLQR 373 Score = 36.6 bits (83), Expect = 8e-07 Identities = 17/64 (26%), Positives = 34/64 (53%) Query: 13 KQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLIQMF 72 + L+ + +L + LIL ++ + S +WL + +R Y+ V R +PLL+Q+ Sbjct: 80 RALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLI 139 Query: 73 LVYY 76 + Y+ Sbjct: 140 VWYF 143 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: 226 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 250 Length of database: 377 Length adjustment: 27 Effective length of query: 223 Effective length of database: 350 Effective search space: 78050 Effective search space used: 78050 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: 48 (23.1 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