Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate Ac3H11_2554 Amino acid ABC transporter, permease protein
Query= uniprot:A0A0H3PA28 (219 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2554 Length = 222 Score = 97.4 bits (241), Expect = 2e-25 Identities = 60/199 (30%), Positives = 107/199 (53%), Gaps = 6/199 (3%) Query: 13 LMQGLFLTLKIALATCIISIVFGTFLAITK-NYGDRLSKFLAACYIDIFRNTPLLLWMLA 71 L+ G +T++I A+ ++ V G + I + N R+ L Y+ R TPLL+ + Sbjct: 15 LLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLFI 74 Query: 72 ACFVLPVFFGQFPQAFWGTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYSQGFGKFFTL 131 F LP F P G IG +Y+ + ++E++RG + SI KGQ EAA S G + Sbjct: 75 LFFGLPQFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSSGLAM 134 Query: 132 FYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILA-KLTSFEEILAMI 190 ++LPQ ++IP L ++ + +K++A ++ L I +L + + I++ S E LA Sbjct: 135 RTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLEVYLA-- 192 Query: 191 GVVAGIYFIICFSLSMLVR 209 +A +YFI+ + ++++R Sbjct: 193 --IAVVYFILTGATTLVLR 209 Lambda K H 0.331 0.144 0.428 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: 122 Number of extensions: 5 Number of successful extensions: 1 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: 219 Length of database: 222 Length adjustment: 22 Effective length of query: 197 Effective length of database: 200 Effective search space: 39400 Effective search space used: 39400 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: 45 (21.9 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