Align Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate Ac3H11_2554 Amino acid ABC transporter, permease protein
Query= TCDB::Q9HU30 (231 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2554 Length = 222 Score = 116 bits (290), Expect = 4e-31 Identities = 70/216 (32%), Positives = 117/216 (54%), Gaps = 12/216 (5%) Query: 11 QLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTS-KYAALRFLGGTYTTIVRGVPETLWVL 69 QLLAG +T++++ A++ +G ++GLL I + + K + L Y +RG P + + Sbjct: 14 QLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLF 73 Query: 70 MIYFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHREA 129 +++FG FG + L F G + LG+ GAY +EV RGA+ SI +G EA Sbjct: 74 ILFFGLPQ--------FG---ILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEA 122 Query: 130 GQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVASNA 189 +++G+S G +VLPQ +P LGN ++ L+K++ALVSL+T+ ++M + Q + Sbjct: 123 ARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISV 182 Query: 190 TKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRG 225 + Y+ A +Y LT + L +E R G Sbjct: 183 SYRSLEVYLAIAVVYFILTGATTLVLRRIELRLRAG 218 Lambda K H 0.327 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: 107 Number of extensions: 3 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: 231 Length of database: 222 Length adjustment: 22 Effective length of query: 209 Effective length of database: 200 Effective search space: 41800 Effective search space used: 41800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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