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 Pf6N2E2_4281 Amino acid ABC transporter, permease protein
Query= TCDB::Q9HU30 (231 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4281 Length = 265 Score = 129 bits (323), Expect = 7e-35 Identities = 76/229 (33%), Positives = 120/229 (52%), Gaps = 15/229 (6%) Query: 2 ILDLHGFGEQLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRG 61 +L +H L G +TL L L ++ LLG + A+A+ S A + Y + RG Sbjct: 48 LLGVHLAPNGFLQGAVLTLFLCLCSIVASSLLGFITALARLSSSAVAFGIASFYASFFRG 107 Query: 62 VPETLWVLMIYFGTVSGLNALGDLFGKPDLALSP--FAAGTLALGLCFGAYATEVFRGAL 119 P + +L+IY G P L + P AAG +AL L +GAY +E+FR + Sbjct: 108 TPLLIQILLIYLGL-------------PQLGVVPGAIAAGIIALSLNYGAYLSEIFRAGI 154 Query: 120 LSIPRGHREAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEI 179 L +P G REA ALGLS IFWR+ LPQ R +P N ++ +LKD++L+S++ + E+ Sbjct: 155 LGVPHGQREASLALGLSETVIFWRVTLPQAMRTIIPPTTNQFISMLKDSSLISVMGVWEV 214 Query: 180 MRKAQVASNATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRGFVR 228 M AQ ++ TAA IY +++ + + +ER G+ +++ Sbjct: 215 MFLAQSYGRSSYRYIEMLTTAAIIYWLMSIALELIQARMERHYGKAYLK 263 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: 155 Number of extensions: 6 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: 265 Length adjustment: 24 Effective length of query: 207 Effective length of database: 241 Effective search space: 49887 Effective search space used: 49887 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