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 PP_0281 PP_0281 Amino acid ABC transporter, permease protein
Query= TCDB::Q9HU30 (231 letters) >FitnessBrowser__Putida:PP_0281 Length = 230 Score = 318 bits (814), Expect = 7e-92 Identities = 154/230 (66%), Positives = 190/230 (82%) Query: 1 MILDLHGFGEQLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVR 60 M +DLHGFG ++AGT MT+KL+L A+ +GL+LGLLGA+AKTS + L++LGG Y+T+VR Sbjct: 1 MNIDLHGFGPAMMAGTLMTVKLALCALLLGLVLGLLGALAKTSPFKPLQWLGGFYSTLVR 60 Query: 61 GVPETLWVLMIYFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALL 120 GVPE LWVL+IYFGTV +N+LG+ P L LS FAAG +ALGLCFGAYATEVFRGA+L Sbjct: 61 GVPELLWVLLIYFGTVGLMNSLGEALNMPGLELSAFAAGVIALGLCFGAYATEVFRGAIL 120 Query: 121 SIPRGHREAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIM 180 +IP+GHREAG ALGLS GRI RI+LPQ+WR+ALPGLGNL++IL+KDTALVS+I L+EIM Sbjct: 121 AIPKGHREAGLALGLSKGRILSRIILPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIM 180 Query: 181 RKAQVASNATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRGFVRNE 230 R +Q+ TKEPFTFYM AA IYL LTV+ M +HF+E+RA RGF R E Sbjct: 181 RHSQIGVTVTKEPFTFYMVAACIYLGLTVLAMTGMHFMEKRAARGFARAE 230 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: 208 Number of extensions: 7 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: 231 Length of database: 230 Length adjustment: 23 Effective length of query: 208 Effective length of database: 207 Effective search space: 43056 Effective search space used: 43056 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