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 AO353_11990 AO353_11990 ABC transporter permease
Query= TCDB::Q9HU30 (231 letters) >FitnessBrowser__pseudo3_N2E3:AO353_11990 Length = 231 Score = 323 bits (827), Expect = 2e-93 Identities = 155/229 (67%), Positives = 193/229 (84%) Query: 1 MILDLHGFGEQLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVR 60 M +DL+GFG L AG MT+KL+L+A+C+GL+LGLLGA+AKTS Y L++LGGTY+T+VR Sbjct: 1 MTIDLYGFGPALAAGALMTVKLALSALCLGLVLGLLGALAKTSPYKPLQWLGGTYSTLVR 60 Query: 61 GVPETLWVLMIYFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALL 120 G+PE LWVL+IYFGTV+ + ALG+ FG PDLAL+ FAAG +ALGLCFGAYATEVFRGA+L Sbjct: 61 GIPELLWVLLIYFGTVNLMRALGEFFGNPDLALNAFAAGVIALGLCFGAYATEVFRGAIL 120 Query: 121 SIPRGHREAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIM 180 +IP+GHREAG ALGLS RIF R++LPQ+WR+ALPGLGNL++IL+KDTALVS+I L+EIM Sbjct: 121 AIPKGHREAGVALGLSKLRIFTRLILPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIM 180 Query: 181 RKAQVASNATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRGFVRN 229 R AQ TK+PFTFYM AA +YL LT++ M +H LE+RA RGF RN Sbjct: 181 RHAQNGVTMTKQPFTFYMVAAFMYLGLTILAMTGMHLLEKRAARGFARN 229 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: 211 Number of extensions: 9 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: 231 Length adjustment: 23 Effective length of query: 208 Effective length of database: 208 Effective search space: 43264 Effective search space used: 43264 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 Apr 09 2024. 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