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 WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease
Query= TCDB::Q9HU30 (231 letters) >NCBI__GCF_900115975.1:WP_092487756.1 Length = 234 Score = 136 bits (343), Expect = 3e-37 Identities = 77/222 (34%), Positives = 123/222 (55%), Gaps = 8/222 (3%) Query: 12 LLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLWVLMI 71 + G +TL++++ +V +G LLGL+G +++ S+ LRFL Y RG P + + ++ Sbjct: 12 IFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFIV 71 Query: 72 YFGTVSGLNALG----DLFGKPDLA----LSPFAAGTLALGLCFGAYATEVFRGALLSIP 123 YFG L L D +G +A L F A +A L GAY E+FR + SI Sbjct: 72 YFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSIE 131 Query: 124 RGHREAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKA 183 RG EA ++LG++ G+ ++LPQ ++ +P LGN ++ +LKDT+L+S+I E+ R Sbjct: 132 RGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTRNG 191 Query: 184 QVASNATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRG 225 Q+ T E F ++T IYL +T + + +LERR G Sbjct: 192 QLIIARTYESFAIWLTVGFIYLIMTFTLSRIVDYLERRYKTG 233 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: 109 Number of extensions: 5 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: 234 Length adjustment: 23 Effective length of query: 208 Effective length of database: 211 Effective search space: 43888 Effective search space used: 43888 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