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 GFF2975 HP15_2919 amino acid ABC transporter, permease protein
Query= TCDB::Q9HU30 (231 letters) >FitnessBrowser__Marino:GFF2975 Length = 223 Score = 134 bits (336), Expect = 2e-36 Identities = 78/210 (37%), Positives = 116/210 (55%), Gaps = 10/210 (4%) Query: 12 LLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLWVLMI 71 L+ G TL +S + +G LG+ + +K LR+ Y I RG P + VL I Sbjct: 19 LIKGIPYTLLISFGGLLIGFALGIFFGLLSINKKWFLRWPATAYIEIFRGTPILVQVLFI 78 Query: 72 YFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHREAGQ 131 ++G L DL G P + P AG A+ L GAY +EV RG + SI +G EAG Sbjct: 79 FYG-------LPDLIGGP---IDPLTAGIAAIALNSGAYISEVVRGGVQSIDKGQTEAGL 128 Query: 132 ALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVASNATK 191 +LGLS + FW +V PQ +R +P LGN ++ +KDT+L S+I + E++R+ Q+ T Sbjct: 129 SLGLSRTQTFWSVVWPQAFRRMIPPLGNQAIVSIKDTSLFSVIGVGELVRQGQIYIANTF 188 Query: 192 EPFTFYMTAAAIYLSLTVVIMVALHFLERR 221 F Y A +YL++T+ + + L F+ERR Sbjct: 189 TAFEVYFVVAILYLAITLSLSIILRFVERR 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: 132 Number of extensions: 8 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: 223 Length adjustment: 22 Effective length of query: 209 Effective length of database: 201 Effective search space: 42009 Effective search space used: 42009 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