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_086510333.1 BZY95_RS12915 glutamine ABC transporter permease GlnP
Query= TCDB::Q9HU30 (231 letters) >NCBI__GCF_002151265.1:WP_086510333.1 Length = 218 Score = 112 bits (280), Expect = 6e-30 Identities = 70/214 (32%), Positives = 110/214 (51%), Gaps = 10/214 (4%) Query: 8 FGEQLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLW 67 F QLL G MT+ +++ +C G+++G + I + L + Y ++RG P + Sbjct: 11 FMPQLLKGAQMTIFITVVGLCGGMVVGAIAGIMRAYGNWLLNYTAMVYIEVIRGTPIVVQ 70 Query: 68 VLMIYFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHR 127 V+ +YF L L + + P +A +A+ + GAY E+ RG+L SI RG Sbjct: 71 VMFLYFA----LPVLASI------RIDPLSAAMIAIVINAGAYIAEIVRGSLQSISRGLA 120 Query: 128 EAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVAS 187 EAG ALGL ++ IV P +R +P LGN ++I LKDT+L +I + E+ R Q Sbjct: 121 EAGLALGLPRWKVLLYIVGPLAFRRLIPPLGNQFIISLKDTSLFIVIGVGELTRTGQEIM 180 Query: 188 NATKEPFTFYMTAAAIYLSLTVVIMVALHFLERR 221 A + A +YL +T + + L F+ERR Sbjct: 181 AANFRAVEIWSAIAIMYLIMTGSLTLMLRFIERR 214 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: 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: 218 Length adjustment: 22 Effective length of query: 209 Effective length of database: 196 Effective search space: 40964 Effective search space used: 40964 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