Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, 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 AZOBR_RS27130 AZOBR_RS27130 polyamine ABC transporter substrate-binding protein
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__azobra:AZOBR_RS27130 Length = 259 Score = 171 bits (432), Expect = 2e-47 Identities = 93/250 (37%), Positives = 139/250 (55%), Gaps = 7/250 (2%) Query: 7 ILLAAAATLAFALDASAAD--KLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMKT 64 + + A A AS AD LRI TEGAYPPFN G G ++++ ALC ++K Sbjct: 8 LAMGLCALAAAVPTASRADGPPLRIATEGAYPPFNMTSPDGTLGGLEVELANALCERIKR 67 Query: 65 ECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFK 124 C +V DWDGIIP L ++++D I+A+M+IT ER +A+ F+ PY FVA Sbjct: 68 RCTLVAQDWDGIIPGLLSRRYDAIMATMNITPERAKAIAFSAPYMVVPAYFVAATGGGID 127 Query: 125 TDKDSLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLADKFV 184 + +L GK +GAQ +T ++E + V++K YDT N DL SGR+D + Sbjct: 128 GTEATLAGKSVGAQTSTTHYRYVEKHFGKTVSLKNYDTASNLLADLKSGRIDAAITTGAT 187 Query: 185 QYDWLKSDAGKEFEFKGEPVFDND----KIGIAVRKGD-PLREKLNAALKEIVADGTYKK 239 DW+K+DA K + G+P+ D + +G+ +RK D L+ +AA+ +V DGT + Sbjct: 188 ASDWVKADASKSLQLVGKPLVDAEVFGPGVGVGLRKEDADLKAAFDAAIASVVQDGTLAR 247 Query: 240 INDKYFPFSI 249 I KY F++ Sbjct: 248 IAAKYVDFTV 257 Lambda K H 0.317 0.135 0.392 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: 158 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: 250 Length of database: 259 Length adjustment: 24 Effective length of query: 226 Effective length of database: 235 Effective search space: 53110 Effective search space used: 53110 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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