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_RS00685 AZOBR_RS00685 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__azobra:AZOBR_RS00685 Length = 278 Score = 166 bits (419), Expect = 6e-46 Identities = 100/276 (36%), Positives = 149/276 (53%), Gaps = 33/276 (11%) Query: 5 KKILLAAAATLAFALDASAAD-----KLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALC 59 KKI+ A A A+ +AA+ K+RI TEGAY P+N D SG+ +GF+ D+ LC Sbjct: 2 KKIVAALALGAIVAVAGTAAEAKDWKKIRIATEGAYAPWNATDPSGKLIGFEPDLALELC 61 Query: 60 AKMKTECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPK 119 ++K ECE+V DWDG+IPA+ K+D I+A+MSITDER++ + F PY T F K Sbjct: 62 KRIKAECEIVAQDWDGMIPAIQQGKYDAIMAAMSITDEREKVIAFAGPYGTEPSMFGTMK 121 Query: 120 S------------VDFKTD---------KDSLKGKVIGAQRATIAGTWLEDNMADVVTIK 158 + D D D+LKGK +G Q +TI ++E + V ++ Sbjct: 122 NSPLAKATFPGERYDLSKDDPKAAIAALADALKGKTVGVQTSTIQANFME-KLLPQVAVR 180 Query: 159 LYDTQENAYLDLSSGRLDGVLADKFVQYDWLKSDAGKEFEFKGEPVFD----NDKIGIAV 214 YD +NA +D+++GR+D + D+ LK+DAG G P F +G+ + Sbjct: 181 TYDKLDNAGIDMAAGRVDAIFGDRSAVDAILKADAGNGMTLFG-PAFARGVLGKGVGVGL 239 Query: 215 RKGD-PLREKLNAALKEIVADGTYKKINDKYFPFSI 249 RK D L+E N A+ E DGT K++ ++F + I Sbjct: 240 RKADGDLKELFNKAIAEANQDGTITKLSTQHFGYDI 275 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: 215 Number of extensions: 14 Number of successful extensions: 4 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: 278 Length adjustment: 25 Effective length of query: 225 Effective length of database: 253 Effective search space: 56925 Effective search space used: 56925 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