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 WP_043529788.1 JH15_RS09820 ABC transporter substrate-binding protein
Query= TCDB::Q9HU31 (250 letters) >NCBI__GCF_000759345.1:WP_043529788.1 Length = 256 Score = 162 bits (410), Expect = 6e-45 Identities = 94/252 (37%), Positives = 137/252 (54%), Gaps = 7/252 (2%) Query: 1 MKNYKKILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCA 60 MK + L AA A + A +++RIG + Y P G+ GFD+D+G ALC Sbjct: 1 MKKLLGVTLLGAAIAAGSAQARDYEEVRIGVDVPYEPMEYRTPEGELTGFDIDLGNALCD 60 Query: 61 KMKTECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKS 120 ++ ECE + WDGIIP L ++K+D I++SM+I DER++ V F+DPY+T + AP Sbjct: 61 EIGVECEWIVQGWDGIIPGLMSRKYDAIMSSMTINDERREQVLFSDPYFTPPSAWFAPAD 120 Query: 121 VDFKTD-KDSLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVL 179 D + +L+GK IG QR T+ ++ DN DV + Y T ++ LD+ SGRLD + Sbjct: 121 TDIEMPYPQTLEGKTIGVQRGTLQDNYVTDNFGDVADVNRYATADDMVLDMDSGRLDILF 180 Query: 180 ADKFVQYDWLKSDAGKEFEFKGEPV-----FDNDKIGIAVRKGD-PLREKLNAALKEIVA 233 D V L ++ GE + + D GIA RK D L EK N AL + Sbjct: 181 LDFPVGKATLLDSEEGNYKVVGEMITEPKEYFGDGFGIAFRKRDEALAEKFNDALATLRD 240 Query: 234 DGTYKKINDKYF 245 +GTY +I ++YF Sbjct: 241 NGTYDEIYNRYF 252 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: 205 Number of extensions: 11 Number of successful extensions: 3 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: 256 Length adjustment: 24 Effective length of query: 226 Effective length of database: 232 Effective search space: 52432 Effective search space used: 52432 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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