Align ArgT aka B2310, component of Histidine/Arginine/Lysine (basic amino acid) uptake porter, HisJ/ArgT/HisP/HisM/HisQ [R, R, C, M, M, respectively] (Gilson et al. 1982). HisJ binds L-His (preferred), but 1-methyl-L-His and 3-methyl-L-His also bind, while the dipeptide carnosine binds weakly; D-histidine and the histidine degradation products, histamine, urocanic acid and imidazole do not bind. L-Arg, homo-L-Arg, and post-translationally modified methylated Arg-analogs also bind with the exception of symmetric dimethylated-L-Arg. L-Lys and L-Orn show weaker interactions with HisJ and methylated and acetylated Lys variants show poor binding.The carboxylate groups of these amino acids and their variants are essential (characterized)
to candidate PP_4486 PP_4486 lysine / arginine / ornithine ABC transporter - periplasmic binding protein
Query= TCDB::P09551 (260 letters) >FitnessBrowser__Putida:PP_4486 Length = 261 Score = 231 bits (589), Expect = 1e-65 Identities = 112/259 (43%), Positives = 160/259 (61%), Gaps = 2/259 (0%) Query: 1 MKKSILALSLLVGLSTAASSYAALPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMC 60 MKK L +L + + + S A P ++IG + Y PF+ K G GFD D+GN +C Sbjct: 1 MKKLALLGALALSVFSLVSQAAEKP--LKIGIEAAYPPFAFKQPDGSIAGFDYDIGNALC 58 Query: 61 KRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAK 120 + M+ KCTWV +FD LIP+LK +KIDAI+SS+SITD R++ + F+ + Y +RL+ Sbjct: 59 EEMKTKCTWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTKRYYLTPARLVMKD 118 Query: 121 GSPIQPTLDSLKGKHVGVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAA 180 G+ + +LD LKGK +GV +GS + +A E +KG VV Y Q+ +Y D+AAGRLD Sbjct: 119 GTTVSDSLDELKGKKIGVQRGSIHDRFAKEVLGAKGATVVPYGTQNEIYLDVAAGRLDGT 178 Query: 181 LQDEVAASEGFLKQPAGKDFAFAGSSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELR 240 + D +GFLK AGK FAF G + D KYFGDG G+ +RK D N A+ +R Sbjct: 179 VADATLLEDGFLKTDAGKGFAFVGPAFTDAKYFGDGIGIAVRKGDKANVDRINAAIDAIR 238 Query: 241 QDGTYDKMAKKYFDFNVYG 259 +G Y ++ KYF+F++YG Sbjct: 239 ANGKYKEIESKYFNFDIYG 257 Lambda K H 0.315 0.132 0.369 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: 9 Number of successful extensions: 1 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: 260 Length of database: 261 Length adjustment: 25 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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 (21.6 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