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 GFF4245 PS417_21745 ABC transporter substrate-binding protein
Query= TCDB::P09551 (260 letters) >FitnessBrowser__WCS417:GFF4245 Length = 261 Score = 239 bits (610), Expect = 4e-68 Identities = 115/259 (44%), Positives = 167/259 (64%), Gaps = 2/259 (0%) Query: 1 MKKSILALSLLVGLSTAASSYAALPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMC 60 MKK +L +L LS + A + ++IG + Y PF+SK G VGFD D+GN +C Sbjct: 1 MKKLVLLGAL--ALSVLSMQAFAEGKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALC 58 Query: 61 KRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAK 120 + M+VKCTWV +FD LIP+LK +KIDAI+SS+SITD R++ + F+++ Y +RL+ + Sbjct: 59 EEMKVKCTWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNRYYLTPARLVLKE 118 Query: 121 GSPIQPTLDSLKGKHVGVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAA 180 G+ + +LD LKGK +GV +GS + +A E KG +V Y++Q+ +Y D+ AGRLD Sbjct: 119 GTAVSDSLDELKGKKIGVQRGSIHDRFAKEVLAPKGATIVPYSSQNEIYLDVEAGRLDGT 178 Query: 181 LQDEVAASEGFLKQPAGKDFAFAGSSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELR 240 + D EGFL PAGK +AF G + D KYFGDG G+ +RK D E N A+ +R Sbjct: 179 VADATLLQEGFLDTPAGKGYAFTGPAFTDAKYFGDGIGIAVRKGDKENLDRINAAIAAIR 238 Query: 241 QDGTYDKMAKKYFDFNVYG 259 +G Y ++ KKYF+F++YG Sbjct: 239 ANGKYKEIEKKYFNFDIYG 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: 211 Number of extensions: 10 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