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 AO356_01470 AO356_01470 ABC transporter substrate-binding protein
Query= TCDB::P09551 (260 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_01470 Length = 259 Score = 237 bits (604), Expect = 2e-67 Identities = 120/255 (47%), Positives = 164/255 (64%), Gaps = 5/255 (1%) Query: 6 LALSLLVGLSTAASSYAALPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMCKRMQV 65 LALS+L + S+ A + +R+G + Y PFS K G GFD+D+G+ +C++M+V Sbjct: 10 LALSVL-----SLSAVAEDAKPIRLGIEAGYPPFSMKTPDGKLAGFDVDIGDALCEQMKV 64 Query: 66 KCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQ 125 KC WV +FD LIP+LK KKIDAI+SS++ITD R++ + F+ K Y +R + +GS I+ Sbjct: 65 KCVWVEQEFDGLIPALKVKKIDAILSSMTITDDRKKNVDFTIKYYHTPARFVMKEGSNIK 124 Query: 126 PTLDSLKGKHVGVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQDEV 185 L LKGK VGVL+ ST + +A E G+D+V Y +Q D+ AGRLDA L D V Sbjct: 125 DPLTELKGKKVGVLRASTHDRFATEVLVPAGIDLVRYGSQQEANLDMVAGRLDAMLADSV 184 Query: 186 AASEGFLKQPAGKDFAFAGSSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELRQDGTY 245 EGFLK AGK FAF G + +D KYFG G G+ +RK D L FN A+ E+R +GTY Sbjct: 185 NLDEGFLKTDAGKGFAFVGPTYEDAKYFGGGAGIAVRKGDKALADQFNAAITEIRANGTY 244 Query: 246 DKMAKKYFDFNVYGD 260 K+ KYF F+VYG+ Sbjct: 245 KKVQDKYFAFDVYGN 259 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: 218 Number of extensions: 6 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 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