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 BPHYT_RS35100 BPHYT_RS35100 ABC transporter substrate-binding protein
Query= TCDB::P09551 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS35100 Length = 263 Score = 243 bits (620), Expect = 3e-69 Identities = 122/256 (47%), Positives = 171/256 (66%), Gaps = 5/256 (1%) Query: 6 LALSLLVGLSTAASSYAALPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMCKRMQV 65 L+ +L L+ + S++A P T+R+G D +Y P +K G F GFD+DLGNE+CKR+ Sbjct: 12 LSTALSAALAFSTSAFAVEPTTLRLGIDPSYPPMDAKAPDGSFKGFDVDLGNEICKRIHA 71 Query: 66 KCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQ 125 +C WV +F +IP+L+A+KIDAI+SS++IT+KR+Q+I FS KL+ SRLIA +GS + Sbjct: 72 RCQWVELEFSGMIPALQARKIDAILSSMAITEKREQQILFSSKLFQFKSRLIARQGSALA 131 Query: 126 PTLDSLKGKHVGVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQDEV 185 ++L GK +GV G+ E YA + W G VVAY +QD V++DL GRLD AL V Sbjct: 132 GGTNALAGKQIGVQSGTQFEGYALKNWAPLGAHVVAYKSQDEVFADLQNGRLDGALLGSV 191 Query: 186 AASEGFLKQPAGKDFAFAGSSVKDKKYFGD-GTGVGLRKDDAELTAAFNKALGELRQDGT 244 A GFL+ PAGK FAF G + GD G G+GLRKD+ + A+ N A+ + +DGT Sbjct: 192 EADIGFLRTPAGKGFAFVGEPLS----MGDRGVGIGLRKDETAVQASINAAIASMLKDGT 247 Query: 245 YDKMAKKYFDFNVYGD 260 Y ++AKKYFDF+ YG+ Sbjct: 248 YAQIAKKYFDFDPYGN 263 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: 11 Number of successful extensions: 2 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: 263 Length adjustment: 25 Effective length of query: 235 Effective length of database: 238 Effective search space: 55930 Effective search space used: 55930 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