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 Pf6N2E2_5395 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
Query= TCDB::P09551 (260 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5395 Length = 244 Score = 231 bits (590), Expect = 8e-66 Identities = 111/244 (45%), Positives = 159/244 (65%), Gaps = 1/244 (0%) Query: 17 AASSYAALPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMCKRMQVKCTWVASDFDA 76 A+SS A +T+RIG + Y PF+SK ++G VGFD D+GN +C +MQVKC W+ +FD Sbjct: 2 ASSSLFAAEKTLRIGIEAAYPPFASKTSEGKIVGFDYDIGNALCAQMQVKCEWIEGEFDG 61 Query: 77 LIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLDSLKGKHV 136 LIP+LK KKID +SS++IT++R++ + F+ K Y SRL+ +G+ + +LKGK V Sbjct: 62 LIPALKVKKIDLALSSMTITEERKKSVDFTHKYYFTSSRLVMKEGAVVDDQYVNLKGKTV 121 Query: 137 GVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQDEVAASEGFLKQPA 196 GV + +T + YA E KGV V Y+N + +Y DLA+GRLDA D + E FL P Sbjct: 122 GVQRATTTDRYATEVLEPKGVSVKRYSNNEEIYMDLASGRLDAIFADTIPL-EDFLSMPR 180 Query: 197 GKDFAFAGSSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELRQDGTYDKMAKKYFDFN 256 GK +AF G +KD KY G+G G+ +RK + +L A NKA+ +R +G Y K+ KYF + Sbjct: 181 GKGYAFVGPELKDPKYVGEGAGIAVRKGNTQLVADLNKAIDGIRANGEYQKIQGKYFKSD 240 Query: 257 VYGD 260 +YGD Sbjct: 241 IYGD 244 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: 203 Number of extensions: 10 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: 244 Length adjustment: 24 Effective length of query: 236 Effective length of database: 220 Effective search space: 51920 Effective search space used: 51920 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: 46 (22.3 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