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 AO353_29015 AO353_29015 ABC transporter substrate-binding protein
Query= TCDB::P09551 (260 letters) >FitnessBrowser__pseudo3_N2E3:AO353_29015 Length = 262 Score = 260 bits (665), Expect = 2e-74 Identities = 127/263 (48%), Positives = 178/263 (67%), Gaps = 7/263 (2%) Query: 1 MKKSILALSLLV----GLSTAASSYAALPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLG 56 M K I A+SL+ GL+ AA + +R+G D TY P K+ G GF +D+ Sbjct: 1 MNKMIAAVSLVFLTASGLAGAADWSG---KVLRLGIDPTYPPLEYKNQDGTLTGFGVDIA 57 Query: 57 NEMCKRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRL 116 + +C + KC WV S +D +IP L A+K DAI SS+++T KRQ++IAFSDK+ A +RL Sbjct: 58 DALCAELHAKCVWVESSWDGMIPGLLARKFDAIASSMTVTPKRQEQIAFSDKVSNAPARL 117 Query: 117 IAAKGSPIQPTLDSLKGKHVGVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGR 176 + +GS +QPT++SLKGK +GV QGSTQEA+A W +GV++++Y NQD VY+DL GR Sbjct: 118 VIKRGSDLQPTVESLKGKRIGVEQGSTQEAFAKAVWGKQGVEILSYQNQDQVYADLVVGR 177 Query: 177 LDAALQDEVAASEGFLKQPAGKDFAFAGSSVKDKKYFGDGTGVGLRKDDAELTAAFNKAL 236 LDA+LQ + AS GFL +P GKD+ FAG ++ + ++FG G G+G+RK D EL NKAL Sbjct: 178 LDASLQGSIQASYGFLNKPVGKDYEFAGGTLDNPEFFGVGDGIGVRKSDVELREDLNKAL 237 Query: 237 GELRQDGTYDKMAKKYFDFNVYG 259 + +GTY K+ KKYFDF++YG Sbjct: 238 ATILANGTYAKINKKYFDFDIYG 260 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: 247 Number of extensions: 12 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: 262 Length adjustment: 25 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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