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 H281DRAFT_06484 H281DRAFT_06484 amino acid ABC transporter substrate-binding protein, PAAT family
Query= TCDB::P09551 (260 letters) >FitnessBrowser__Burk376:H281DRAFT_06484 Length = 266 Score = 265 bits (676), Expect = 1e-75 Identities = 130/242 (53%), Positives = 169/242 (69%) Query: 16 TAASSYAALPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMCKRMQVKCTWVASDFD 75 TA S+ AA + VR G + +YAPF SK G+ GFDID+GN +C +++ KC WV + FD Sbjct: 22 TAGSAAAADIKEVRFGVEASYAPFESKSPSGELQGFDIDVGNAVCAKLKAKCVWVENSFD 81 Query: 76 ALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLDSLKGKH 135 LIP+L+A+K +AI S ++ITD+R+Q + F+D +Y +++IA KGS + PT SLKGKH Sbjct: 82 GLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPNQMIAKKGSGLLPTPASLKGKH 141 Query: 136 VGVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQDEVAASEGFLKQP 195 VGVLQG+ QE YA W GVDVV Y QD +Y+DLA+GRLDA+ QD AAS+GFLK+P Sbjct: 142 VGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLASGRLDASFQDAEAASKGFLKKP 201 Query: 196 AGKDFAFAGSSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELRQDGTYDKMAKKYFDF 255 G F FAG +V D+K G G G G+RK DA L A N+AL EL+ DGT D+ A KYFD Sbjct: 202 QGAGFEFAGPAVSDEKLLGAGVGFGIRKGDAALKDALNQALKELKADGTIDRFAAKYFDV 261 Query: 256 NV 257 V Sbjct: 262 KV 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: 240 Number of extensions: 11 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: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 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