GapMind for catabolism of small carbon sources

 

Aligments for a candidate for argT in Burkholderia phytofirmans PsJN

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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS35100 BPHYT_RS35100 ABC
           transporter substrate-binding protein
          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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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