GapMind for catabolism of small carbon sources

 

Aligments for a candidate for argT in Paraburkholderia bryophila 376MFSha3.1

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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06484 H281DRAFT_06484 amino
           acid ABC transporter substrate-binding protein, PAAT
           family
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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