GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Pseudomonas fluorescens GW456-L13

Align BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized)
to candidate PfGW456L13_4606 High-affinity leucine-specific transport system, periplasmic binding protein LivK (TC 3.A.1.4.1)

Query= TCDB::Q9L3M3
         (381 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4606
          Length = 375

 Score =  284 bits (726), Expect = 3e-81
 Identities = 152/356 (42%), Positives = 213/356 (59%), Gaps = 2/356 (0%)

Query: 4   SLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGING 63
           S L A  + A +A    A   + I +AGP TGP A +G     GA+ A   INA GG++G
Sbjct: 9   SKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGAKMAIEQINAKGGVDG 68

Query: 64  EQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGR 123
           ++++    DD  DPKQ ++VANK   DGVKFV+GH  S  + PAS++Y + G++   P  
Sbjct: 69  KKLEAVEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEGVIMITPAA 128

Query: 124 DEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKA 183
             PD+   G    FRT G D  QG  AG Y+AD  K   +AV+HDK  YG+G+A   KK 
Sbjct: 129 TSPDITARGYKMVFRTIGLDSAQGPAAGNYIADFVKPKIVAVLHDKQQYGEGIASAVKKT 188

Query: 184 MNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKAT 243
           +   GV   ++EG+N GDKDFS++IAK+K+A V  +Y+GG H E GLI+RQ+A++GLKA 
Sbjct: 189 LEGKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSAEKGLKAK 248

Query: 244 LVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA-YTLYSY 302
            +  +G+ ++ ++ IA DA  G L T       +PAN  L + FKA   +P   +   +Y
Sbjct: 249 FMGPEGVGNDSISQIAKDASEGLLVTLPKSFDQDPANVALADAFKAKKEDPSGPFVFPAY 308

Query: 303 AAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358
           +A+  IA   KAA S D   VA+A+   G F T  GD+SFDEKGD K   +++YEW
Sbjct: 309 SAVTVIADGIKAAKSEDSAKVAEAI-HAGTFKTPTGDLSFDEKGDLKDFKFVVYEW 363


Lambda     K      H
   0.314    0.132    0.383 

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: 453
Number of extensions: 22
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: 381
Length of database: 375
Length adjustment: 30
Effective length of query: 351
Effective length of database: 345
Effective search space:   121095
Effective search space used:   121095
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 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:

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