GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braC in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_2921 High-affinity leucine-specific transport system, periplasmic binding protein LivK (TC 3.A.1.4.1)

Query= TCDB::Q9L3M3
         (381 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2921 High-affinity
           leucine-specific transport system, periplasmic binding
           protein LivK (TC 3.A.1.4.1)
          Length = 375

 Score =  280 bits (717), Expect = 4e-80
 Identities = 150/356 (42%), Positives = 212/356 (59%), Gaps = 2/356 (0%)

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

Query: 64  EQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGR 123
           +Q+     DD  DPKQ ++VANK   DG+KFV+GH  S  + PAS++Y + G++   P  
Sbjct: 69  KQLVAVEYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITPAA 128

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

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

Query: 244 LVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA-YTLYSY 302
            +  +G+ ++ ++ IA ++  G L T       +PAN  L + FKA   +P   +   SY
Sbjct: 249 FMGPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGPFVFPSY 308

Query: 303 AAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358
           +A+  IA A KAA S D   VA+A+   G F T  GD+SFD+ GD K   +++YEW
Sbjct: 309 SAVTVIADAIKAAKSEDAGKVAEAI-HAGTFKTPTGDLSFDKNGDLKDFKFVVYEW 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: 23
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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