GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artJ in Pseudomonas putida KT2440

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate PP_0227 PP_0227 periplasmic cystine-binding protein

Query= TCDB::Q9HU31
         (250 letters)



>lcl|FitnessBrowser__Putida:PP_0227 PP_0227 periplasmic
           cystine-binding protein
          Length = 264

 Score =  129 bits (325), Expect = 5e-35
 Identities = 68/224 (30%), Positives = 131/224 (58%), Gaps = 10/224 (4%)

Query: 27  LRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMKTECEVVTSDWDGIIPALNAKKFD 86
           + +G EG YPPF+  D +G+  GF++++ + L  ++  + ++  + WDGI+ AL +K+ D
Sbjct: 40  INVGLEGTYPPFSFQDENGKLTGFEVELSELLAKELGVKAKIQPTKWDGILAALESKRLD 99

Query: 87  FIVASMSITDERKQAVDFTDPYYTNKLQFVAPK----SVDFKTDKDSLKGKVIGAQRATI 142
            +V  ++I++ERK+  DF++PY  + +Q +  K     ++ K  +D L GK +G    T 
Sbjct: 100 VVVNQVTISEERKKKYDFSEPYTVSGIQALILKKKAEQLNIKGAQD-LAGKKVGVGLGTN 158

Query: 143 AGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLADKFVQYDWLKSDAGKEFEFKGE 202
              W++ ++     ++ Y+   + + DL +GR+D +L D+    ++  +   K+ E  G+
Sbjct: 159 YEQWVKKDVPQ-ADVRTYEDDPSKFADLRNGRIDAILIDRLAALEY--AQKAKDTELAGD 215

Query: 203 PVFDNDKIGIAVRKGDP-LREKLNAALKEIVADGTYKKINDKYF 245
             F   + G+A+RKG+P L   +N A+ ++ ADGT  K+++KYF
Sbjct: 216 -AFSRLESGVALRKGEPELLAAINKAIDKLKADGTLAKLSEKYF 258


Lambda     K      H
   0.317    0.135    0.392 

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: 174
Number of extensions: 9
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: 250
Length of database: 264
Length adjustment: 24
Effective length of query: 226
Effective length of database: 240
Effective search space:    54240
Effective search space used:    54240
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 (21.7 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 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