GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Pseudomonas fluorescens FW300-N2E2

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate Pf6N2E2_667 Dihydrolipoamide acetyltransferase component (E2) of acetoin dehydrogenase complex (EC 2.3.1.-)

Query= BRENDA::Q0SH24
         (400 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_667
          Length = 370

 Score = 75.5 bits (184), Expect = 2e-18
 Identities = 79/252 (31%), Positives = 118/252 (46%), Gaps = 31/252 (12%)

Query: 15  GAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSED 74
           G    P++++ G  G + + W     AL+   RV+A+D  GHGES        + +LS  
Sbjct: 129 GEGGTPLLLVHG-FGGDLNNWLFNHEALAAGRRVIALDLPGHGESGKVLQRGDLDELSGV 187

Query: 75  VLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGE-----PQAWI 129
           VLALLD L ++A H VG SMGGA++      APRRV SL+L+ +A    E      Q ++
Sbjct: 188 VLALLDHLDINAVHLVGHSMGGAVSLNTARLAPRRVRSLTLIGSAGLGSEINGSYLQGFV 247

Query: 130 ERAAASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDAL--- 186
           E  AA+R     +L   +V  + +  L  R     +   +M+     EG  A    L   
Sbjct: 248 E--AANR----NALKPQLVQLFSNAELVNR-----QMLDDMLKYKRLEGVDAALQQLSSR 296

Query: 187 --ADWDFTADLSRI----SAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVA 240
             AD     DL  +      PTLV+ G +D   P +  + L+     A+ EVL    H+ 
Sbjct: 297 LFADGRQQTDLREVVQAGQVPTLVVWGSDDAIIPVTHSEGLS-----AQVEVLPGQGHMV 351

Query: 241 NLEQAGAVTALL 252
            +E A  V +L+
Sbjct: 352 QMEAAEQVNSLI 363


Lambda     K      H
   0.318    0.132    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: 313
Number of extensions: 18
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: 400
Length of database: 370
Length adjustment: 30
Effective length of query: 370
Effective length of database: 340
Effective search space:   125800
Effective search space used:   125800
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: 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