GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaC in Azospirillum brasilense Sp245

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate AZOBR_RS05920 AZOBR_RS05920 3-oxoadipate enol-lactonase (Enol-lactone hydrolase) (Beta-ketoadipate enol-lactone hydrolase)

Query= BRENDA::Q0SH24
         (400 letters)



>FitnessBrowser__azobra:AZOBR_RS05920
          Length = 259

 Score =  181 bits (458), Expect = 3e-50
 Identities = 100/230 (43%), Positives = 134/230 (58%), Gaps = 3/230 (1%)

Query: 15  GAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSED 74
           G  D P V+LL SLG+N  +WDPQ   L+   RV+  D RGHG S AP GPY + DL++D
Sbjct: 16  GPQDGPPVLLLHSLGTNHHVWDPQAEVLARRFRVIRPDMRGHGLSEAPPGPYGMEDLADD 75

Query: 75  VLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQAWIERAAA 134
             A+LD+LGV      G+S+GG IAQ +   AP RV  L L+ T+     P  W ERA  
Sbjct: 76  AFAVLDALGVGRCFVGGVSIGGMIAQTMALKAPHRVGGLVLVDTSMATAVPAMWRERAGQ 135

Query: 135 SRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWDFTAD 194
            R       ADA+ ARW ++G A  D   ++  R M+  T+ EG+A C +ALA  D +A 
Sbjct: 136 VRASSVAPFADAITARWVTQGFA--DSPEMQGLRTMLHQTAAEGFAGCAEALATADLSAR 193

Query: 195 LSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQ 244
           +  I+AP+LVI G++D STP +  Q L   + +    VL  AAH+ NLEQ
Sbjct: 194 VGDIAAPSLVIVGDQDQSTPVAAAQALCAAL-KGTLVVLPDAAHIPNLEQ 242


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: 317
Number of extensions: 18
Number of successful extensions: 3
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: 259
Length adjustment: 28
Effective length of query: 372
Effective length of database: 231
Effective search space:    85932
Effective search space used:    85932
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: 48 (23.1 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