GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Azospirillum brasilense Sp245

Align 3-oxoadipate enol-lactonase 2; EC 3.1.1.24; 3-oxoadipate enol-lactonase II; Beta-ketoadipate enol-lactone hydrolase II; Enol-lactone hydrolase II (uncharacterized)
to candidate AZOBR_RS05920 AZOBR_RS05920 3-oxoadipate enol-lactonase (Enol-lactone hydrolase) (Beta-ketoadipate enol-lactone hydrolase)

Query= curated2:P00632
         (267 letters)



>FitnessBrowser__azobra:AZOBR_RS05920
          Length = 259

 Score =  155 bits (393), Expect = 6e-43
 Identities = 88/230 (38%), Positives = 126/230 (54%), Gaps = 2/230 (0%)

Query: 23  GQADRPALIFSNSLGTNLSMWQQQIAYFQDKYFVICYDTRGHGASSTPVGPYRIDQLGTD 82
           G  D P ++  +SLGTN  +W  Q      ++ VI  D RGHG S  P GPY ++ L  D
Sbjct: 16  GPQDGPPVLLLHSLGTNHHVWDPQAEVLARRFRVIRPDMRGHGLSEAPPGPYGMEDLADD 75

Query: 83  VIALLDHLQIPQATFCGISMGGLTGQWLAIHFPERFNQVIVANTAAKIGEAQAWQARAQL 142
             A+LD L + +    G+S+GG+  Q +A+  P R   +++ +T+        W+ RA  
Sbjct: 76  AFAVLDALGVGRCFVGGVSIGGMIAQTMALKAPHRVGGLVLVDTSMATAVPAMWRERAGQ 135

Query: 143 VREQGLTPIAQTAATRWFTPGFIEDSPEIVEKLSHDLAQGSAEGYASCCEALAEADVRPQ 202
           VR   + P A     RW T GF  DSPE ++ L   L Q +AEG+A C EALA AD+  +
Sbjct: 136 VRASSVAPFADAITARWVTQGF-ADSPE-MQGLRTMLHQTAAEGFAGCAEALATADLSAR 193

Query: 203 LQRISIPVLVIAGAQDPVTTVADGQFLCEHIVHSTLEVLEASHISNVEQP 252
           +  I+ P LVI G QD  T VA  Q LC  +  + + + +A+HI N+EQP
Sbjct: 194 VGDIAAPSLVIVGDQDQSTPVAAAQALCAALKGTLVVLPDAAHIPNLEQP 243


Lambda     K      H
   0.321    0.134    0.405 

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: 198
Number of extensions: 6
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: 267
Length of database: 259
Length adjustment: 25
Effective length of query: 242
Effective length of database: 234
Effective search space:    56628
Effective search space used:    56628
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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:

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