GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Azospirillum brasilense Sp245

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate AZOBR_RS18155 AZOBR_RS18155 enoyl-CoA hydratase

Query= BRENDA::P77467
         (262 letters)



>FitnessBrowser__azobra:AZOBR_RS18155
          Length = 248

 Score =  134 bits (338), Expect = 1e-36
 Identities = 92/255 (36%), Positives = 135/255 (52%), Gaps = 8/255 (3%)

Query: 9   VEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAG-RGFCAGQDLN 67
           V+  V T+TL+RP++LN+   EM AQL   + +   DD IRC++LTGAG R FC G D+ 
Sbjct: 1   VDGFVATITLDRPQKLNAVTPEMAAQLVAAVARCNADDDIRCVVLTGAGPRAFCCGSDI- 59

Query: 68  DRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAA 127
            R +D    A +     +  Y   +R L K   P I AVNG A G G   A+  DI IA+
Sbjct: 60  -RELDRYDTAWNFRNRED--YCDAIRGLRK---PSIAAVNGYAFGGGLETAMSCDIRIAS 113

Query: 128 RSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDD 187
            +A+F     KLG I   G    L    G + A  + L G+ + A++A  WG++ +VV  
Sbjct: 114 ENAQFGAPEIKLGWIGGGGVAAFLSHSIGTSNAAMMILTGDPIPADKALAWGLVSEVVPA 173

Query: 188 ETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREG 247
           + L   AQ++A  +A++        K  + +A T  ++  ++ ERD Q +   +AD  EG
Sbjct: 174 DRLLARAQEIAAIVASRAPIAAETAKLNLKAAHTMPVEKAIEYERDLQTICFATADAAEG 233

Query: 248 VSAFLAKRSPQFTGK 262
            +AF  KRSP F  K
Sbjct: 234 RAAFKEKRSPVFRRK 248


Lambda     K      H
   0.321    0.136    0.403 

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: 136
Number of extensions: 8
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: 262
Length of database: 248
Length adjustment: 24
Effective length of query: 238
Effective length of database: 224
Effective search space:    53312
Effective search space used:    53312
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 (21.8 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