GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaG in Burkholderia phytofirmans PsJN

Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate BPHYT_RS07240 BPHYT_RS07240 2-keto-4-pentenoate hydratase

Query= BRENDA::Q1XGK3
         (264 letters)



>FitnessBrowser__BFirm:BPHYT_RS07240
          Length = 273

 Score =  160 bits (405), Expect = 3e-44
 Identities = 95/258 (36%), Positives = 138/258 (53%), Gaps = 5/258 (1%)

Query: 10  VLALAEHIENAELNVHDIGKVTNDFPEMTFADAYDVQWEIRR----RKEARGNKIVGLKM 65
           V  +A+ +  A+     +  V N   E+   DA D  + ++R    R+ A G ++VG K+
Sbjct: 9   VQRIADALWRAQQTGVPVAPVRNAIAELG-GDALDAAYAVQRVNTERQLAAGRRLVGRKI 67

Query: 66  GLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVDCSKLIHPKIEAEISVVTKAPLHGPGC 125
           GLTS A   Q+GV+ P +G L D  S+ DG  +  S+   PK+EAEI++V    L     
Sbjct: 68  GLTSKAVQTQLGVDQPDFGMLFDDMSIADGEEIALSRTQQPKVEAEIALVLARDLPHERN 127

Query: 126 HLGDVIAAIDYVIPTVEVIDSRYENFKFDLISVVADNASSTRFITGGRMASLEEVDLRTL 185
            + D+I A  Y +P +E++ SR  N+   L   VADNASS  F+ G R   L   D+   
Sbjct: 128 TIADLIGATAYALPAIEIVGSRIANWDIRLTDTVADNASSGLFVLGNRPVKLGAFDIVHC 187

Query: 186 GVVMEKNGEVVELGAGAAVLGHPLSSVAMLANLLAERGEHIPAGTFIMTGGITAAVPVAP 245
           G+ ME+ G+ V +G GAA LG+PL +   LAN +   G  + AG  ++TG +     V  
Sbjct: 188 GMAMERRGDPVSVGVGAACLGNPLYAAVWLANTMTRVGAPLKAGDIVLTGALGPMAAVQA 247

Query: 246 GDNITVRYQGLGSVSARF 263
           GD  T   +GLGSVSA F
Sbjct: 248 GDVFTAHIEGLGSVSASF 265


Lambda     K      H
   0.319    0.136    0.395 

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: 181
Number of extensions: 9
Number of successful extensions: 1
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: 264
Length of database: 273
Length adjustment: 25
Effective length of query: 239
Effective length of database: 248
Effective search space:    59272
Effective search space used:    59272
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