GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praD in Klebsiella michiganensis M5al

Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate BWI76_RS03850 BWI76_RS03850 2-oxo-hepta-3-ene-1,7-dioic acid hydratase

Query= BRENDA::B0VXM8
         (267 letters)



>FitnessBrowser__Koxy:BWI76_RS03850
          Length = 267

 Score =  177 bits (449), Expect = 2e-49
 Identities = 102/255 (40%), Positives = 147/255 (57%), Gaps = 8/255 (3%)

Query: 14  AELLNEAEREKREVARITEEVPDLSAEEAYKIQEELIKIKTNSGHRIIGPKMGLTSQAKM 73
           A+ LN+AE+++ ++  I+ + P ++ E+AY +Q E + +K   G  + G K+GLTS+A  
Sbjct: 11  AQRLNQAEKQREQIRAISLDHPTITIEDAYAVQREWVNMKIAEGRVLKGHKIGLTSKAMQ 70

Query: 74  AQMKVKEPIYGYLFDYMFVPSGGAIHMSELIHPKVEVEIAFILGEDLEGPHVTSTQVLSA 133
           A  ++ EP YG L D MF   GG I     I P++EVE+AF+L + L GP+ T   V +A
Sbjct: 71  ASSQISEPDYGALLDDMFFHDGGDIPTDRFIVPRIEVELAFVLAKPLRGPNCTLFDVYNA 130

Query: 134 TKYVAPALEIIDSRYQDF------TFTLPDVIADNASSSRVVIGNTMTPIHSLKTDLDLI 187
           T YV PALE+ID+R  +          + D I+DNA+++ V++G    PI   + DL  I
Sbjct: 131 TDYVIPALELIDARCHNIDPETQRPRKVFDTISDNAANAGVILGG--RPIKPDELDLRWI 188

Query: 188 GAALYINGELKACGAGAAVFNHPANSVAVLANMLARKGERLKAGDIILTGGITEAIQLSA 247
            A LY NG ++  G  A V NHPAN VA LAN LA    +L+AG IIL G  T  +    
Sbjct: 189 SALLYRNGVIEETGVAAGVLNHPANGVAWLANKLAPYDVQLEAGQIILGGSFTRPVPARK 248

Query: 248 GDTVIGQLDQLGDVS 262
           GDT       +G +S
Sbjct: 249 GDTFHVDYGNMGAIS 263


Lambda     K      H
   0.316    0.134    0.364 

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: 170
Number of extensions: 5
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: 267
Length of database: 267
Length adjustment: 25
Effective length of query: 242
Effective length of database: 242
Effective search space:    58564
Effective search space used:    58564
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 (21.6 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