GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaG in Cupriavidus basilensis 4G11

Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate RR42_RS05105 RR42_RS05105 2-keto-4-pentenoate hydratase

Query= BRENDA::Q1XGK3
         (264 letters)



>FitnessBrowser__Cup4G11:RR42_RS05105
          Length = 263

 Score =  161 bits (407), Expect = 1e-44
 Identities = 91/222 (40%), Positives = 127/222 (57%)

Query: 42  AYDVQWEIRRRKEARGNKIVGLKMGLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVDCS 101
           AY VQ    +R  A G ++VG K+GLTS A   Q+GV  P +G L    +V +G  +D  
Sbjct: 33  AYQVQEINTQRWLAAGRRLVGRKIGLTSRAVQQQLGVGEPDFGMLFADMAVAEGEEIDLR 92

Query: 102 KLIHPKIEAEISVVTKAPLHGPGCHLGDVIAAIDYVIPTVEVIDSRYENFKFDLISVVAD 161
           +++ P+IEAEI++V   PL      + D+I A  Y +P  E++ SR  N+   L   +AD
Sbjct: 93  RVLQPRIEAEIALVLAHPLAHERHTIADLIRATAYALPAAEIVGSRVANWDIRLNDTIAD 152

Query: 162 NASSTRFITGGRMASLEEVDLRTLGVVMEKNGEVVELGAGAAVLGHPLSSVAMLANLLAE 221
           NASS  F  G R   L ++DL   G+ ME+ GE V LGAGAA LG+PL +   LA+ +  
Sbjct: 153 NASSGLFALGSRPVKLADLDLIGCGMAMERRGEQVSLGAGAACLGNPLHAALWLADTMVR 212

Query: 222 RGEHIPAGTFIMTGGITAAVPVAPGDNITVRYQGLGSVSARF 263
            G  + AG  +MTG +   VPVA GD   +  +GLG +S RF
Sbjct: 213 VGRPLQAGDIVMTGALGPMVPVAAGDVFDLEIEGLGRLSTRF 254


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: 180
Number of extensions: 5
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: 263
Length adjustment: 25
Effective length of query: 239
Effective length of database: 238
Effective search space:    56882
Effective search space used:    56882
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