GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaG in Acidovorax sp. GW101-3H11

Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate Ac3H11_4809 2-oxo-hepta-3-ene-1,7-dioic acid hydratase (EC 4.2.-.-)

Query= metacyc::MONOMER-15110
         (260 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4809
          Length = 271

 Score =  172 bits (436), Expect = 7e-48
 Identities = 105/267 (39%), Positives = 147/267 (55%), Gaps = 11/267 (4%)

Query: 1   MDKTVIKDLARFLVDAEVEKKEVLKLTNEHPDLTVEDGYAIQEQLVQMKLEQGYRIVGPK 60
           +D  +I+ LA  L  AE  + +V   +  HP +TV+DGYAI    V MK+ +G  + G K
Sbjct: 2   LDDALIQQLASELHQAEKTRVQVEHFSKRHPGMTVQDGYAISRAWVAMKIAEGRTVRGHK 61

Query: 61  MGLTSQAKMKQMNVNEPIYGYIFDYMV-VNGQELSMSELIHPKVEAEIAFILGKDIEG-- 117
           +GLTS+A      + EP +G + D M    G ++ M   I P+VE E+AF+L K + G  
Sbjct: 62  IGLTSRAMQVASQITEPDFGTLLDDMFFAEGCDIPMQRFILPRVEVELAFVLHKPLRGEP 121

Query: 118 --PGITGAQVLAATEYVVPALEIIDSRYQNFQF------TLPDVIADNASSSRVFLGSTI 169
             P +    VLAATEYVVPA+EIID+R +           + D I+DNA+++ +  G   
Sbjct: 122 GRPPVNIFDVLAATEYVVPAIEIIDARIEQHDRHTGGMRKVFDTISDNAANAGIVTGGRP 181

Query: 170 KRPDNMELDLLGVTLSINGQIKDLGAGAAVVGHPANSVAMLANMLARKGLKLKAGQIILS 229
            RPD ++L   G  L  NG I++ G  AAV+ HPA  VA LAN LA  G  L AG+++L 
Sbjct: 182 VRPDAVDLRWCGALLYKNGVIEESGLAAAVLNHPATGVAWLANKLAPYGEGLAAGEVVLG 241

Query: 230 GGITGAVMLNVGDSVTGKFDGLGTIDF 256
           G  T  V    GD+    +  LG I F
Sbjct: 242 GSFTRPVSAAAGDTFHADYGPLGNIAF 268


Lambda     K      H
   0.317    0.137    0.374 

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: 8
Number of successful extensions: 4
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: 260
Length of database: 271
Length adjustment: 25
Effective length of query: 235
Effective length of database: 246
Effective search space:    57810
Effective search space used:    57810
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