GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praD in Ruegeria conchae TW15

Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate WP_010441603.1 G7G_RS0111655 2-oxo-hepta-3-ene-1,7-dioic acid hydratase

Query= BRENDA::Q1XGK3
         (264 letters)



>NCBI__GCF_000192475.1:WP_010441603.1
          Length = 266

 Score =  159 bits (403), Expect = 4e-44
 Identities = 93/256 (36%), Positives = 134/256 (52%), Gaps = 6/256 (2%)

Query: 14  AEHIENAELNVHDIGKVTNDFPEMTFADAYDVQWEIRRRKEARGNKIVGLKMGLTSWAKM 73
           A  + +AE + + IG ++   PEM   DAY+VQ  I R K A G  +VG K+GLTS A  
Sbjct: 10  AADLLDAERSGNQIGLLSLRHPEMGMDDAYEVQNAIYRAKLAEGRSVVGWKIGLTSKAMQ 69

Query: 74  AQMGVETPIYGFLADYFSVPDGGVVDCSKLIHPKIEAEISVVTKAPLHGPGCHLGDVIAA 133
             + ++ P  G L D     +G  V   + I P+IEAEI+ VTK+PL G      DVIAA
Sbjct: 70  YALNIDIPDSGILFDDMIFDNGATVPADRFIQPRIEAEIAFVTKSPLGGDNVSREDVIAA 129

Query: 134 IDYVIPTVEVIDSRYENFKFD------LISVVADNASSTRFITGGRMASLEEVDLRTLGV 187
            DYV P +E++D+R +    +      +   ++DNA++   + G     ++  DLR +G 
Sbjct: 130 TDYVAPAIEILDTRIQRVDPETGKTRTVFDTISDNAANAGIVLGAARHKIDAADLRWVGA 189

Query: 188 VMEKNGEVVELGAGAAVLGHPLSSVAMLANLLAERGEHIPAGTFIMTGGITAAVPVAPGD 247
           +  +NGE+ E G GA VL  P+ SV  LA  +A  G+ I  G  I++G     V    G 
Sbjct: 190 LTFRNGEIEETGLGAGVLNDPIESVVWLARRMATYGQSIEPGQIILSGSFIRPVECPSGT 249

Query: 248 NITVRYQGLGSVSARF 263
            I   +   GSV  RF
Sbjct: 250 EIHADFGAFGSVDIRF 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: 182
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: 264
Length of database: 266
Length adjustment: 25
Effective length of query: 239
Effective length of database: 241
Effective search space:    57599
Effective search space used:    57599
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 24 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