GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Pseudomonas fluorescens FW300-N2E2

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate Pf6N2E2_1004 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= reanno::pseudo5_N2C3_1:AO356_20240
         (272 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1004
          Length = 252

 Score =  139 bits (351), Expect = 5e-38
 Identities = 86/256 (33%), Positives = 132/256 (51%), Gaps = 27/256 (10%)

Query: 17  ERLKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQ 76
           +RL +KV L+TG   GIG AI   FA + A +++ D+   +          +   V A  
Sbjct: 13  KRLHNKVALVTGGGMGIGRAIAELFAEEGATVIVGDVHQPEPY--------KNDSVVAKH 64

Query: 77  ADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPL-EMTEEDWRRCFAIDLDGAWY 135
            DVSK +D + +    V  HG++DVLVN AG+     P+ E+T +DW R   I+ +G +Y
Sbjct: 65  LDVSKLEDWELLVAEVVREHGKVDVLVNNAGLVGSYLPIDEITLDDWNRVIDINQNGVFY 124

Query: 136 GCKAVLPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRV 195
           G + V+P M  Q  GSI+N++S+       G   Y  +K  +  +++   + Y   G+RV
Sbjct: 125 GMRTVVPVMKRQHAGSIVNVSSIWGIVGASGVSAYQASKAAVRMMSKNAALSYVANGIRV 184

Query: 196 NAIAPGYIETQLNVDYWNGFADPHAERQRA------LDLHPPRRVGQPIEVAMTAVFLAS 249
           N++ PG +ET            P  +RQ A      +   P +R   P E+A  A+FLAS
Sbjct: 185 NSLHPGLVET------------PMIDRQAADITAAVVAATPMKRAADPKEIAYAALFLAS 232

Query: 250 DEAPFINASCITIDGG 265
           DEA FI  + + +DGG
Sbjct: 233 DEASFITGAELVVDGG 248


Lambda     K      H
   0.321    0.137    0.419 

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: 159
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: 272
Length of database: 252
Length adjustment: 25
Effective length of query: 247
Effective length of database: 227
Effective search space:    56069
Effective search space used:    56069
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 (21.9 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