GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Rhizobium etli CFN 42

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_011427206.1 RHE_RS20550 beta-ketoacyl-ACP reductase

Query= SwissProt::Q9NKW1
         (441 letters)



>NCBI__GCF_000092045.1:WP_011427206.1
          Length = 241

 Score =  106 bits (264), Expect = 9e-28
 Identities = 81/253 (32%), Positives = 111/253 (43%), Gaps = 37/253 (14%)

Query: 8   KVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGGTA 67
           +V +VTG   GIG   +      G +V     G             D+         G A
Sbjct: 3   RVALVTGGTRGIGAAISTALKNAGYRVAATYAGN------------DEKAHAFHDVTGVA 50

Query: 68  VANYDSVED----GEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHAK 123
           V  +D V D    GE I +   +  G V+IL+NNAGI RD  F KMT   W  V   +  
Sbjct: 51  VFKWD-VSDYAACGEGITKVEGE-IGPVEILVNNAGITRDAMFHKMTPQQWHEVINTNLT 108

Query: 124 GAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKSK 183
           G + ++   W+ MR+++FGRI+  SS  G  G  GQANY + K   +G +  LAQEG +K
Sbjct: 109 GLFNMTHQVWSGMRDRSFGRIVNISSINGQKGQMGQANYSAAKAGDLGFTKALAQEGAAK 168

Query: 184 NIHCNTIAP-----IAASRLTESVMPPEILEQM------KPDYIVPLVLYLCHQDT---- 228
           NI  N I P          + E V+   I+ Q+      +P+ I   V +L   D     
Sbjct: 169 NITVNAICPGYIGTEMVLAVPEKVLNERIIPQIPVGRLGEPEEIARCVTFLVSDDAGFIT 228

Query: 229 ----TETGGVFEV 237
               T  GG F V
Sbjct: 229 GSTLTANGGQFFV 241


Lambda     K      H
   0.313    0.131    0.371 

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: 232
Number of extensions: 13
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: 441
Length of database: 241
Length adjustment: 28
Effective length of query: 413
Effective length of database: 213
Effective search space:    87969
Effective search space used:    87969
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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