GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Sinorhizobium meliloti 1021

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate SMc03878 SMc03878 acetoacetyl-CoA reductase

Query= SwissProt::Q9NKW1
         (441 letters)



>FitnessBrowser__Smeli:SMc03878
          Length = 241

 Score =  112 bits (279), Expect = 2e-29
 Identities = 77/258 (29%), Positives = 116/258 (44%), Gaps = 32/258 (12%)

Query: 8   KVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGGTA 67
           +V +VTG   GIG    +     G KV  N  G     +    ++   V +         
Sbjct: 3   RVALVTGGSRGIGAAICVALKAAGYKVAANYAGNDERAKAFEQESGIPVYK-------WD 55

Query: 68  VANYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHAKGAYK 127
           V++Y +  DG   V+  +   G VDIL+NNAGI RD  F KMT   W  V   +  G + 
Sbjct: 56  VSSYQACVDGIARVEADL---GPVDILVNNAGITRDAMFHKMTPEQWGEVIGTNLTGVFN 112

Query: 128 LSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKSKNIHC 187
           ++   W+ MR++ FGRI+  SS  G  G  GQ NY + K   +GL+  LAQEG +K I  
Sbjct: 113 MTHPLWSGMRDRGFGRIVNISSINGQKGQMGQVNYSAAKAGDLGLTKALAQEGAAKGITV 172

Query: 188 NTIAP-----IAASRLTESVMPPEILEQM------KPDYIVPLVLYLCHQDTTETGGVFE 236
           N I P          + E V+   I+ Q+      +P+ +   V++L   D         
Sbjct: 173 NAICPGYIGTEMVRAVPEKVLNERIIPQIPVGRLGEPEEVARCVVFLASDD--------- 223

Query: 237 VGAGWVSKVRLQRSAGVY 254
             AG+++   +  + G Y
Sbjct: 224 --AGFITGSTISANGGQY 239


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: 223
Number of extensions: 12
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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