GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Sinorhizobium meliloti 1021

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate SM_b21143 SM_b21143 mercuric reductase

Query= SwissProt::P85207
         (461 letters)



>FitnessBrowser__Smeli:SM_b21143
          Length = 473

 Score =  238 bits (606), Expect = 4e-67
 Identities = 141/446 (31%), Positives = 231/446 (51%), Gaps = 8/446 (1%)

Query: 2   KTYDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHH 61
           K +D ++IG G  G   A R + +G  V  +E    GG C+N GC+PTKA++ +A  +H 
Sbjct: 19  KHFDAVIIGAGQAGPSLAGRLSGVGKTVALIERKLFGGTCVNTGCMPTKAMVASAYAIHT 78

Query: 62  LKGAEGFGLKAKP-ELDLKKLGAWRDGVVKKLTGGVAGLLKGNK-VELLRGFARFKGPRE 119
            +    +G+   P  +D  ++ A ++ V      GV   LKG K   +  G ARF+GPRE
Sbjct: 79  ARRGAEYGMTTGPVSVDFGRVMARKEKVRLDARSGVEKWLKGMKNCTVFEGHARFEGPRE 138

Query: 120 IEVNGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVEEG-IPKRLLVIGGGAVG 178
           + +  E    +   +  G     +   P   DV   T +  ++   +P+ L+V+GG  +G
Sbjct: 139 VRIGDELISGERIFVNVGGRAA-VADLPGVNDVPYLTNSSIMDLAELPEHLVVVGGSYIG 197

Query: 179 LELGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKKQD 238
           LE  Q++ R GS+VT+IE    ++   D E +  +R+ LE EG+++RT  + + +    D
Sbjct: 198 LEFAQMFRRFGSDVTVIEKGARLIGREDPEVSDAIREILENEGVRIRTNAECIRFSNHAD 257

Query: 239 GLHVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSA 298
            + V ++   G  + E+    +L+A GR P T+ LGL+KAGVK DERG+I+V+  + T+ 
Sbjct: 258 SVAVGVDCTSG--EPEVSGSHVLLATGRHPNTDDLGLDKAGVKTDERGYIEVDDSLRTNV 315

Query: 299 PGVYAIGDVARPPLLAHKAMKEGLVAAENAAGKNA--LFDFQVPSVVYTGPEWAGVGLTE 356
           P ++A+GD        H +  +  + A N    +   + D      +Y  P     G+TE
Sbjct: 316 PHIFAMGDCNGRGAFTHTSYNDFEIVAANLIDNDPRRVSDRIQTYALYIDPPLGRAGMTE 375

Query: 357 EEARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAE 416
            EARK G+ + VG  P +  GRA+  G  +G +KV+ DAETD +LG  ++G    E +  
Sbjct: 376 TEARKKGHKLLVGTRPMTRVGRAVEKGETQGFMKVIVDAETDEILGASILGTGGDEAVQS 435

Query: 417 ATLALEMGATVSDLGLTIHPHPTLSE 442
               +      + +   +H HPT+SE
Sbjct: 436 ILDVMYAKKPYTMIARAVHIHPTVSE 461


Lambda     K      H
   0.316    0.138    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: 583
Number of extensions: 35
Number of successful extensions: 6
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: 461
Length of database: 473
Length adjustment: 33
Effective length of query: 428
Effective length of database: 440
Effective search space:   188320
Effective search space used:   188320
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: 51 (24.3 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