GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Pseudomonas simiae WCS417

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Cla h 8; EC 1.1.1.138 (characterized)
to candidate GFF4186 PS417_21440 3-ketoacyl-ACP reductase

Query= SwissProt::P0C0Y5
         (267 letters)



>FitnessBrowser__WCS417:GFF4186
          Length = 247

 Score =  122 bits (307), Expect = 6e-33
 Identities = 83/249 (33%), Positives = 132/249 (53%), Gaps = 7/249 (2%)

Query: 16  LSLKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKA 75
           +SL+GKV +VTGAS  +G+G   A      GA V  T A+ A GAE     L++  G++ 
Sbjct: 1   MSLQGKVALVTGAS--RGIGQAIALELGRQGAVVIGT-ATSASGAERIAATLKEN-GVQG 56

Query: 76  KAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQVDLNG 135
              +  V S ES   ++ ++ A FG     + NAG T D+ ++    + W  VV  +LN 
Sbjct: 57  TGLELNVTSDESVAAVLAEITAQFGAPAILVNNAGITRDNLMMRMKDDEWYDVVDTNLNS 116

Query: 136 TFHCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRD 195
            F  +K V     +   G ++   S+ G + N    Q +Y  AKAG    +R+LA E   
Sbjct: 117 LFRLSKGVLRGMTKARWGRIINIGSVVGAMGN--AGQVNYASAKAGLEGFSRALAREVGS 174

Query: 196 FA-RVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFASDASTYTT 254
            +  VNS++PG+IDT ++  +P+  ++   + IP+GR G A+E+     + ASD + Y T
Sbjct: 175 RSITVNSVAPGFIDTDMTRELPEAQREALLTQIPLGRLGQAQEIANVVTFLASDGAAYVT 234

Query: 255 GADLLIDGG 263
           GA + ++GG
Sbjct: 235 GATIPVNGG 243


Lambda     K      H
   0.316    0.131    0.383 

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: 161
Number of extensions: 8
Number of successful extensions: 3
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: 267
Length of database: 247
Length adjustment: 24
Effective length of query: 243
Effective length of database: 223
Effective search space:    54189
Effective search space used:    54189
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: 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