GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mt2d in Pseudomonas fluorescens FW300-N1B4

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Cla h 8; EC 1.1.1.138 (characterized)
to candidate Pf1N1B4_451 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= SwissProt::P0C0Y5
         (267 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_451
           3-oxoacyl-[acyl-carrier protein] reductase (EC
           1.1.1.100)
          Length = 247

 Score =  123 bits (308), Expect = 4e-33
 Identities = 83/249 (33%), Positives = 131/249 (52%), Gaps = 7/249 (2%)

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

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

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

Query: 196 FA-RVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFASDASTYTT 254
            +  VNS++PG+IDT ++  +P+  ++   + IP+GR G A+E+     + ASD + Y T
Sbjct: 175 RSITVNSVAPGFIDTDMTRELPEAQREALQTQIPLGRLGQAQEIASVVAFLASDGAAYVT 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: 159
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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