GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N2E2

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate Pf6N2E2_446 Glutathione reductase (EC 1.8.1.7)

Query= SwissProt::P85207
         (461 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_446
          Length = 452

 Score =  257 bits (657), Expect = 5e-73
 Identities = 164/444 (36%), Positives = 238/444 (53%), Gaps = 12/444 (2%)

Query: 4   YDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHHLK 63
           +DL VIG G GG  AA   A  G KV   E+  +GG C+NVGC+P K L++ A      +
Sbjct: 5   FDLYVIGAGSGGVRAARFAAGFGAKVAVAESRYLGGTCVNVGCVPKKLLVYGAHYAEDFE 64

Query: 64  GAEGFGLKA-KPELDLKKLGAWRDGVVKKLTGGVAGLLKGNKVELLRGFARFKGPREIEV 122
            A  +G  A +P  D   L A +D  + +L G    LL  + V L  G AR  GP E+E+
Sbjct: 65  QASAYGWTAGEPSFDWATLIANKDREINRLNGIYRSLLVNSGVVLHEGHARLTGPNEVEI 124

Query: 123 NGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVEEGIPKRLLVIGGGAVGLELG 182
           NG+ Y A+  +IATG  P+ +   P  E    S  A  ++E +PKR++V+GGG + +E  
Sbjct: 125 NGQRYTAKHILIATGGWPV-IPDIPGREHAISSNEAFFLKE-LPKRVIVVGGGYIAVEFA 182

Query: 183 QIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKKQDG-LH 241
            I+H +G++ +L+      L   D      L + L + GL ++        EK  DG L 
Sbjct: 183 GIFHGMGAQTSLLYRGGLFLRGFDGAVRKHLAEELTRRGLDLQFDADIKCIEKLDDGSLR 242

Query: 242 VLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSAPGV 301
           V L+  Q      ++ D +  A GRRP  + LGLE   V VDE+GF+QVN + ET+ P +
Sbjct: 243 VELKNGQ-----TLLTDCVFYATGRRPMLDNLGLENTAVTVDEKGFVQVNEKYETTEPSI 297

Query: 302 YAIGDVARPPLLAHKAMKEGLVAAENA--AGKNALFDFQ-VPSVVYTGPEWAGVGLTEEE 358
            AIGDV     L   A+ EG+  A       +  L D++ +P+ V++ P    VGLTEE+
Sbjct: 298 LAIGDVIGRVQLTPVALAEGMAVARRLFKPEQYRLVDYRMIPTAVFSLPNIGTVGLTEEQ 357

Query: 359 ARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAEAT 418
           AR+ G+ V++ +  F     +LT      L+K+V DA TD +LG  +VGP AGE++    
Sbjct: 358 AREEGHEVQIFESRFRPMKLSLTECQERTLMKLVVDARTDKVLGCHMVGPDAGEIVQGLA 417

Query: 419 LALEMGATVSDLGLTIHPHPTLSE 442
           +AL+ GAT  D   TI  HPT +E
Sbjct: 418 IALKAGATKRDFDETIGVHPTAAE 441


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: 498
Number of extensions: 26
Number of successful extensions: 5
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: 452
Length adjustment: 33
Effective length of query: 428
Effective length of database: 419
Effective search space:   179332
Effective search space used:   179332
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