GapMind for catabolism of small carbon sources

 

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

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate Pf1N1B4_5014 Glutathione reductase (EC 1.8.1.7)

Query= SwissProt::P85207
         (461 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5014 Glutathione reductase
           (EC 1.8.1.7)
          Length = 452

 Score =  249 bits (635), Expect = 2e-70
 Identities = 159/443 (35%), Positives = 238/443 (53%), Gaps = 10/443 (2%)

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

Query: 64  GAEGFG-LKAKPELDLKKLGAWRDGVVKKLTGGVAGLLKGNKVELLRGFARFKGPREIEV 122
            ++GFG    + + D   L A +D  + +L G    LL  + V L  G A+   P  +E 
Sbjct: 65  QSQGFGWTPGEAKFDWATLIANKDREINRLNGIYRNLLVNSGVTLHEGHAKIVDPHTVEF 124

Query: 123 NGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVEEGIPKRLLVIGGGAVGLELG 182
           +G+ Y A++ +IATG  P  +   P  E    S +A  ++E +PKR+LV+GGG + +E  
Sbjct: 125 DGKRYTAKNILIATGGWPQ-IPEIPGHEHAISSNQAFFLKE-LPKRVLVVGGGYIAVEFA 182

Query: 183 QIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKKQDGLHV 242
            I+H LG+E TL+      L   D      L++ L K G+ ++        EK+ DG   
Sbjct: 183 GIFHGLGAETTLLYRGDLFLRGFDGAVRKHLQEELTKRGMNLQFNADIERIEKQADGS-- 240

Query: 243 LLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSAPGVY 302
           L    + G + E   D +  A GRRP  + LGLE  GVK+D++GF++V+ + +T+ P + 
Sbjct: 241 LKATLKDGRKLE--ADCVFYATGRRPMLDNLGLENTGVKLDKKGFVEVDEQYQTAEPSIL 298

Query: 303 AIGDVARPPLLAHKAMKEGLVAAENAAGKNAL--FDFQ-VPSVVYTGPEWAGVGLTEEEA 359
           A+GDV     L   A+ EG+  A            D++ +P+ V++ P    VGLTEEEA
Sbjct: 299 ALGDVIGRVQLTPVALAEGMAVARRLFKPEQYRPVDYKMIPTAVFSLPNIGTVGLTEEEA 358

Query: 360 RKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAEATL 419
           R+AG+ V + +  F      LT      L+K+V DA+TD +LG  +VGP+AGE++    +
Sbjct: 359 REAGHEVVIFESRFRPMKLTLTECQERTLMKLVVDAKTDKVLGCHMVGPEAGEIVQGLAI 418

Query: 420 ALEMGATVSDLGLTIHPHPTLSE 442
           AL+ GAT  D   TI  HPT +E
Sbjct: 419 ALKAGATKRDFDETIGVHPTAAE 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: 536
Number of extensions: 25
Number of successful extensions: 4
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 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, the preprint on GapMind for carbon sources, 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