GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5014
          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 (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