GapMind for catabolism of small carbon sources

 

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

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Pf1N1B4_4763 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43)

Query= reanno::BFirm:BPHYT_RS11290
         (321 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4763 2-ketogluconate
           6-phosphate reductase (EC 1.1.1.43)
          Length = 341

 Score =  311 bits (798), Expect = 1e-89
 Identities = 167/317 (52%), Positives = 220/317 (69%), Gaps = 3/317 (0%)

Query: 2   KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVA---ALKDADGGIGSSVKITPAMLE 58
           K++V +K L   ++A L +  +V  +D+   +       AL  A G +G+S+K+   +L+
Sbjct: 3   KQVVLYKKLSPLLMARLHEQTEVTLIDSLDAEGLAQLRRALPRAQGLLGASLKLDAGLLD 62

Query: 59  GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118
            A  L+A++++SVG D +D+  LT R I+L+NTPDVLTE+TADT F+LILA+ARRVVELA
Sbjct: 63  LAPNLEAIASVSVGVDNYDIDYLTERRILLSNTPDVLTETTADTGFALILATARRVVELA 122

Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178
             V+AG W  +IGP  FG DV GKTLGI+G+GRIG A+A+R   GF M V+Y + S  P 
Sbjct: 123 NMVRAGQWNRNIGPTHFGSDVHGKTLGIIGMGRIGEALAQRGHFGFGMPVVYHSHSPKPA 182

Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238
            E+ + A+   L++LL  ADFVCL +PLT  T+ LIGA +   M+   I IN SRG  VD
Sbjct: 183 VEQRFNAQYRSLSDLLQQADFVCLTLPLTAATEGLIGAEQFALMRPETIFINISRGKVVD 242

Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298
           E ALIEAL++  I  AGLDVFE EPL +DSPLL+L NVVA PHIGSATHETR AMAR A 
Sbjct: 243 EPALIEALRHKRIRAAGLDVFEREPLGNDSPLLQLNNVVATPHIGSATHETREAMARCAV 302

Query: 299 ENLVAALDGTLTSNIVN 315
           +NL+AAL G   +N+VN
Sbjct: 303 DNLLAALAGERPANLVN 319


Lambda     K      H
   0.317    0.131    0.366 

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: 252
Number of extensions: 3
Number of successful extensions: 1
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: 321
Length of database: 341
Length adjustment: 28
Effective length of query: 293
Effective length of database: 313
Effective search space:    91709
Effective search space used:    91709
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 (21.7 bits)
S2: 49 (23.5 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