GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4763
          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 (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