GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pseudomonas fluorescens FW300-N2C3

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate AO356_24675 AO356_24675 bifunctional glyoxylate/hydroxypyruvate reductase B

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_24675
          Length = 325

 Score =  321 bits (823), Expect = 1e-92
 Identities = 173/317 (54%), Positives = 219/317 (69%), Gaps = 3/317 (0%)

Query: 2   KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVA---ALKDADGGIGSSVKITPAMLE 58
           K +V +K+L   ++A LQ  AQV  ++            AL  A G +G+S+K+  A+L+
Sbjct: 3   KHVVLYKALSPQLMARLQAQAQVTLIERLDAQGLAQLRDALPTAHGLLGASLKLDAALLD 62

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

Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178
             V++G WQ SIGP  FG DV GKTLGI+G+GRIG A+A+R   GF M VLY + S  P 
Sbjct: 123 NLVRSGGWQQSIGPRHFGTDVHGKTLGIIGMGRIGEALAQRGHFGFGMPVLYHSHSPKPA 182

Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238
            E+ +GAR   L  LL  ADFVCL +PLT ET+ LI A     M+   + IN SRG  VD
Sbjct: 183 VEQRFGARYCSLETLLQQADFVCLTLPLTAETQGLIDAQAFARMRPETLFINISRGKVVD 242

Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298
           E ALI+AL+NG I GAGLDVFE EPL +DSPLL++ NVVA PH+GSATHETR AMAR A 
Sbjct: 243 EAALIDALRNGQIRGAGLDVFEHEPLSADSPLLQMDNVVATPHMGSATHETREAMARCAV 302

Query: 299 ENLVAALDGTLTSNIVN 315
           +NL+AAL G    N+VN
Sbjct: 303 DNLLAALAGERPENLVN 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: 264
Number of extensions: 8
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: 325
Length adjustment: 28
Effective length of query: 293
Effective length of database: 297
Effective search space:    87021
Effective search space used:    87021
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: 48 (23.1 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