GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pseudomonas fluorescens FW300-N2E3

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate AO353_26885 AO353_26885 bifunctional glyoxylate/hydroxypyruvate reductase B

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



>FitnessBrowser__pseudo3_N2E3:AO353_26885
          Length = 328

 Score =  322 bits (826), Expect = 6e-93
 Identities = 172/320 (53%), Positives = 224/320 (70%), Gaps = 3/320 (0%)

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

Query: 59  GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118
            A RL+A++++SVG D +D+  L RR I+L+NTPDVLTE+TADT F+LILA+ARRVVELA
Sbjct: 63  LAPRLEAIASVSVGVDNYDIDYLNRRQILLSNTPDVLTETTADTGFALILATARRVVELA 122

Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178
             V+AG W  +IGPA FG DV GKTLGI+G+GRIG A+A+R   GF M +LY + S  P 
Sbjct: 123 NLVRAGQWNRNIGPAHFGTDVHGKTLGIIGMGRIGEALAQRGHFGFGMPILYHSHSVKPA 182

Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238
            E+ + A+   L  LL  ADF+CL +PLT ET+ LIGA +   M+  +I IN SRG  VD
Sbjct: 183 VEQRFNAQYRSLPALLQQADFICLTLPLTAETEGLIGAEQFALMRPESIFINISRGKVVD 242

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

Query: 299 ENLVAALDGTLTSNIVNREV 318
           +NL+AAL G   +N+VN +V
Sbjct: 303 DNLLAALAGERPANLVNGQV 322


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: 328
Length adjustment: 28
Effective length of query: 293
Effective length of database: 300
Effective search space:    87900
Effective search space used:    87900
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