GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pseudomonas simiae WCS417

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF932 PS417_04730 bifunctional glyoxylate/hydroxypyruvate reductase B

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



>FitnessBrowser__WCS417:GFF932
          Length = 324

 Score =  322 bits (824), Expect = 1e-92
 Identities = 175/320 (54%), Positives = 221/320 (69%), Gaps = 4/320 (1%)

Query: 2   KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDA---FVAALKDADGGIGSSVKITPAMLE 58
           K ++A+  +  +++  LQQ  +V+  +    D    F  AL  A G IG   K+    L+
Sbjct: 3   KTVLAFSRVTPEMIERLQQDFEVIAPNPKLGDISAQFNEALPHAHGLIGVGRKLGREQLQ 62

Query: 59  GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118
           GA++L+ +S++SVG+D +DVA    RGI+L NTPDVLTESTAD  F+L+++SARRV EL 
Sbjct: 63  GASKLEVVSSVSVGYDNYDVAYFNERGIMLTNTPDVLTESTADLAFALLMSSARRVAELD 122

Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178
            W KAG W+ S+G  LFG DV GKTLGIVG+G IG AVARR  LGFNM +LY+  S  P 
Sbjct: 123 AWTKAGQWKASVGAPLFGCDVHGKTLGIVGMGNIGAAVARRGRLGFNMPILYSGNSRKPA 182

Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238
            E+  GA+   L ELLA ADFVCL VPL+ +T+HLI   EL  MK SAILIN SRG  VD
Sbjct: 183 LEQELGAQFRSLDELLAEADFVCLVVPLSDKTRHLISTRELGLMKSSAILINISRGPVVD 242

Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298
           E ALI+ALQN TI GAGLDV+E EPL ++SPL +L+N V LPHIGSATHETR AMA  A 
Sbjct: 243 EPALIDALQNQTIRGAGLDVYEQEPL-AESPLFQLSNAVTLPHIGSATHETREAMANRAL 301

Query: 299 ENLVAALDGTLTSNIVNREV 318
           +NL +AL G    ++VN +V
Sbjct: 302 DNLRSALLGQRPQDLVNPQV 321


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: 258
Number of extensions: 8
Number of successful extensions: 2
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: 324
Length adjustment: 28
Effective length of query: 293
Effective length of database: 296
Effective search space:    86728
Effective search space used:    86728
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