GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pseudomonas putida KT2440

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate PP_0762 PP_0762 Glycerate dehydrogenase

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



>FitnessBrowser__Putida:PP_0762
          Length = 321

 Score =  141 bits (356), Expect = 2e-38
 Identities = 96/300 (32%), Positives = 149/300 (49%), Gaps = 11/300 (3%)

Query: 13  DVLAYLQQHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVG 72
           D+    QQ  Q     AT+ +     L+ A   + + V +  A L    +LK +   + G
Sbjct: 21  DLSPLKQQFDQFELFAATRPEQVAERLQGAVAVVSNKVMLDAATLAANPQLKLILVAATG 80

Query: 73  FDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGP 132
            +  D+A    +GI + N     T S A    +L+LA A R+ +  + V  G W  +   
Sbjct: 81  TNNVDLAAARAQGITVCNCQGYGTPSVAQHTLALLLALATRLCDYNQAVADGQWAKASQF 140

Query: 133 ALFG---VDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVE 189
            L     V+++GKTLG++G G +GGAVAR A   F M+VL       P+      A R+ 
Sbjct: 141 CLLDFPIVELEGKTLGLLGHGELGGAVARLAE-AFGMRVLSGQIPGRPER-----ADRLP 194

Query: 190 LAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNG 249
           L ELL   D + L  PL   T+H++GA EL  +K +A+++N +RG  +DE+AL +AL+ G
Sbjct: 195 LDELLPQVDALTLHCPLNEHTRHMLGARELALLKPNALVVNTARGGLIDEQALADALRGG 254

Query: 250 TIHGAGLDVFETEPLPSDSPLLK--LANVVALPHIGSATHETRHAMARNAAENLVAALDG 307
            + GA  DV   EP  + +PLL+  +  ++  PH      E+R  +    +EN  A   G
Sbjct: 255 HLGGAATDVLSVEPPVNGNPLLEPGIPRLIITPHSAWGAVESRQRIVGQLSENAQAFFAG 314


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: 194
Number of extensions: 9
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: 321
Length adjustment: 28
Effective length of query: 293
Effective length of database: 293
Effective search space:    85849
Effective search space used:    85849
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