GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pedobacter sp. GW460-11-11-14-LB5

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate CA265_RS09010 CA265_RS09010 3-phosphoglycerate dehydrogenase

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



>FitnessBrowser__Pedo557:CA265_RS09010
          Length = 315

 Score =  127 bits (320), Expect = 3e-34
 Identities = 92/291 (31%), Positives = 142/291 (48%), Gaps = 17/291 (5%)

Query: 25  VQVDATQHDAFVAALKDADG-GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTR 83
           V  +    D    ALK+ D   + S+ K+   +++    +K +    VG D  DV     
Sbjct: 24  VDTETVPQDQLAEALKNYDAITVRSATKVRKELIDAVPNIKLIGRGGVGMDNIDVEYARS 83

Query: 84  RGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKA-GHWQHSIGPALF--GVDVQ 140
           +GI + NTP   + S A+ VFS +    R + +    +   G  Q +     +  G ++ 
Sbjct: 84  QGINVVNTPAASSLSVAELVFSHLFTGIRFLQDANRKMPVEGSTQFNNLKKAYAKGTELS 143

Query: 141 GKTLGIVGLGRIGGAVARRAALGFNMKVLYTNR--SANPQAEEAYGARRVE-------LA 191
           GKT+GI+G GRIG A A+  ALG  M VL  +   S +    E  G + V        L 
Sbjct: 144 GKTIGIIGFGRIGRATAK-VALGLGMNVLAYDLYPSESEITLEFQGGKSVSIPIKTVSLD 202

Query: 192 ELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTI 251
           E++  +DF  L  P     K ++GA E   MK    ++N SRG T+DE ALI+AL +G +
Sbjct: 203 EVITGSDFFSLHTPFAD--KPILGAEEFAKMKNGVGIVNCSRGGTIDELALIDALNSGKV 260

Query: 252 HGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLV 302
             AGLDVF+ EP P  + +L    +   PHIG++T+E +  +    A  ++
Sbjct: 261 SFAGLDVFDNEPTPL-AEILTHPKISLTPHIGASTNEAQERIGTELATLII 310


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: 215
Number of extensions: 11
Number of successful extensions: 3
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: 315
Length adjustment: 27
Effective length of query: 294
Effective length of database: 288
Effective search space:    84672
Effective search space used:    84672
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