GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Shewanella oneidensis MR-1

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 200048 SO0862 D-3-phosphoglycerate dehydrogenase (NCBI ptt file)

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



>FitnessBrowser__MR1:200048
          Length = 409

 Score =  137 bits (345), Expect = 4e-37
 Identities = 100/288 (34%), Positives = 144/288 (50%), Gaps = 11/288 (3%)

Query: 33  DAFVAALKDADG-GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANT 91
           +A   ++KDA   GI S  +++  +L+ A +L A+    +G +Q D+A     GI + N 
Sbjct: 45  EALHESIKDAHFIGIRSRTQLSADVLKRAEKLIAIGCFCIGTNQVDLATAESLGIPVFNA 104

Query: 92  PDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGR 151
           P   T S A+ V   I+   R + E       G W  +   A    +V+GKTLG++G G 
Sbjct: 105 PFSNTRSVAELVLGEIIMLMRGIPERNAIAHRGGWMKT---AAGSYEVRGKTLGVIGYGH 161

Query: 152 IGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETK 211
           IG  +   A     M+V++ +         A     +E  +LLA AD V L VP TP+TK
Sbjct: 162 IGTQLGILAET-LGMRVVFFDIEDKLPLGNAQQIHSME--QLLAQADVVSLHVPETPQTK 218

Query: 212 HLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSD---- 267
            +I  AE  +M+K +I INASRG  VD  AL  AL+   + GA +DVF  EP  +D    
Sbjct: 219 DMISTAEFAAMRKGSIFINASRGTVVDIDALTVALKERHLAGAAIDVFPVEPQSNDDEFI 278

Query: 268 SPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315
           SPL  L NV+  PH+G +T E +  +    A  L    D   T + VN
Sbjct: 279 SPLRGLDNVLLTPHVGGSTAEAQENIGIEVAGKLAKYSDNGSTVSAVN 326


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: 268
Number of extensions: 13
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: 409
Length adjustment: 29
Effective length of query: 292
Effective length of database: 380
Effective search space:   110960
Effective search space used:   110960
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: 49 (23.5 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