GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kguD in Escherichia coli BW25113

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 16992 b2913 D-3-phosphoglycerate dehydrogenase (NCBI)

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



>lcl|FitnessBrowser__Keio:16992 b2913 D-3-phosphoglycerate
           dehydrogenase (NCBI)
          Length = 410

 Score =  132 bits (333), Expect = 1e-35
 Identities = 96/277 (34%), Positives = 138/277 (49%), Gaps = 14/277 (5%)

Query: 45  GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVF 104
           G+ S   +T  ++  A +L A+    +G +Q D+    +RGI + N P   T S A+ V 
Sbjct: 58  GLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVI 117

Query: 105 SLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRA-ALG 163
             +L   R V E       G W      A    + +GK LGI+G G IG  +   A +LG
Sbjct: 118 GELLLLLRGVPEANAKAHRGVWNKL---AAGSFEARGKKLGIIGYGHIGTQLGILAESLG 174

Query: 164 FNMKVLYTNRSANPQAEEAYGARRVE-LAELLATADFVCLQVPLTPETKHLIGAAELKSM 222
             +   Y   +  P       A +V+ L++LL  +D V L VP  P TK+++GA E+  M
Sbjct: 175 MYV-YFYDIENKLPLGN----ATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLM 229

Query: 223 KKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPL----PSDSPLLKLANVVA 278
           K  ++LINASRG  VD  AL +AL +  + GA +DVF TEP     P  SPL +  NV+ 
Sbjct: 230 KPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLL 289

Query: 279 LPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315
            PHIG +T E +  +    A  L+   D   T + VN
Sbjct: 290 TPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVN 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: 251
Number of extensions: 18
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: 410
Length adjustment: 29
Effective length of query: 292
Effective length of database: 381
Effective search space:   111252
Effective search space used:   111252
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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