GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kguD in Echinicola vietnamensis KMM 6221, DSM 17526

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Echvi_2777 Echvi_2777 Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like

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



>lcl|FitnessBrowser__Cola:Echvi_2777 Echvi_2777 Haloacid
           Dehalogenase superfamily, subfamily IB, phosphoserine
           phosphatase-like
          Length = 630

 Score =  132 bits (332), Expect = 2e-35
 Identities = 91/275 (33%), Positives = 135/275 (49%), Gaps = 10/275 (3%)

Query: 45  GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVF 104
           GI S  +IT  +LE A RL A+    +G +Q D+     +GI + N P   T S  +   
Sbjct: 279 GIRSKTQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAI 338

Query: 105 SLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGF 164
           S I+   R + +    +  G W  S   +    +V+GK LGI+G G IG  ++  A    
Sbjct: 339 SEIIFLMRNLHDKTLKMHQGIWNKSASGSF---EVRGKKLGIIGYGNIGAQLSVLAE-NM 394

Query: 165 NMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKK 224
            M V Y +         A   +   L ELL T D + L V    E K+++   ++  MKK
Sbjct: 395 GMNVFYYDIVERLALGNA--TKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKK 452

Query: 225 SAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSP----LLKLANVVALP 280
            AIL+N SRG  VD  AL +AL++G + GA +DVF TEP  +D P    L+   N +  P
Sbjct: 453 GAILVNLSRGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTP 512

Query: 281 HIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315
           HIG +T E +  +A+     ++  ++   T N VN
Sbjct: 513 HIGGSTLEAQENIAQFVPGKIIEYINSGNTFNSVN 547


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: 337
Number of extensions: 17
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: 630
Length adjustment: 33
Effective length of query: 288
Effective length of database: 597
Effective search space:   171936
Effective search space used:   171936
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: 51 (24.3 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 paper from 2022 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