GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cola:Echvi_2777
          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:

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