GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mak in Echinicola vietnamensis KMM 6221, DSM 17526

Align Mannokinase (EC 2.7.1.7) (characterized)
to candidate Echvi_3894 Echvi_3894 Transcriptional regulator/sugar kinase

Query= reanno::Smeli:SMc03109
         (298 letters)



>FitnessBrowser__Cola:Echvi_3894
          Length = 291

 Score = 72.4 bits (176), Expect = 1e-17
 Identities = 52/161 (32%), Positives = 79/161 (49%), Gaps = 5/161 (3%)

Query: 1   MFIGIDWGGTKMEVIALDRDGETRARHRVPTPTSGYEDCIRAVV-ELVASAESTAGERGS 59
           + +G+D GGT +    + +DGE   +  +PTP+   ++ I + + + +AS  S   E   
Sbjct: 6   LILGLDIGGTSINA-GIMKDGELIEKREIPTPSQEPQEVILSTIADFIASYFSH--EIDG 62

Query: 60  IGIGIPGSPNPRTGIVRN-SNAVLINGKPLGRDLAAALGREVRLANDANCLAVSEAVDGA 118
           IGIGIPG  +   GIV N  N    N   L   L   L + V + NDANC A+ E   G 
Sbjct: 63  IGIGIPGLVDAEKGIVYNLENIPAFNKVALKDYLERTLEKPVYINNDANCFALGEYKFGG 122

Query: 119 GKDAGVVFGVIVGTGHGGGLAIGKKVHAGYQGVAAEIGHYP 159
                 + G+ +GTG G G+    +++ G+   A E G  P
Sbjct: 123 ANKHRHMVGITLGTGIGTGVITNGELYPGFLCGAGEWGGVP 163


Lambda     K      H
   0.319    0.140    0.436 

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: 170
Number of extensions: 11
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: 298
Length of database: 291
Length adjustment: 26
Effective length of query: 272
Effective length of database: 265
Effective search space:    72080
Effective search space used:    72080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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