GapMind for catabolism of small carbon sources

 

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

Align Glucosamine-6-phosphate deaminase; EC 3.5.99.6; GlcN6P deaminase; GNPDA; Glucosamine-6-phosphate isomerase (uncharacterized)
to candidate Echvi_3893 Echvi_3893 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase

Query= curated2:Q0SP13
         (268 letters)



>FitnessBrowser__Cola:Echvi_3893
          Length = 775

 Score = 81.6 bits (200), Expect = 5e-20
 Identities = 49/144 (34%), Positives = 75/144 (52%), Gaps = 2/144 (1%)

Query: 114 LEKECEEYEKKIKSFGGIMLFVGGIGPDGHIAFNEPGSSLTSRTRIKTLTQDTIIANSRF 173
           ++K C EYE+KI+  GGI  F+GGIGPDGHIAFN  GS + S TR+     +T    +  
Sbjct: 192 IDKWCGEYEQKIREKGGIGFFLGGIGPDGHIAFNTRGSDIFSTTRLTETNFETQAVAAGD 251

Query: 174 FEGNVNKVPKSALTVGIGTIMDSQEI--LIIVNGHNKARALKHAIEKGINHMWTISALQL 231
             G      +  +T+G+ TI+ + E   +II  G  KA+ +K ++E  + ++   + LQ 
Sbjct: 252 LGGIEVSANRLVITIGLDTIVYNPEAVGIIIAAGEAKAQIVKDSLETDLTNIHPATVLQK 311

Query: 232 HKNAIIVSDKNATYELKVGTVEYF 255
            KN      K    +L      Y+
Sbjct: 312 LKNGRFYLTKGGASKLTDSINTYY 335


Lambda     K      H
   0.317    0.135    0.391 

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: 432
Number of extensions: 19
Number of successful extensions: 1
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: 268
Length of database: 775
Length adjustment: 33
Effective length of query: 235
Effective length of database: 742
Effective search space:   174370
Effective search space used:   174370
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 (21.6 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