GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoK in Arenitalea lutea P7-3-5

Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate WP_026009921.1 P735_RS0102615 sugar kinase

Query= BRENDA::Q9WXS2
         (339 letters)



>NCBI__GCF_000283015.1:WP_026009921.1
          Length = 335

 Score =  239 bits (609), Expect = 9e-68
 Identities = 135/341 (39%), Positives = 198/341 (58%), Gaps = 8/341 (2%)

Query: 1   MKVVTFGEIMLRLSPPDHK-RIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNP 59
           M   TFGEIM+RL+P ++  +I  + SF+V Y G+E+NVA+ L  +G    ++TKLP N 
Sbjct: 1   MSFTTFGEIMMRLTPSNYSNKINSSSSFNVDYAGSESNVASSLGVLGNKVSYITKLPENQ 60

Query: 60  LGDAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFD 119
           LGDA    LR +G+ T  I RGG+R+G Y +E+GAS RPS V+YDR +S+ SE ++++F+
Sbjct: 61  LGDATIRSLRAYGIDTGNIIRGGHRMGTYIIELGASIRPSSVIYDRKYSSFSEIEKDEFN 120

Query: 120 WEKILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLW-TKEEAQ 178
           WE IL+  +W   SGITP L K+         ++A + GV V+ D+NYR  LW    +A+
Sbjct: 121 WEDILNDKKWLFLSGITPVLSKQCAEETIKVSQIAKQLGVKVAFDMNYRRSLWKDAADAR 180

Query: 179 KVMIPFMEYVDVLIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTRKYNFKTVG 238
           K+    +E  D+L  N + ++ V  ++  G    T +L  E   + A+    K+  K + 
Sbjct: 181 KIFDKILENTDLLFGNADVLKDVYNLNPSG----TSRL--ENTKEAAQMAADKFGIKHIA 234

Query: 239 ITLRESISATVNYWSVMVFENGQPHFSNRYEIHIVDRVGAGDSFAGALIYGSLMGFDSQK 298
            T+RE  SA+VN  S +   N + + S   E+ I DR G GD+FA A ++G    +D +K
Sbjct: 235 FTIREHCSASVNKVSGVFLTNSKYYSSKTIEVAITDRFGTGDAFAAAFLHGIEHQWDDKK 294

Query: 299 KAEFAAAASCLKHTIPGDFVVLSIEEIEKLASGATSGRVER 339
             +FA AA  LKHTI GD    S  EI  +  G  SG V R
Sbjct: 295 VIDFATAAFALKHTIQGDQHTSSEREILSIMEGHISGHVLR 335


Lambda     K      H
   0.319    0.136    0.397 

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: 283
Number of extensions: 14
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: 339
Length of database: 335
Length adjustment: 28
Effective length of query: 311
Effective length of database: 307
Effective search space:    95477
Effective search space used:    95477
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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