GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoK in Sphingomonas koreensis DSMZ 15582

Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate Ga0059261_2965 Ga0059261_2965 Sugar kinases, ribokinase family

Query= BRENDA::Q9WXS2
         (339 letters)



>FitnessBrowser__Korea:Ga0059261_2965
          Length = 336

 Score =  187 bits (476), Expect = 3e-52
 Identities = 119/341 (34%), Positives = 172/341 (50%), Gaps = 15/341 (4%)

Query: 2   KVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLG 61
           ++V FGE++LRL+ P  + + QT   DV  GGAEANV   LA +G     V+ +P+N LG
Sbjct: 4   RIVCFGELLLRLTAPGRELLMQTPRLDVVVGGAEANVGIGLANLGHSVSMVSAVPDNALG 63

Query: 62  DAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWE 121
            AA   +R  G  T  +     R+G+YFL  GA  R S +VYDRA SA + A  + FDW+
Sbjct: 64  RAAVQFVRSQGADTSGVQYRDGRMGLYFLTQGAGLRASDIVYDRADSAFANAPADAFDWK 123

Query: 122 KILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWT--KEEAQK 179
            +L GA   H SGITP LG         A + A E GV +S D NYRARLW     + + 
Sbjct: 124 TLLSGASMLHLSGITPALGPATAEAALRAARAAKELGVAISFDGNYRARLWEAWDSDPRA 183

Query: 180 VMIPFMEYVDVLIANEEDIEKVLG--ISVEGLDLKTGKLNREAYAKIAEEVTRKY-NFKT 236
           V+   +   D +  N  D+  +LG   S +G D +     REA    AE     + N K 
Sbjct: 184 VLTELVSLADTMFGNHRDVSLLLGKTFSGDGADRR-----REA----AEAAFAAFPNLKR 234

Query: 237 VGITLRESISATVNYWSVMVFENGQPHFSNRYEI-HIVDRVGAGDSFAGALIYGSLMGFD 295
           +  T R    A  +  +  V    + + +    +  I+DR+G GD++A  +++G L G D
Sbjct: 235 IASTARHVDDADRHRIAARVDTPERGYQTEEVVVAGIIDRIGGGDAYAAGILHGVLSGQD 294

Query: 296 SQKKAEFAAAASCLKHTIPGDFVVLSIEEIEKLASGATSGR 336
            +       A +CLKH++PGD  +    +I+    G    R
Sbjct: 295 LEGTVASGLALTCLKHSLPGDASLFRQADIDAFLEGGLDVR 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: 263
Number of extensions: 9
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: 339
Length of database: 336
Length adjustment: 28
Effective length of query: 311
Effective length of database: 308
Effective search space:    95788
Effective search space used:    95788
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 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