GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Shewanella oneidensis MR-1

Align hexokinase (EC 2.7.1.1) (characterized)
to candidate 202608 SO3507 conserved hypothetical protein (NCBI ptt file)

Query= BRENDA::Q96Y14
         (299 letters)



>FitnessBrowser__MR1:202608
          Length = 300

 Score =  104 bits (260), Expect = 2e-27
 Identities = 77/245 (31%), Positives = 120/245 (48%), Gaps = 28/245 (11%)

Query: 3   IIVGVDAGGTKTKAVAYDCEGNFIGEGSSGPGNYHNVGLTRAIENIK--------EAVKI 54
           + +GVD GG+K +A  Y  +G  +G G +G  N  + GL +  E+I+        +A   
Sbjct: 11  LFIGVDGGGSKCRATIYTADGTVLGTGVAGRANPLH-GLAQTFESIEASAHQALLDAGMK 69

Query: 55  AAKGEADVVGMGVAGLD------SKFDWENFTPLASLIAPKVIIQHDGVIALFAETLGEP 108
           A      V G+G+AG++         +W++  P A++      +  D   A      G  
Sbjct: 70  ATDSHLLVAGLGLAGVNVPRLYQDVVNWQH--PFAAMY-----VTTDLHTACIGAHRGAD 122

Query: 109 GVVVIAGTGSVVEGYNGKEFLRVGGRGWLLSDDGSAYWVGRKALRKVLKMMDGLENKTIL 168
           G V+I GTGS    + G   L +GG G+ L D GS  W+G KA   VL  +DG    T L
Sbjct: 123 GAVIITGTGSCGYAHVGDASLSIGGHGFALGDKGSGAWLGLKAAEHVLLALDGFATPTAL 182

Query: 169 YNKVLKTINVKDLDELV--MWSYTSSCQIDLVASIAKAVDEAANEGDTVAMDILKQGAEL 226
              +L  + VKD   +V  +   +SSC     A +A+ V + AN GD VA+ I+++GA+ 
Sbjct: 183 TEMLLSHLGVKDALGIVEHLAGKSSSC----YAQLARNVLDCANAGDQVAIAIVQEGADY 238

Query: 227 LASQA 231
           ++  A
Sbjct: 239 ISEMA 243


Lambda     K      H
   0.317    0.137    0.395 

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: 225
Number of extensions: 15
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: 299
Length of database: 300
Length adjustment: 27
Effective length of query: 272
Effective length of database: 273
Effective search space:    74256
Effective search space used:    74256
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: 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