GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguK in Dyella japonica UNC79MFTsu3.2

Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate N515DRAFT_0916 N515DRAFT_0916 Sugar or nucleoside kinase, ribokinase family

Query= metacyc::MONOMER-12748
         (320 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0916
          Length = 312

 Score = 72.0 bits (175), Expect = 2e-17
 Identities = 77/258 (29%), Positives = 109/258 (42%), Gaps = 18/258 (6%)

Query: 42  AIGLARLGFKVAWLSRVGNDSLGRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGD 101
           A+GLARLG  VA+  R+G D+ G + LD LR  G+D   ++ +    TG  + S     D
Sbjct: 51  AMGLARLGNAVAFHGRLGADAWGSYCLDALRDAGIDVASLQPEAALRTGITV-SLSTPRD 109

Query: 102 DPRVEYFRRGSAASHLAISDLDPALLR-ARHLHATGIPPALSDSARELSGHLMHTQRSAG 160
              V +     A + L   D+  ALL  A HLH +     L  + R     L    R AG
Sbjct: 110 RSLVTF---SGAIAALRAEDVSDALLAGAGHLHVSSF--YLQKALRADIRQLFARARKAG 164

Query: 161 HSVSFDPNLRPALWPSEALMIREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQ 220
            ++S DP   P     E     ++  +       LP   E R LTG +      A  LD 
Sbjct: 165 LTLSLDPGFDP-----EQRWGDDLRGVLEDVDVFLPNEEELRALTGENHVRKALA-ALDN 218

Query: 221 GAEAVVIKLGAHGAYYRTQLDAGFVEGVP--VAQVVDTVGAGDGFAVGLISALLESRGIL 278
           G   +V K G  G      L  G +   P    + VD+ GAGD F  G + A L    + 
Sbjct: 219 GRTLIVAKRGRQGC---AVLHDGKLLVAPALAVEAVDSTGAGDSFDAGFLHAWLRGLPLR 275

Query: 279 EAVQRANWIGSRAVQSRG 296
           + ++  N  GS + +  G
Sbjct: 276 DCLRWGNACGSLSTRGIG 293


Lambda     K      H
   0.321    0.138    0.414 

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: 254
Number of extensions: 22
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: 320
Length of database: 312
Length adjustment: 27
Effective length of query: 293
Effective length of database: 285
Effective search space:    83505
Effective search space used:    83505
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 (21.9 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