GapMind for catabolism of small carbon sources

 

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

Align 6-phosphogluconate dehydrogenase, decarboxylating; EC 1.1.1.44 (uncharacterized)
to candidate N515DRAFT_2996 N515DRAFT_2996 3-hydroxyisobutyrate dehydrogenase

Query= curated2:Q931R3
         (468 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2996
          Length = 286

 Score = 82.4 bits (202), Expect = 2e-20
 Identities = 84/276 (30%), Positives = 127/276 (46%), Gaps = 24/276 (8%)

Query: 1   MTQQIGVIGLAVMGKNLAWNIESHGYSVSVFNRSSEKTDLMVEESKGKNIHPTYSLEEFV 60
           MT +   +GL  MG  +A +++S G   +V NR+  K D +  E  G    P   LE+  
Sbjct: 1   MTFKAAFVGLGAMGAPMAGHLKSKGLLHAVANRTQAKADALARE-LGVVAPP---LEQLA 56

Query: 61  NSLEKPRKILLMVQAGKATDATIDSLLPLLDDGDILIDGGNTNYQDTIRRNKA-LAQSAI 119
              E    I L V A     ATID++LP L  G +++D  +T   DT +R  A LA + +
Sbjct: 57  AQCE---VIALCVTADADVLATIDTMLPHLKRGAVVVD-HSTVAPDTAKRAAARLATAGV 112

Query: 120 NFIGMGVSGGEIGALTGP-SLMPGGQEEAYNKVADILDAIAAKAKDGASCVTYIGPNGAG 178
           +F+   VSGG  GA  G  S+M GG      +   +L+A A +       VT++G  GAG
Sbjct: 113 DFLDAPVSGGVEGAKNGKLSVMVGGDAAVLERARPVLEAYALR-------VTHLGDVGAG 165

Query: 179 HYVKMVHNGIEYADMQLIAESYAMMKELLGMSHEDIAQTFKDWNAGELESYLIEITGDIF 238
              K V+  +     Q + E  A + E LG+  E +  T     AG   S+ +E  G   
Sbjct: 166 QATKAVNQVLVAGIAQAVCEGLA-LGEALGLEAERLLPTL---GAGAAGSWFLEKRGATM 221

Query: 239 MKLDEN---KEALVEKILDTAGQKGTGKWTSINALE 271
           ++ + +   K AL+ K L    +   G  T    +E
Sbjct: 222 LRDEFSVGFKLALLHKDLGIVKRIAEGAGTDRTVIE 257


Lambda     K      H
   0.315    0.134    0.384 

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: 212
Number of extensions: 7
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: 468
Length of database: 286
Length adjustment: 30
Effective length of query: 438
Effective length of database: 256
Effective search space:   112128
Effective search space used:   112128
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: 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