GapMind for catabolism of small carbon sources

 

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

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate N515DRAFT_1253 N515DRAFT_1253 2-dehydro-3-deoxy-L-fuconate dehydrogenase (EC 1.1.1.-)

Query= BRENDA::Q1J2J0
         (255 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1253
          Length = 248

 Score =  157 bits (396), Expect = 3e-43
 Identities = 98/246 (39%), Positives = 134/246 (54%), Gaps = 9/246 (3%)

Query: 15  RLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAAREL-DGTFERLNVTD 73
           RL G+HALVT    GIG   A   A+ GARV   D++       + E  +   ERL+VTD
Sbjct: 4   RLAGKHALVTAAGAGIGRATALAFAREGARVLATDIDEQALAALSAEAPELRTERLDVTD 63

Query: 74  ADAVADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFGRTML 133
              +  L    P  DVL N AG V      DT D  W+   ++N+D +F  C+     ML
Sbjct: 64  PVQIDRLVASHPPFDVLFNCAGYVHAGTILDTDDAAWKRSFAINVDSMFHLCQRVLPAML 123

Query: 134 ARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVAPGYT 193
            RG G+IV+ +S++  I   P  + AY+ +KAAVI LT+S+A ++  RG+R NA+ PG  
Sbjct: 124 ERGGGSIVNMSSVASSIKGVPN-RFAYSTTKAAVIGLTKSVAADFVGRGIRCNAICPGTV 182

Query: 194 ATP------LTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLV 247
            TP          G E   WR  +++  P+GRL  P EIA   LYLASD A+F TG   +
Sbjct: 183 KTPSLGDRVRALGGDEDAVWR-GFVERQPMGRLGNPEEIAMLALYLASDEAAFTTGTVHI 241

Query: 248 VDGGYT 253
           VDGG++
Sbjct: 242 VDGGWS 247


Lambda     K      H
   0.319    0.134    0.408 

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: 160
Number of extensions: 10
Number of successful extensions: 4
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: 255
Length of database: 248
Length adjustment: 24
Effective length of query: 231
Effective length of database: 224
Effective search space:    51744
Effective search space used:    51744
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: 46 (22.3 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