GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Phaeobacter inhibens BS107

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate GFF983 PGA1_c10000 short chain dehydrogenase / reductase

Query= reanno::Burk376:H281DRAFT_00644
         (263 letters)



>FitnessBrowser__Phaeo:GFF983
          Length = 250

 Score =  109 bits (273), Expect = 5e-29
 Identities = 70/247 (28%), Positives = 126/247 (51%), Gaps = 4/247 (1%)

Query: 12  GLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGIADVSKQAQ 71
           G    ++ G  GIGLA+A+A     AEV I    Q  ++E  +    LH    DV  +A 
Sbjct: 5   GKHALITGGGTGIGLAMAQALAAEGAEVTITGRRQEVLEEVATE--GLHPLAMDVRDEAD 62

Query: 72  VDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKAVPV 131
           V   ID A    G + + V NAGIA    A+ ++    W + ++TNL+  F  +R+++  
Sbjct: 63  VIAKIDAATAARGPIQICVPNAGIAEGK-ALHKMSMEFWRNMMATNLDGAFLTIRESMKS 121

Query: 132 LKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAILPGV 191
           +++T D   ++ +SS+AG  G      Y+++K  ++GL +SL+ +   +    NA+ PG 
Sbjct: 122 MRQT-DWGRVMTVSSIAGLRGLQGAPCYSASKHGLIGLTRSLSEDYLGTPYTFNALCPGY 180

Query: 192 VEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSNVTG 251
           V+   +DR +++ +   G+      +  +     +R++  D++AA  L+L  P   ++ G
Sbjct: 181 VDTPIIDRNVTSISQRAGVSEEDALKIMVSANRHKRLILPDEVAAALLWLCGPGSQSING 240

Query: 252 QAISVDG 258
           Q I + G
Sbjct: 241 QTIEIAG 247


Lambda     K      H
   0.318    0.134    0.375 

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: 128
Number of extensions: 7
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: 263
Length of database: 250
Length adjustment: 24
Effective length of query: 239
Effective length of database: 226
Effective search space:    54014
Effective search space used:    54014
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 (21.7 bits)
S2: 47 (22.7 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