GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh3 in Herbaspirillum seropedicae SmR1

Align D-gluconate dehydrogenase 21.7 kD subunit (EC 1.1.99.3) (characterized)
to candidate HSERO_RS16745 HSERO_RS16745 gluconate 2-dehydrogenase

Query= metacyc::MONOMER-12747
         (251 letters)



>FitnessBrowser__HerbieS:HSERO_RS16745
          Length = 240

 Score =  271 bits (693), Expect = 9e-78
 Identities = 134/248 (54%), Positives = 178/248 (71%), Gaps = 12/248 (4%)

Query: 4   QDRDNPRREFLRKSLTLIPVVTVASTGLGGSLLAAASETAIAATPATPGKQPAGSGQGYE 63
           QD++ PRR FLR+ L ++P    A++ LGG+   A S+ A+A + + PGK  A     Y 
Sbjct: 3   QDKE-PRRRFLRQVLAIVP----AASTLGGATTVAVSQAAMADS-SEPGKPRA-----YT 51

Query: 64  PGYFTAEEWAFIKAAVERLIPADEMGPGALEAGVPEYIDRQMNTPYAAGALWYMQGPFKA 123
           P YFTA EWAF+ AAV+ LIP+D+ G GALE GVPE+IDRQM TPY AG LWYMQGPF  
Sbjct: 52  PTYFTAAEWAFLNAAVDHLIPSDQYGAGALETGVPEFIDRQMETPYGAGKLWYMQGPFHP 111

Query: 124 DAAPEMGWQSKLVPKDIYRLGIAATDAWCKELKGQTFAAQDSATRDDLLKQLEAGTPQFD 183
           D+ PE+G+Q  LVP+DIYR GIAA + WC +  G+ FA  D A + ++LK ++ G   F+
Sbjct: 112 DSVPELGYQLSLVPRDIYRQGIAACNDWCSKNHGKVFAELDKAKQLEVLKMMDGGKISFE 171

Query: 184 AVPAKLFFNLLLQNTKEGFFSDPIHGGNKGLVGWTLIGFPGARADFMDWVER-NEQYPFP 242
            VPAK FFN +L NTKEG+F+DP++GGN+ + GW ++GFPGARADF DWV++ N +YP+ 
Sbjct: 172 TVPAKTFFNFMLGNTKEGYFADPMYGGNQKMGGWKMVGFPGARADFADWVDQYNVKYPYG 231

Query: 243 AVSIRGER 250
            VSI GE+
Sbjct: 232 PVSILGEK 239


Lambda     K      H
   0.317    0.135    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: 262
Number of extensions: 14
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: 251
Length of database: 240
Length adjustment: 24
Effective length of query: 227
Effective length of database: 216
Effective search space:    49032
Effective search space used:    49032
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: 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