GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Sinorhizobium meliloti 1021

Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate SMa0060 SMa0060 gluconolactonase

Query= BRENDA::Q64374
         (299 letters)



>FitnessBrowser__Smeli:SMa0060
          Length = 311

 Score =  130 bits (327), Expect = 4e-35
 Identities = 83/278 (29%), Positives = 138/278 (49%), Gaps = 10/278 (3%)

Query: 17  GESPVWEEASQSLLFVDIPSKIICRWDTVSNQVQRVAVDAPVSSVALRQLGGYVATIGTK 76
           GES +W    ++L +VDI  K I R +  + +         V+S+ +R+ GG++  +   
Sbjct: 16  GESILWCGDEKALYWVDIVGKRIHRLEPENGRHDTWPTPDFVTSIGMRKDGGFIVGLSRN 75

Query: 77  FCALNWENQSVFV-LAMVDEDKKNNRFNDGKVDPAGRYFAGTMAEET----APAVLERHQ 131
            C   W     F   AM + D   NR N+G+V P G ++  TM        +P  ++R  
Sbjct: 76  VCL--WTPDGPFEEFAMPEPDLPENRLNEGRVAPDGSFWVATMQSNLDAGGSPKDMDRQS 133

Query: 132 GSLYSLFPDHSVKKYF-DQVDISNGLDWSLDHKIFYYIDSLSYTVDAFDYDLQTGQISNR 190
           G++Y + P   V +   ++  I+N + W+ D++ F++ D+L+  +  FD DL   +I NR
Sbjct: 134 GAVYRIDPTGHVSQLTPNEYGITNTMGWTRDNR-FFFADTLANEIYMFDCDLAARRIDNR 192

Query: 191 RIVYKMEKDEQIPDGMCIDAEGKLWVACYNGGRVIRLDPETGKRLQTVKLPVDKTTSCCF 250
           R +        +PDG C+DA+ +LW     GG  +      G+ +  ++LP    TSC F
Sbjct: 193 RTIVAGFA-RGLPDGSCLDADDRLWNCRVAGGAAVAGFDGAGRLMHLIELPASWPTSCTF 251

Query: 251 GGKDYSEMYVTCARDGLNAEGLLRQPDAGNIFKITGLG 288
           GG   S +YVT AR  +  + L   P  G +F + G+G
Sbjct: 252 GGPVLSTLYVTSARFTMTGDHLDMHPLEGGLFAVEGVG 289


Lambda     K      H
   0.319    0.137    0.419 

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: 271
Number of extensions: 21
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: 299
Length of database: 311
Length adjustment: 27
Effective length of query: 272
Effective length of database: 284
Effective search space:    77248
Effective search space used:    77248
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: 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