GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Sinorhizobium meliloti 1021

Align L-asparaginase (EC 3.5.1.1) (characterized)
to candidate SMc00035 SMc00035 hypothetical protein

Query= reanno::Phaeo:GFF3567
         (333 letters)



>FitnessBrowser__Smeli:SMc00035
          Length = 336

 Score =  227 bits (578), Expect = 4e-64
 Identities = 135/333 (40%), Positives = 180/333 (54%), Gaps = 5/333 (1%)

Query: 2   MTNPVPMTEVWRGPLLESLHLGHAVVCNAKGEIVRSWGDPDAVIYPRSSAKMIQALPLIT 61
           M+NPV + EV RG L+ES H G  V  +  G+ + S G+ DA I+PRS+ K +QALPLI 
Sbjct: 1   MSNPV-LVEVTRGNLVESRHRGMIVAVDGDGKTLFSLGETDAHIFPRSACKAMQALPLIE 59

Query: 62  SGAAAKYGLTSEQLALACASHNGAEIHTSRVNAWLDQLSMTDHDFRCGPQLPDDIPARNA 121
           SGAA   G    +LALAC+SH+G   H +     L           CG     D     A
Sbjct: 60  SGAADANGFGDRELALACSSHSGEPEHVALAAKMLSAAGRDVQALECGAHWSSDQKTLIA 119

Query: 122 LIKTDTSPCQVHNNCSGKHAGFLTLSQHLGAGPE-YVEIDHPVQQACRSAFEQVTEEV-- 178
             ++  +P  +HNNCSGKHAGF+    H G   + Y+  DHP+QQ  R    ++T  V  
Sbjct: 120 QARSLEAPSALHNNCSGKHAGFVCACCHSGTEVKGYIGYDHPIQQEIRGVMAELTGAVLD 179

Query: 179 SPGYGIDGCSAPNFATSVKGLARAMAWFAAASDRSDRDADAAQELVSAMMAHPELVAGET 238
               G+DGCS P +A S++GLA   A  A+        A A++ L+ A MA P  VAG  
Sbjct: 180 RDNCGVDGCSIPTYALSMRGLAHGFARMASGVGLGAERARASKRLIEACMAEPFFVAGTK 239

Query: 239 RACTNLMRAMGGTVAIKTGAEAVFIAILPEQKLGVALKITDGATRASECAIASILVGLGV 298
           RACT LM+   G +  KTGAE VF A +PE+ +G+ALK  DG TRA+E  +A+ L     
Sbjct: 240 RACTRLMKTAPGRIFAKTGAEGVFCAAIPEKGIGIALKCEDGTTRAAEAMVAATLARFFS 299

Query: 299 LDAD-HPATLKYRNAPLINRRGIDCGSIRPSAE 330
            DA+ H A +   N  + N  GI  G +R   E
Sbjct: 300 DDAEIHEALMAQANHAMRNWNGIHVGDVRVVTE 332


Lambda     K      H
   0.318    0.131    0.398 

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: 350
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: 333
Length of database: 336
Length adjustment: 28
Effective length of query: 305
Effective length of database: 308
Effective search space:    93940
Effective search space used:    93940
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 (21.8 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