GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroL in Acidovorax sp. GW101-3H11

Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate Ac3H11_3086 Regulatory protein of benzoate catabolism

Query= curated2:Q2W095
         (195 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3086
          Length = 311

 Score = 96.3 bits (238), Expect = 5e-25
 Identities = 63/182 (34%), Positives = 99/182 (54%), Gaps = 9/182 (4%)

Query: 12  LAPLLSG------RIGRTIVLVGLMGAGKSCVGRRLAARLGLDFVDSDAEFEAASGSSIS 65
           L  LLSG      R GR I LVGL GAGKS +G  LA  L + F++   E E+ +G S+ 
Sbjct: 123 LHELLSGGSNDTARHGR-IALVGLRGAGKSTLGPLLARALDVPFIELSREIESLAGCSVR 181

Query: 66  DYFARFGEAAFREGERKVIARLLD-GPPVVLATGGGAFVDPTTRERIKAAGTSVWIRADL 124
           +    +G  A+R  ER+ +   +     VV+AT GG   DP T   + A  T+VW+RA  
Sbjct: 182 EIHDLYGTTAYRRYERRALEETIQIHSEVVIATPGGIVSDPATFNELLAHCTTVWLRAAP 241

Query: 125 ELLLKRTVGR-DHRPLLKQGDPREILGRLMEARYPIYAEADIIVESTDEVPEATVIRVME 183
           E  + R V + D RP+    +  + L R+++ R   Y++ADI ++++ + PE ++  +  
Sbjct: 242 EEHMGRVVAQGDMRPMAASKEAMDDLKRILDGRAAFYSKADITIDTSGQTPEQSLAALHA 301

Query: 184 GL 185
           G+
Sbjct: 302 GV 303


Lambda     K      H
   0.321    0.140    0.395 

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: 144
Number of extensions: 7
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: 195
Length of database: 311
Length adjustment: 24
Effective length of query: 171
Effective length of database: 287
Effective search space:    49077
Effective search space used:    49077
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 Aug 03 2021. The underlying query database was built on Aug 03 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