GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Pseudomonas fluorescens GW456-L13

Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate PfGW456L13_3607 Amino acid ABC transporter, permease protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_772
         (248 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3607
          Length = 281

 Score =  109 bits (273), Expect = 5e-29
 Identities = 66/220 (30%), Positives = 112/220 (50%), Gaps = 13/220 (5%)

Query: 16  VGSEIYFDWYLSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNV 75
           VG  +  D +L G   T+ +   +  ++LLLG +  + R   + +  G+A+ Y   FR  
Sbjct: 65  VGLHLGPDGFLQGAALTLFLCFCSIWLSLLLGFVTALARLSRSAVAFGVASFYASFFRGT 124

Query: 76  PLLVQLFIWYFLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQ 135
           PLL+Q+ + Y  +P L                  A  + ++ L L   A + E  R GI 
Sbjct: 125 PLLIQILLIYLGLPQL-------------GVVPGAISAGIIALSLNYGAYLSEIFRAGIM 171

Query: 136 ALPRGQEAAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELL 195
           A+  GQ  AA A+G      + +++LPQA R IIPP TS+F+++ K+SS+ S++G+ E++
Sbjct: 172 AVAPGQREAAMALGLGPVATFLHIVLPQAMRTIIPPTTSQFISMLKDSSLISVMGVWEVM 231

Query: 196 AQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRSVEK 235
              +     S    E  T A +IY+ L++ L L+   +E+
Sbjct: 232 FLAQSYGRSSYRYIEMLTTAAVIYWLLSIGLELIQNRLER 271


Lambda     K      H
   0.326    0.140    0.433 

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: 179
Number of extensions: 12
Number of successful extensions: 2
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: 248
Length of database: 281
Length adjustment: 25
Effective length of query: 223
Effective length of database: 256
Effective search space:    57088
Effective search space used:    57088
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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