GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized)
to candidate AO353_12325 AO353_12325 ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_16285
         (248 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_12325
          Length = 319

 Score =  127 bits (319), Expect = 3e-34
 Identities = 68/211 (32%), Positives = 120/211 (56%), Gaps = 14/211 (6%)

Query: 28  GLGWTIAIAIVAWIIALMLGSVLGVMRTVPNRLVSGIATCYVELFRNVPLLVQLFIWYFL 87
           GL  T+ +++V+ ++ L++G   G+ R   N  +  ++T Y+EL R  PLLVQ+FI+YF 
Sbjct: 120 GLWTTLWLSLVSGVLGLLIGLATGLCRLSNNPTLRDLSTVYIELVRGTPLLVQIFIFYFF 179

Query: 88  VPDLLPQNLQDWYKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPRGQESAARA 147
           +  +L                S   + +  L LFT A V E +R+G+Q++ RGQ  AAR+
Sbjct: 180 IGTVL--------------NLSREFAGIAALSLFTGAYVAEIIRSGVQSIARGQNEAARS 225

Query: 148 MGFKLPQIYWNVLLPQAYRIVIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSAN 207
           +G    Q   +V+LPQA++ V+PPL  +F+++ K++S+ S+I + ELL   ++    S +
Sbjct: 226 LGLSAGQSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELLKSGREVITTSFS 285

Query: 208 LFEAFTLATLIYFTLNMSLMLLMRMVEKKVA 238
            FE       +Y  +N+ L  +   +E+++A
Sbjct: 286 PFEILFCVAGLYLLINLPLSKIASRLERRLA 316


Lambda     K      H
   0.326    0.139    0.432 

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: 198
Number of extensions: 5
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: 319
Length adjustment: 26
Effective length of query: 222
Effective length of database: 293
Effective search space:    65046
Effective search space used:    65046
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