GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_3326
          Length = 260

 Score =  106 bits (265), Expect = 4e-28
 Identities = 66/218 (30%), Positives = 111/218 (50%), Gaps = 13/218 (5%)

Query: 25  FITGLGWTIAIAIVAWIIALMLGSVLGVMRTVPNRLVSGIATCYVELFRNVPLLVQLFIW 84
           F  G   T+ + +++  + L+LG+   + RT    +V   A+ Y+ + R  PLLVQ+   
Sbjct: 52  FSDGARTTLWLTLISGSVGLVLGTGAALARTARWAVVRWAASFYIWVIRGTPLLVQILFV 111

Query: 85  YFLVPDLLPQ-NLQDWYKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPRGQES 143
           YF +P L+P  NL D            + + V+ LGL   A   E +R G+ A+PRGQ  
Sbjct: 112 YFALPVLVPGLNLPD------------FAAAVLALGLNVGAYNAEAIRAGLLAVPRGQTE 159

Query: 144 AARAMGFKLPQIYWNVLLPQAYRIVIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAE 203
           AA+A+G     ++++V+ PQA++I +PPL S F+ + K+SS+A  IG++EL     +   
Sbjct: 160 AAKALGLGRMHVFFDVVFPQAFKISLPPLVSNFVALLKDSSLAYAIGVVELTNVGNRIQS 219

Query: 204 FSANLFEAFTLATLIYFTLNMSLMLLMRMVEKKVAVPG 241
            +       +   + Y  L   +  +   VE +  V G
Sbjct: 220 ATFQPIATLSTVAITYLLLTTLVTQISNAVEYRFDVEG 257


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: 161
Number of extensions: 10
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: 260
Length adjustment: 24
Effective length of query: 224
Effective length of database: 236
Effective search space:    52864
Effective search space used:    52864
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