GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Pseudomonas simiae WCS417

Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized)
to candidate GFF1094 PS417_05550 amino acid ABC transporter permease

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4771
         (248 letters)



>FitnessBrowser__WCS417:GFF1094
          Length = 223

 Score =  123 bits (308), Expect = 4e-33
 Identities = 68/212 (32%), Positives = 119/212 (56%), Gaps = 6/212 (2%)

Query: 28  GLAWTIGIAIAAWIIALTLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYFL 87
           G+  T+ + +   +  + LG++L +MR   ++++S +A  YV  FR++PLL+ +  +Y  
Sbjct: 18  GMVMTLQLMVMGVVGGIALGTVLALMRLSSSKLLSRVAGAYVNYFRSIPLLLVITWFYLA 77

Query: 88  VPDLLPADLQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQALPKGQESAARA 147
           VP +L      W   +  P   AF S VV   +F  A  CE VR G+Q++PKGQ +AA+A
Sbjct: 78  VPFVL-----RWITGEDTPI-GAFTSCVVAFMMFEAAYFCEIVRAGVQSIPKGQMAAAQA 131

Query: 148 MGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNTSVASLIGLMELLAQTKQTAEFSAN 207
           MG    Q    ++LPQA+R + P L  + + +F++TS+   +GL++ L   +   +    
Sbjct: 132 MGMTYGQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNSARSNGDIIGR 191

Query: 208 LFEAFTLATLIYFTLNMSLMLLMRVVEKKVAV 239
             E    A ++YF ++ S  LL++ ++K+ AV
Sbjct: 192 SNEFLIFAGVVYFIISFSASLLVKRLQKRFAV 223


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: 137
Number of extensions: 4
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: 223
Length adjustment: 23
Effective length of query: 225
Effective length of database: 200
Effective search space:    45000
Effective search space used:    45000
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: 46 (22.3 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