GapMind for catabolism of small carbon sources

 

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

Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate AO353_16280 AO353_16280 amino acid ABC transporter permease

Query= TCDB::Q88NY3
         (248 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_16280
          Length = 223

 Score =  128 bits (322), Expect = 8e-35
 Identities = 69/212 (32%), Positives = 123/212 (58%), Gaps = 6/212 (2%)

Query: 28  GLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLFIWYFL 87
           G+  T+ + +   +  ++LG+LL +MR   ++L+S IA AYV  FR++PLL+ +  +Y  
Sbjct: 18  GMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYFRSIPLLLVITWFYLA 77

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

Query: 148 MGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSAN 207
           +G    Q+   ++LPQA+R + P L  + + +F+++S+   +GL++ L  T+ + +    
Sbjct: 132 LGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNATRASGDIIGR 191

Query: 208 LFEAFTLATLIYFTLNMGLMLLMRMVEKKVAV 239
             E   +A L+YFT++     L++ ++K+ AV
Sbjct: 192 ANEFLIIAGLVYFTISFAASRLVKRLQKRFAV 223


Lambda     K      H
   0.325    0.139    0.425 

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: 142
Number of extensions: 6
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 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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