GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Pseudomonas fluorescens FW300-N1B4

Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate Pf1N1B4_772 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)

Query= TCDB::Q52813
         (400 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_772
          Length = 248

 Score = 87.0 bits (214), Expect = 5e-22
 Identities = 48/129 (37%), Positives = 75/129 (58%)

Query: 269 FMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIP 328
           F+S+ + L  +T + + E VR GI+ +P+GQ  AA A+G     +   V++PQA RIIIP
Sbjct: 111 FLSVVVCLGLFTTARVCEQVRTGIQALPRGQEAAARAMGFKLPQIYWNVLLPQAYRIIIP 170

Query: 329 PLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSLFM 388
           PLTS++LN+ KNSS+A  IG  +L+A        S    E   +  ++Y +L++   L M
Sbjct: 171 PLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLM 230

Query: 389 NWFNAKMAL 397
                K+A+
Sbjct: 231 RSVEKKVAV 239



 Score = 53.9 bits (128), Expect = 5e-12
 Identities = 25/68 (36%), Positives = 42/68 (61%)

Query: 93  LVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFWY 152
           L G+  T+ +AV     A ++G ++G+ R   N +++ + T YVE+FRN+P L+ +F WY
Sbjct: 26  LSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWY 85

Query: 153 LGVLSVLP 160
             V  +LP
Sbjct: 86  FLVPDLLP 93


Lambda     K      H
   0.327    0.141    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: 293
Number of extensions: 18
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 400
Length of database: 248
Length adjustment: 27
Effective length of query: 373
Effective length of database: 221
Effective search space:    82433
Effective search space used:    82433
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: 48 (23.1 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