GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Pseudomonas fluorescens GW456-L13

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate PfGW456L13_3607 Amino acid ABC transporter, permease protein

Query= TCDB::Q52665
         (434 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3607
          Length = 281

 Score = 81.6 bits (200), Expect = 3e-20
 Identities = 63/203 (31%), Positives = 101/203 (49%), Gaps = 9/203 (4%)

Query: 226 GFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASL- 284
           G  L L +   +I +SL LG + AL R S   +   ++     F RG PL+  +    L 
Sbjct: 77  GAALTLFLCFCSIWLSLLLGFVTALARLSRSAVAFGVASFYASFFRGTPLLIQILLIYLG 136

Query: 285 LLQYFLPPGTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQ 344
           L Q  + PG     I   +I ++L   AY++E+ R G+ A+  GQ EAA ALGL      
Sbjct: 137 LPQLGVVPGA----ISAGIIALSLNYGAYLSEIFRAGIMAVAPGQREAAMALGLGPVATF 192

Query: 345 RLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPY 404
             I++PQA++  IP   S FI + KD++L++ +G+++ +    +  RS       Y E  
Sbjct: 193 LHIVLPQAMRTIIPPTTSQFISMLKDSSLISVMGVWEVMFLAQSYGRSSY----RYIEML 248

Query: 405 IFVALIFFLFNFSMSRYSMYLER 427
              A+I++L +  +      LER
Sbjct: 249 TTAAVIYWLLSIGLELIQNRLER 271


Lambda     K      H
   0.329    0.143    0.457 

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: 352
Number of extensions: 12
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: 434
Length of database: 281
Length adjustment: 29
Effective length of query: 405
Effective length of database: 252
Effective search space:   102060
Effective search space used:   102060
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 (21.8 bits)
S2: 49 (23.5 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