GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0548 in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate AO356_27675 AO356_27675 sugar ABC transporter permease

Query= reanno::Dino:3607126
         (288 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27675
          Length = 311

 Score =  121 bits (303), Expect = 2e-32
 Identities = 84/279 (30%), Positives = 138/279 (49%), Gaps = 7/279 (2%)

Query: 14  IGPAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMGRTF 73
           + P+V  L L  I PL   ++ S+  YNL      EF+GLEN+   LTD  F      T 
Sbjct: 32  VSPSVALLLLWMIVPLGMTVYFSMIRYNLLYPGENEFVGLENFTYFLTDSGFMPGATNTL 91

Query: 74  FLLGTALPLQIALGLGIALVLHQPGLTLVKTLARLSLVLPMATTYAVVGLLGQ-VMFNQK 132
            L+G+ L + I LG+ I+ +L        + + R+ L+ P      V  L+ + ++F+  
Sbjct: 92  LLVGSVLLISIVLGVLISALLEASEF-FGRGIVRVLLISPFFIMPTVGALIWKNLIFHPV 150

Query: 133 FGV---VNQLLGGADINWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEVEEAA 189
            G+   V +L G   ++W+         II    WQW PF  L+L+  +  +  E +EAA
Sbjct: 151 SGILASVWKLFGAQPVDWLA--HYPLLSIIIIVSWQWLPFAILILMTAMQSLDQEQKEAA 208

Query: 190 RLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFISLMI 249
           RL+      +  ++ LP L   +  VL++ T   L +F  +FT T GGPG ++  ++ +I
Sbjct: 209 RLDGAGPIAIFWHLTLPHLARPIAVVLMIETIFLLSVFAEIFTTTNGGPGYASTNLAYLI 268

Query: 250 QRVGFRGFDQGLASAQAIILLIITIVLAQIYIRVFYKEV 288
                  FD G+ASA  +I ++I  + A I +R+  K +
Sbjct: 269 YNQALVQFDVGMASAGGLIAVVIANIAAIILVRMIGKNL 307


Lambda     K      H
   0.329    0.144    0.440 

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: 271
Number of extensions: 14
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: 288
Length of database: 311
Length adjustment: 27
Effective length of query: 261
Effective length of database: 284
Effective search space:    74124
Effective search space used:    74124
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: 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