GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0548 in Marinobacter adhaerens HP15

Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate GFF2208 HP15_2162 sugar ABC transporter, permease protein

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



>FitnessBrowser__Marino:GFF2208
          Length = 288

 Score =  153 bits (386), Expect = 5e-42
 Identities = 84/235 (35%), Positives = 135/235 (57%), Gaps = 8/235 (3%)

Query: 50  FIGLENYWTVLTDEVFWQAMGRTFFLLGTALPLQIALGLGIALVLHQPGLTLVKTLARLS 109
           F+G E +  VLTDE    ++ R F   G  L +QI LG+G+AL++ + G+    +L  + 
Sbjct: 47  FVGTEWFKEVLTDERLQDSLIRQFIFSGAVLLIQIPLGIGVALMMPKSGIK--GSLCLIL 104

Query: 110 LVLPMATTYAVVGLLGQVMFNQKFGV----VNQLLGGADINWIGDPENAFAMIIFWDVWQ 165
           L +P+   + VVG + Q+      G+    +NQL  G D N+ GD  +A+  ++  DVW 
Sbjct: 105 LAIPLLIPWNVVGTIWQIFARGDIGLFGWGINQL--GIDYNYTGDTLDAWLTVLLMDVWH 162

Query: 166 WTPFVALVLLAGLTMVPGEVEEAARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLK 225
           WTP VAL+  +GL  +P    +AA ++  SKW V RY+QLP L   L+  ++LR  D+  
Sbjct: 163 WTPLVALLCYSGLRAIPEAFYQAAEIDRASKWAVFRYIQLPRLKSVLIIAVLLRFMDSFM 222

Query: 226 LFDMVFTLTRGGPGSSTEFISLMIQRVGFRGFDQGLASAQAIILLIITIVLAQIY 280
           ++   F LT GGPGSST F+S  +  +    FD G A+A ++I  +I ++++ ++
Sbjct: 223 IYIEPFVLTGGGPGSSTTFLSQTLTTMAIGQFDLGRAAAFSLIYFLIVLLISWLF 277


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: 15
Number of successful extensions: 3
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: 288
Length adjustment: 26
Effective length of query: 262
Effective length of database: 262
Effective search space:    68644
Effective search space used:    68644
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: 47 (22.7 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