GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02871 in Dinoroseobacter shibae DFL-12

Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized)
to candidate 3607127 Dshi_0549 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= reanno::Smeli:SMc02871
         (279 letters)



>FitnessBrowser__Dino:3607127
          Length = 272

 Score =  129 bits (323), Expect = 9e-35
 Identities = 83/265 (31%), Positives = 136/265 (51%), Gaps = 5/265 (1%)

Query: 16  AALIAYTLIALFPVFLTIVNSFKSRNAIFREPLAVPTPETFSLIGYETVLKQGDFIGYFQ 75
           A L+    + +FP +  +  S K++      P       T S   Y   L +   +    
Sbjct: 12  ALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLS--NYREALFEDGVLRTLI 69

Query: 76  NSIIVTVVSIALVLLFGAMAAFALSEYRFRGNTLMGLYLALGIMI-PIRLGTVAILQGMV 134
           NS+I+ + +  L L+ G  AAFAL+ + FRG   +  +     MI PI L     L    
Sbjct: 70  NSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIAR- 128

Query: 135 ATGLVNTLTALILVYTAQGLPLAVFILSEFMRTVSDDLKNAGRIDGLSEYAIFLRLVLPL 194
             GL++    LIL+Y    LP+ ++I+++  R +  DL  A R++G S++ I  ++ LPL
Sbjct: 129 NLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPL 188

Query: 195 IRPAMATVAVFTMIPIWNDLWFPLILAPAEATKTVTLGSQIFIGQFVTNWNAVLSALSLA 254
             P +A  A+F+ I  WN+L F LIL  +EA KT    +  F+  +   +  +++  +L 
Sbjct: 189 AMPGVAVSAIFSFIFSWNELMFGLILTRSEA-KTAPAMAVSFMEGYNLPYGKIMATSTLI 247

Query: 255 IFPVLVLYVIFSRQLIRGITAGAVK 279
           + PVL+  +I S+QL+RG+T GAVK
Sbjct: 248 VIPVLIFALIASKQLVRGLTMGAVK 272


Lambda     K      H
   0.330    0.142    0.409 

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: 231
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: 279
Length of database: 272
Length adjustment: 25
Effective length of query: 254
Effective length of database: 247
Effective search space:    62738
Effective search space used:    62738
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