GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_01112 in Pseudomonas simiae WCS417

Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease

Query= reanno::Burk376:H281DRAFT_01112
         (364 letters)



>lcl|FitnessBrowser__WCS417:GFF2365 PS417_12060 sugar ABC
           transporter permease
          Length = 325

 Score =  147 bits (372), Expect = 3e-40
 Identities = 102/334 (30%), Positives = 171/334 (51%), Gaps = 20/334 (5%)

Query: 34  APSVEAPGLRTRLARNPEWFTVALIVVTCLIVGAINPRFFQ-FATLFDLLHSATTMSLFA 92
           AP   AP  R RL  + + F + L+ +   +V A +  +F  +    D+L   +   + A
Sbjct: 8   APVTAAP--RNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILA 65

Query: 93  LGTLVVLASGGIDVSFTAIAALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGL 152
           +G   V+ + GID+S  +I A    G+  A+ A       A +   G   G +LG+VNG 
Sbjct: 66  VGMTYVILTKGIDLSVGSILAFA--GLCSAMVATQGYGLLAAVSA-GMFAGAMLGVVNGF 122

Query: 153 LVHRLKAPSLIVTIGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAV 212
           +V  L  P  + T+G   + RG+       +   ++P +            + A G+  +
Sbjct: 123 MVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDA------------YLALGIGKI 170

Query: 213 LPVSVLALVAA--AVVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGM 270
            P+ V  ++ A  A++ W +L  T  GR VYA+GG+   A   G  +R +   V+  +G+
Sbjct: 171 GPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGL 230

Query: 271 LAGIAGILHVSNNRLANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIK 330
           LAG+AG++  +    A P   V  ELD IAAV++GG  ++GGTG++VGTL G +L+ +I 
Sbjct: 231 LAGLAGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVIN 290

Query: 331 SVLILVGVPSTWQKVIIGAFILLAGTLFALQRKR 364
           + L L+GV S +Q+V  G  I+ A  +   ++K+
Sbjct: 291 NGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRKKK 324


Lambda     K      H
   0.328    0.141    0.426 

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: 268
Number of extensions: 8
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: 364
Length of database: 325
Length adjustment: 29
Effective length of query: 335
Effective length of database: 296
Effective search space:    99160
Effective search space used:    99160
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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