GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gguB in Pseudomonas fluorescens FW300-N2C3

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate AO356_28515 AO356_28515 sugar ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28515 AO356_28515 sugar
           ABC transporter permease
          Length = 378

 Score =  265 bits (676), Expect = 2e-75
 Identities = 148/372 (39%), Positives = 225/372 (60%), Gaps = 10/372 (2%)

Query: 22  SNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHID 81
           S  +   ++IA+  I +FF + T G    P NL+NL+ Q S   I+A GM+LVI++G ID
Sbjct: 9   SRYKMLALVIAVALIWLFFSWQTEGGFVTPRNLSNLLRQMSITGILACGMVLVIISGEID 68

Query: 82  LSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGG-IIGAAQGYWIAYHRIPSFIVTL 140
           LSVGS++  +G +AAIL V + + P LA L  + + G +IG   GY  AY RIPSFIV L
Sbjct: 69  LSVGSLLGLLGGLAAILDVVYHV-PLLANLSLVALCGLVIGLGNGYMTAYLRIPSFIVGL 127

Query: 141 AGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFY 200
            GML FRG+ L V GG  I P   +   +  G+LP        +T    L +L+     +
Sbjct: 128 GGMLAFRGVLLGVTGGTTIAPVSPELVYVGQGYLP--------HTVGTGLGILLFALTLF 179

Query: 201 LAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALY 260
           L W++R     HG+        +++ ++I   +    Y L++Y G+P  ++++L+L+ ++
Sbjct: 180 LTWKQRRNRALHGLAAHSLVRDVLRVVVIGAVLAGFVYTLNSYDGIPVPVLLLLILLGVF 239

Query: 261 SFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSAT 320
           S+VT +T  GRRVY++G N +AT+LSGIN + +    F  MGV+  LAG++   RL + +
Sbjct: 240 SYVTSQTVFGRRVYSVGSNMEATRLSGINVQAVKLWIFGIMGVMCALAGVVNTARLAAGS 299

Query: 321 PKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVK 380
           P AG   ELD IAACFIGG S  GG G + GA++GA ++  ++NGMS++ +   +Q +VK
Sbjct: 300 PSAGNMGELDAIAACFIGGTSMRGGSGTVYGALLGALVITSLDNGMSMLDVDSYWQMIVK 359

Query: 381 GLVLLAAVFFDV 392
           G +L+ AV+ DV
Sbjct: 360 GSILVLAVWVDV 371


Lambda     K      H
   0.329    0.145    0.422 

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: 535
Number of extensions: 35
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: 398
Length of database: 378
Length adjustment: 30
Effective length of query: 368
Effective length of database: 348
Effective search space:   128064
Effective search space used:   128064
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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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