GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruG in Burkholderia phytofirmans PsJN

Align Fructose import permease protein FruG (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease

Query= SwissProt::Q8G845
         (340 letters)



>FitnessBrowser__BFirm:BPHYT_RS16055
          Length = 335

 Score =  160 bits (404), Expect = 6e-44
 Identities = 101/307 (32%), Positives = 165/307 (53%), Gaps = 14/307 (4%)

Query: 24  PTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVG 83
           P +  +V+ I+M+    +    ++    I ++    +   I+AV MT  ILTGGIDLSVG
Sbjct: 39  PFIGLLVVCIVMVFASDS----FLSGANIENVLRQVSINAIIAVGMTCVILTGGIDLSVG 94

Query: 84  AIVAITAVVGLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLA 143
           +++A+   +   L  AG+ A   + I + +G  FG   G  +    M P I TL+TM +A
Sbjct: 95  SVMALAGTLAAGLMVAGMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVTLATMGIA 154

Query: 144 RGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFGYVFLH 203
           RGLA       L +  G     + + +    + KI   L     V+I  V+ V  +V L 
Sbjct: 155 RGLA-------LIYTGGYPIDGLPDWVSFFGSGKI---LGVQAPVVIMAVIYVIAWVLLE 204

Query: 204 HTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAKNTVGV 263
               GR +YAIGG+  +  L G+ V R + I+Y  +   +A A+IV TA + S +   GV
Sbjct: 205 RMPFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQPNAGV 264

Query: 264 GWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIVIGLMIL 323
           G+ELDA+A+VV+GGT I+GG G ++G+++G+L+  +L+   +  GV      ++ G +IL
Sbjct: 265 GFELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGGIIL 324

Query: 324 VFVVLQR 330
           + + + R
Sbjct: 325 LAIYISR 331


Lambda     K      H
   0.327    0.142    0.400 

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: 296
Number of extensions: 8
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: 340
Length of database: 335
Length adjustment: 28
Effective length of query: 312
Effective length of database: 307
Effective search space:    95784
Effective search space used:    95784
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 (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