GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruG in Paraburkholderia bryophila 376MFSha3.1

Align Fructose import permease protein FruG (characterized)
to candidate H281DRAFT_00427 H281DRAFT_00427 monosaccharide ABC transporter membrane protein, CUT2 family

Query= SwissProt::Q8G845
         (340 letters)



>FitnessBrowser__Burk376:H281DRAFT_00427
          Length = 341

 Score =  159 bits (402), Expect = 1e-43
 Identities = 98/306 (32%), Positives = 167/306 (54%), Gaps = 11/306 (3%)

Query: 26  LAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGAI 85
           L A    IL+++        ++++  I  +    A   +LA+A T  I+TGGIDLSVG +
Sbjct: 32  LLAFASLILLLVFFSFASPAFMQMDNILGILQATAVNGVLAIASTFVIITGGIDLSVGTL 91

Query: 86  VAITAVV-GLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLAR 144
           +  TAV+ G+ L    +P +L +I  +  GA+ G ++GTL  +  + PFIATL  M L +
Sbjct: 92  MTFTAVICGVFLTYWHLPMWLGVIAAIGTGAICGTISGTLTAKMKIPPFIATLGMMLLLK 151

Query: 145 GLASIISTDS-LTFPQGNDFSFISN---VIKIIDNPKISNDLSFNVGVIIALVVVVFGYV 200
           GL+ ++S D  + F    +F  IS    +  ++ +  I N       V+I   + +   V
Sbjct: 152 GLSLVVSADKPIYFTDTENFYMISQDSLIGYLVPSLPIPN------AVLILFFLAIVSSV 205

Query: 201 FLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAKNT 260
            L+ T  GR  +A+G +  +  L G+ V R +  IY     +  +A ++  + + SA+  
Sbjct: 206 TLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAIYGLGGAICGIAGLLIASRLNSAQPA 265

Query: 261 VGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIVIGL 320
           +G G+EL+A+A+VVIGGT ++GG G +LG+++G+ + S+L        V  EW  +V GL
Sbjct: 266 LGQGYELEAIAAVVIGGTSLSGGSGTILGTIIGAFIMSVLTNGLRIMSVAQEWQIVVTGL 325

Query: 321 MILVFV 326
           +I++ V
Sbjct: 326 IIILAV 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: 242
Number of extensions: 11
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: 340
Length of database: 341
Length adjustment: 28
Effective length of query: 312
Effective length of database: 313
Effective search space:    97656
Effective search space used:    97656
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