GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Pseudomonas fluorescens FW300-N2E2

Align Glucose/galactose porter (characterized)
to candidate Pf6N2E2_1003 Fucose permease

Query= TCDB::P0C105
         (412 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1003
          Length = 460

 Score =  269 bits (687), Expect = 1e-76
 Identities = 151/399 (37%), Positives = 227/399 (56%), Gaps = 8/399 (2%)

Query: 12  HTETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAY 71
           H + SS +    A   +T LFFMWG    L D+L  H ++   ++  QS L+Q  +FGAY
Sbjct: 55  HEKLSSTR---LAFIFVTSLFFMWGLSHGLLDVLNKHFQDTLHISRGQSGLVQTAYFGAY 111

Query: 72  FIVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTIL 131
           FI++LP G  ++R  YK GI+ GL + AIG  LFIPA+    +  FL ALFVLA G+  L
Sbjct: 112 FIIALPVGLFMERFGYKAGILAGLALFAIGALLFIPASMVGTFMPFLVALFVLACGLGCL 171

Query: 132 QVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSAATDATVNAEADAVR 191
           + AAN Y   LG P  +  RLT  Q+FN LG  + PV G  +  +   +   N   D V 
Sbjct: 172 ETAANLYAAALGDPAKSEQRLTFAQSFNGLGAFIGPVIGGAVFFAPPIEFNGN-RVDLVS 230

Query: 192 FPYLLLALAFTVLAIIFAILKPPDVQEDEPA---LSDKKEGSAWQYRHLVLGAIGIFVYV 248
             Y  LA+   ++ + FA ++ P+++ ++ +   L    E S W+  +     +  F  V
Sbjct: 231 VTYAALAIIVMLMFVAFARIQLPEIRNEKSSDVLLPSAGEVSLWKKSNFTGALVAQFCNV 290

Query: 249 GAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYIDDGKALAF 308
           GA V +G+F +N+  D    G+S   A++ ++      MVGRF G+  MRY+     L  
Sbjct: 291 GAYVGIGAFFINYAIDHW-QGISAQKASYLLSLGMLAYMVGRFAGTWVMRYVPARSLLIL 349

Query: 309 NAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCLA 368
           N+ V+++L  + +A    I++++V AI LF S+M+PTIF++ + GLG+ T +    L + 
Sbjct: 350 NSLVSMVLCIVAIAGFERISIFAVAAIYLFMSVMYPTIFAMGIRGLGTQTKKAGSCLVMT 409

Query: 369 IVGGAIVPLIQGALADAIGIHLAFLMPIICYAYIAFYGL 407
           +VGGA VPL+ GALAD  GI  AF +P+ C+A IA+YGL
Sbjct: 410 LVGGAFVPLLMGALADHFGIAAAFYVPLACFAAIAWYGL 448


Lambda     K      H
   0.328    0.141    0.420 

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: 554
Number of extensions: 30
Number of successful extensions: 4
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: 412
Length of database: 460
Length adjustment: 32
Effective length of query: 380
Effective length of database: 428
Effective search space:   162640
Effective search space used:   162640
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: 51 (24.3 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