GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proP in Pseudomonas fluorescens FW300-N2E2

Align proline porter II (characterized)
to candidate Pf6N2E2_388 Transporter, MFS superfamily

Query= CharProtDB::CH_024324
         (500 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_388 Transporter, MFS
           superfamily
          Length = 447

 Score =  242 bits (618), Expect = 2e-68
 Identities = 138/430 (32%), Positives = 234/430 (54%), Gaps = 12/430 (2%)

Query: 18  IDDGKLR--KAITAASL-GNAMEWFDFGVYGFVAYAL-GKVFFPGADPSVQMVAALATFS 73
           +DD K +  K + A SL G A+E +D  +YG  A  +   +FFPG D +V  +A+LA+F+
Sbjct: 16  VDDEKKKSMKNVVAGSLFGTALETYDLYLYGTAAALIFAPLFFPGTDEAVSRLASLASFA 75

Query: 74  VPFLIRPLGGLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLIC 133
           + F+ RPLG L  G  GD+ GR+K+L +T++IM +ST  IGL+P+Y ++GIWAPI+L + 
Sbjct: 76  ISFVARPLGSLVLGHFGDRIGRKKLLYLTLIIMGLSTVGIGLLPTYASVGIWAPIMLCVL 135

Query: 134 KMAQGFSVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEA 193
           +  QGF+  GEY+GA + + E++P RKRGF  +  + G + GF+  AG+++++S+++   
Sbjct: 136 RFIQGFAFAGEYSGAVLMLLEHAPRRKRGFYAAINNIGPVFGFIASAGLLLIVSSLLSVE 195

Query: 194 NFLDWGWRIPFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVS-FKE 252
           +F  WGWRIPF  +L L ++G+++R  + E+P F++  +K        +  GP +S    
Sbjct: 196 DFYKWGWRIPFIASLALLVVGVFVRSKVAESPVFEKTAEK------RAVAKGPDLSPAMR 249

Query: 253 IATKYWRSLLTCIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQ 312
           + TKY + LL   G  I    T+Y+   +  SY    L  S    + + +  +   L + 
Sbjct: 250 LFTKYPKQLLLVAGANICHFSTFYLFTVFALSYGQKELGLSNAFVLAVAMVAICTHLVIV 309

Query: 313 PVMGLLSDRFGRRPFVLLGSVALFVLAIPAFILINSNVIGLIFAGLLMLAVILNCFTGVM 372
           P  G ++DR GRR  +L+G     + A P + L ++     +  G  +         G +
Sbjct: 310 PFAGAMADRLGRRTMMLIGFAVTALAAFPFWHLFSTGQFLPMVLGSCLFMAGYGLVYGAV 369

Query: 373 ASTLPAMFPTHIRYSALAAAFNISVLVAGLT-PTLAAWLVESSQNLMMPAYYLMVVAVVG 431
            S     F    R++  A A N+  ++ G T P + A+L+    +    + Y +V+A + 
Sbjct: 370 PSFTGEAFGPSARFTGFAMATNVGGIIGGGTAPIVGAYLLSHYGSPYAISVYTVVLAAIS 429

Query: 432 LITGVTMKET 441
            +      ET
Sbjct: 430 ALCVYLSAET 439



 Score = 25.4 bits (54), Expect = 0.004
 Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 5/95 (5%)

Query: 32  LGNAMEWFDFG-VYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGGLFFGMLG 90
           LG+ +    +G VYG V    G+ F P A  +   +A      +     P+ G +   L 
Sbjct: 353 LGSCLFMAGYGLVYGAVPSFTGEAFGPSARFTGFAMATNVGGIIGGGTAPIVGAY---LL 409

Query: 91  DKYGRQKILAI-TIVIMSISTFCIGLIPSYDTIGI 124
             YG    +++ T+V+ +IS  C+ L     TI I
Sbjct: 410 SHYGSPYAISVYTVVLAAISALCVYLSAETRTINI 444


Lambda     K      H
   0.327    0.142    0.429 

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: 601
Number of extensions: 31
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 500
Length of database: 447
Length adjustment: 33
Effective length of query: 467
Effective length of database: 414
Effective search space:   193338
Effective search space used:   193338
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 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, 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