GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_388
          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.

Links

Downloads

Related tools

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