GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gatY in Pseudomonas fluorescens FW300-N2E2

Align D-tagatose-1,6-bisphosphate aldolase subunit KbaY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Ketose 1,6-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate Pf6N2E2_4660 Fructose-bisphosphate aldolase class II (EC 4.1.2.13)

Query= SwissProt::Q9KIP8
         (286 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4660
          Length = 354

 Score =  163 bits (412), Expect = 6e-45
 Identities = 109/330 (33%), Positives = 170/330 (51%), Gaps = 45/330 (13%)

Query: 1   MSIISTKYLLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGTFKHIALE 60
           M++IS + +L  A   GY VPAFN++N E ++AI+E   +  SPVI+  + G  K+    
Sbjct: 1   MALISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAP 60

Query: 61  EI-YALCSAYSTTYNMPLALHLDHHESLDDIRRKVHAGVRSAMIDGS-------HFPFAE 112
            + + + +A     ++P+ +H DH  S D  +R +  G  S M+DGS          +  
Sbjct: 61  FLRHLILAAIEEFPHIPVCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEY 120

Query: 113 NVKLVKSVVDFCHSQDCSVEAELGRLGGVEDDMSVDAE----------SAFLTDPQEAKR 162
           NV++ +  V   H+   SVE ELG LG +E  M+ + +          S  LTDP+EA  
Sbjct: 121 NVRVTQQTVAMAHACGVSVEGELGCLGSLETGMAGEEDGIGAEGVLDHSQMLTDPEEAAD 180

Query: 163 FVELTGVDSLAVAIGTAHGLY--SKTPKIDFQRLAEIRE----VVDVPLVLHGASDVPDE 216
           FV+ T VD+LA+AIGT+HG Y  +K P  D   +  I+E    + +  LV+HG+S VP E
Sbjct: 181 FVKKTQVDALAIAIGTSHGAYKFTKPPTGDVLAIDRIKEIHKRIPNTHLVMHGSSSVPQE 240

Query: 217 F----------VRRT-----------IELGVTKVNVATELKIAFAGAVKAWFAENPQGND 255
           +          ++ T           I+ GV KVN+ T+L++A  GA++   A NP   D
Sbjct: 241 WLAIINQYGGDIKETYGVPVEEIVEGIKYGVRKVNIDTDLRLASTGAMRRLMATNPSEFD 300

Query: 256 PRNYMRVGMDAMKEVVRNKINVCGSANRIS 285
           PR +    + AM++V   +    G+A   S
Sbjct: 301 PRKFFGATVTAMRDVCIARYEAFGTAGNAS 330


Lambda     K      H
   0.319    0.133    0.384 

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: 250
Number of extensions: 13
Number of successful extensions: 7
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: 286
Length of database: 354
Length adjustment: 27
Effective length of query: 259
Effective length of database: 327
Effective search space:    84693
Effective search space used:    84693
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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