GapMind for catabolism of small carbon sources

 

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

Align BadK (characterized)
to candidate Pf6N2E2_1834 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= metacyc::MONOMER-943
         (258 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1834
          Length = 256

 Score =  175 bits (444), Expect = 7e-49
 Identities = 98/254 (38%), Positives = 145/254 (57%), Gaps = 1/254 (0%)

Query: 3   SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFA 62
           S P++ E  G V I+ LNR +  NAL+ ++  A+  A+   + D G+  IVI G    FA
Sbjct: 2   SAPVVVERNGAVAILRLNRVEKRNALDLSMRVAIASAMQELERDSGVAVIVITGGDSVFA 61

Query: 63  AGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIA 122
           AGAD+  +       V   + + + W  + + +KP++AAV+G A G GCELA+ CDI++A
Sbjct: 62  AGADLNLLVDKGAQQVAELD-LGQYWAPVAKSQKPLIAAVSGFALGAGCELAMMCDILVA 120

Query: 123 GRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVD 182
             SA+F  PE ++G++PGAGGTQRL RA+GK  A  M L+   L+AE A + GLVS +V 
Sbjct: 121 DNSARFGQPEARVGIMPGAGGTQRLLRAVGKPVASLMLLAGELLSAERASQLGLVSELVT 180

Query: 183 DDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADARE 242
           +       + LA   A     AL A+K  L    + +L   +  E RE    F + D  E
Sbjct: 181 EGSALARAIVLAQATATMPPKALRAIKRVLALGADQSLDLALALENREFLLLFDTQDKTE 240

Query: 243 GIQAFLEKRAPCFS 256
           G++AFL+KR P ++
Sbjct: 241 GMRAFLDKRPPRYT 254


Lambda     K      H
   0.321    0.135    0.389 

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: 117
Number of extensions: 7
Number of successful extensions: 2
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: 258
Length of database: 256
Length adjustment: 24
Effective length of query: 234
Effective length of database: 232
Effective search space:    54288
Effective search space used:    54288
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 (21.9 bits)
S2: 47 (22.7 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