GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Pseudomonas putida KT2440

Align BadH (characterized)
to candidate PP_1852 PP_1852 putative enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific)

Query= metacyc::MONOMER-893
         (255 letters)



>FitnessBrowser__Putida:PP_1852
          Length = 249

 Score =  148 bits (373), Expect = 1e-40
 Identities = 93/249 (37%), Positives = 141/249 (56%), Gaps = 11/249 (4%)

Query: 4   LQNKTAVITGGGGGIGGATCRRFAQEGAKIA-VFDLNLDAAEKVAGAIRDAGGTAEAVRC 62
           L+ K A++ GG  GIG A  RR A+EGA++A  +  +   AE++A  I + GG A A+R 
Sbjct: 7   LEGKVALVQGGSRGIGAAIVRRLAREGAQVAFTYVSSAGPAEELAREITENGGKALALRA 66

Query: 63  DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMH 122
           D AD  +V  A+  T   LG +DILVNNAG     P T+ +  +++ ++A+N+       
Sbjct: 67  DSADAAAVQLAVDDTEKALGRLDILVNNAGVLAVAPVTEFDLADFDHMLAVNVRSVFVAS 126

Query: 123 HAVLPGMVERRHGRIVNIAS-DAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVN 181
            A    M   + GRI+NI S +A R+  +G A YA  K  LV  ++ +AR+    GITVN
Sbjct: 127 QAAARYM--GQGGRIINIGSTNAERMPFAGGAPYAMSKSALVGLTRGMARDLGPQGITVN 184

Query: 182 VVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFIT 241
            V PGP DT +  +  SG     +  E+    + +GR G+P+++A  +A+    +AG+IT
Sbjct: 185 NVQPGPVDTDM--NPASG-----EFAESLIPLMAIGRYGEPEEIASFVAYLAGPEAGYIT 237

Query: 242 GQVLSVSGG 250
           G  L+V GG
Sbjct: 238 GASLTVDGG 246


Lambda     K      H
   0.318    0.135    0.398 

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: 195
Number of extensions: 14
Number of successful extensions: 3
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: 255
Length of database: 249
Length adjustment: 24
Effective length of query: 231
Effective length of database: 225
Effective search space:    51975
Effective search space used:    51975
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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