GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas putida KT2440

Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate PP_3726 PP_3726 Enoyl-CoA hydratase/isomerase family protein

Query= SwissProt::Q0AVM1
         (260 letters)



>FitnessBrowser__Putida:PP_3726
          Length = 264

 Score =  151 bits (382), Expect = 1e-41
 Identities = 87/256 (33%), Positives = 146/256 (57%), Gaps = 4/256 (1%)

Query: 5   NIILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFVA 64
           +++ + E  +A + +NRP+  NAL+  TL ++   + +  DDPAV ++++TGSG +SF A
Sbjct: 7   SLLSKVEAGVAWITLNRPEQRNALDIPTLKQLHALLDSHADDPAVRVVVLTGSG-RSFCA 65

Query: 65  GADIAFMQNLSA---MEAREFGALGQKVFRLIEAMEKPVIAAVNGFALGGGCELAMCCDF 121
           GAD+A      A   +E+  +      +   + +++KP IAA+NG A+GGG +L++CCD 
Sbjct: 66  GADLAEWAAAEAAGTLESYGWTETAHALMLRLHSLDKPTIAAINGTAVGGGMDLSLCCDL 125

Query: 122 RIAASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLVNK 181
           RIAA++A+F      +G +P  G +  LPRL+G   AK+LL+  ++  AD A   GLV++
Sbjct: 126 RIAAASARFKAGYTSMGYSPDAGASWHLPRLIGSEQAKRLLFLDELWGADRALAAGLVSE 185

Query: 182 VVQPEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAFGLCFATQD 241
           V   E+L     ++AGR+ +    A   +K    +G +  +   +  E  A  LC  +QD
Sbjct: 186 VCADEQLPAVAAELAGRLANGPTFAYAQTKRLIRDGARRTLAEQLEAERHAGLLCGRSQD 245

Query: 242 QKEGMTAFLEKRKANF 257
             E + A +E+R   F
Sbjct: 246 GAEALQASVERRTPRF 261


Lambda     K      H
   0.319    0.136    0.378 

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: 142
Number of extensions: 3
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: 260
Length of database: 264
Length adjustment: 25
Effective length of query: 235
Effective length of database: 239
Effective search space:    56165
Effective search space used:    56165
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: 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