GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Phaeobacter inhibens BS107

Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized)
to candidate GFF400 PGA1_c04110 putative fatty acid oxidation complex subunit alpha

Query= SwissProt::P94549
         (258 letters)



>FitnessBrowser__Phaeo:GFF400
          Length = 697

 Score =  141 bits (356), Expect = 3e-38
 Identities = 77/165 (46%), Positives = 108/165 (65%), Gaps = 8/165 (4%)

Query: 12  VAVLTIHNPPANALSSRILEELSSCLDQCETDAGVRSIIIHGEGRFFSAGADIKEFTSLK 71
           +AVL   NPP NAL   +   L + +++ E + G R+++I+GEGR + AGADI+EF   K
Sbjct: 13  IAVLAAQNPPVNALGIDVRRGLLAGIERAEKE-GARAVLIYGEGRTYFAGADIREFG--K 69

Query: 72  GNEDSSLLAERGQQLMERIESFPKPIIAAIHGAALGGGLELAMACHIRIAAEDAKLGLPE 131
             E+  L       L  RIE+    +++A+HG ALGGGLE+A++ H RIA   AK+GLPE
Sbjct: 70  PMEEPGL-----PDLCNRIEAAKLIVVSALHGTALGGGLEVALSSHYRIAVPGAKMGLPE 124

Query: 132 LNLGIIPGFAGTQRLPRYVGTAKALELIGSGEPISGKEALDLGLV 176
           ++LGIIPG  GTQRLPR  GT  ALE+I +G  ++  EA D G++
Sbjct: 125 VHLGIIPGAGGTQRLPRVAGTEAALEMITTGRHVAAAEAFDKGVI 169


Lambda     K      H
   0.315    0.134    0.366 

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: 373
Number of extensions: 13
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: 258
Length of database: 697
Length adjustment: 32
Effective length of query: 226
Effective length of database: 665
Effective search space:   150290
Effective search space used:   150290
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: 42 (22.0 bits)
S2: 50 (23.9 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