GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Dechlorosoma suillum PS

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Dsui_0502 Dsui_0502 enoyl-CoA hydratase/carnithine racemase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>FitnessBrowser__PS:Dsui_0502
          Length = 263

 Score =  140 bits (354), Expect = 2e-38
 Identities = 88/247 (35%), Positives = 131/247 (53%), Gaps = 9/247 (3%)

Query: 17  VTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGADIGMMSTYTYM 76
           +TLNRP+ALNALN A++++L AA    + D+A+GA+V+ G E  F AG D+    +   +
Sbjct: 15  LTLNRPEALNALNLAMIEDLRAATARAEHDEAVGAVVLRGGEH-FMAGGDLKWFHSQLAL 73

Query: 77  DVYKGDYITRNWET--------VRSIRKPIIAAVAGFALGGGCELAMMCDIIFAADTAKF 128
              +   +              VR + KP++A+V+G A G G  L + CD+  AAD A F
Sbjct: 74  PPAERQALFEQTIAAVHATTLQVRRMGKPVVASVSGAAAGFGLSLMLACDLAVAADNAYF 133

Query: 129 GQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAASLVD 188
                 +G+ P  G T  LPRAV   +A ++ L     DAA+A   GL++RV+PAA L  
Sbjct: 134 TLAYCHIGLSPDGGATWFLPRAVGAKRAAEIALLGDRFDAAQAREWGLINRVVPAAELEA 193

Query: 189 EAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGMAAFV 248
           E+   A  +A  P  A+   K  +  +   +L E +  E+  F +     D  EG+ AF+
Sbjct: 194 ESAKLARRLAAGPRQALARTKALLQASSGNSLPEQLFAEQGNFAACSVHPDFAEGLGAFL 253

Query: 249 EKRKPVF 255
           EKRKP F
Sbjct: 254 EKRKPAF 260


Lambda     K      H
   0.321    0.134    0.380 

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: 157
Number of extensions: 4
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: 263
Length adjustment: 25
Effective length of query: 233
Effective length of database: 238
Effective search space:    55454
Effective search space used:    55454
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