GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Dechlorosoma suillum PS

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate Dsui_0502 Dsui_0502 enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__PS:Dsui_0502
          Length = 263

 Score =  152 bits (385), Expect = 5e-42
 Identities = 93/262 (35%), Positives = 141/262 (53%), Gaps = 8/262 (3%)

Query: 5   TIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAG 64
           T+ +  E  +  +TLNRP+ LNALN  ++E+L  A ++AE D  +  +++ G G+ F AG
Sbjct: 3   TVLSHLEDGVLTLTLNRPEALNALNLAMIEDLRAATARAEHDEAVGAVVLRG-GEHFMAG 61

Query: 65  ADITQFNQ---LTPAEAWKFSKKGREIMD----KIEALSKPTIAMINGYALGGGLELALA 117
            D+  F+    L PAE     ++    +     ++  + KP +A ++G A G GL L LA
Sbjct: 62  GDLKWFHSQLALPPAERQALFEQTIAAVHATTLQVRRMGKPVVASVSGAAAGFGLSLMLA 121

Query: 118 CDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGL 177
           CD+ +AA+ A   L   ++G+ P  G T  L R +G  RA E+ + GDR     A ++GL
Sbjct: 122 CDLAVAADNAYFTLAYCHIGLSPDGGATWFLPRAVGAKRAAEIALLGDRFDAAQAREWGL 181

Query: 178 VNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFS 237
           +NRVVP A LE E+ KLA ++A     +LA  K ++     + L   L  E   +     
Sbjct: 182 INRVVPAAELEAESAKLARRLAAGPRQALARTKALLQASSGNSLPEQLFAEQGNFAACSV 241

Query: 238 TEDKKEGVSAFLEKREPTFKGK 259
             D  EG+ AFLEKR+P F  K
Sbjct: 242 HPDFAEGLGAFLEKRKPAFGQK 263


Lambda     K      H
   0.315    0.135    0.382 

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: 111
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: 259
Length of database: 263
Length adjustment: 25
Effective length of query: 234
Effective length of database: 238
Effective search space:    55692
Effective search space used:    55692
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: 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