GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Echinicola vietnamensis KMM 6221, DSM 17526

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate Echvi_0343 Echvi_0343 Enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::D3RXI0
         (252 letters)



>FitnessBrowser__Cola:Echvi_0343
          Length = 258

 Score =  106 bits (265), Expect = 4e-28
 Identities = 75/259 (28%), Positives = 129/259 (49%), Gaps = 20/259 (7%)

Query: 6   IKVEKDERVARIKIANPPV-NVLDMETMKEIISAIDEVEGVD---VIVFSGEGKSFSAGA 61
           +K E+  R+  + ++ P   N L+   +  + +A+D  E ++   V++   EGK F +GA
Sbjct: 5   VKFEQKGRIGYVILSRPEKRNALNAAMVSGLQAALDRCEAIETVKVVIIKAEGKVFCSGA 64

Query: 62  EIKE-------HFPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFV 114
           ++++        F +   +      +L  ++     + +A V+G AL GG  L   CDF 
Sbjct: 65  DLQDIERMQDNTFDENLADS-EGLKKLFLRLYTFPKVVIAQVQGHALAGGCGLVSVCDFA 123

Query: 115 LASKNAKLGVPEITLAHYPPVAIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVF 174
            A   AKLG  E+ +   P + +  L R +G   A EL+LTGE + A  A EIGL+ +VF
Sbjct: 124 YAVPTAKLGYTEVRIGFVPAMVLVFLVRKLGEGKAKELLLTGELLVAPAAKEIGLIQEVF 183

Query: 175 EDENFEESVNDFVNSLL-EKSSVALRLTKKALLFSTE---KEYLSLFDVINDVYLSQLVK 230
           E    + +V +    L+ + S  ++ LTKK +    +   +E L     +N    ++  +
Sbjct: 184 EPAALDGAVQEIAERLISQNSGESMALTKKMIAAVQDLPLEEALEYAARMN----AKARE 239

Query: 231 SEDAVEGLKAFLEKRKPEW 249
           +ED   G+ AFL K+K EW
Sbjct: 240 TEDCKRGIAAFLGKKKIEW 258


Lambda     K      H
   0.318    0.136    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: 143
Number of extensions: 6
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: 252
Length of database: 258
Length adjustment: 24
Effective length of query: 228
Effective length of database: 234
Effective search space:    53352
Effective search space used:    53352
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: 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