GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Escherichia coli BW25113

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate 15515 b1393 enoyl-CoA hydratase-isomerase (NCBI)

Query= BRENDA::D3RXI0
         (252 letters)



>FitnessBrowser__Keio:15515
          Length = 255

 Score =  118 bits (296), Expect = 1e-31
 Identities = 84/252 (33%), Positives = 134/252 (53%), Gaps = 9/252 (3%)

Query: 8   VEKDERVARIKIANPPV-----NVLDMETMKEIISAIDEVEGVDVIVFSGEGKSFSAGAE 62
           V + +RV  + +  P       N L M+ + E+ +A  +   + V V +G  + F+AGA+
Sbjct: 6   VSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTS-ISVCVITGNARFFAAGAD 64

Query: 63  IKEHFP-DKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAK 121
           + E    D A  +     QL  ++       +AAV G+ALG G ELA+ CD V+A +NA+
Sbjct: 65  LNEMAEKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENAR 124

Query: 122 LGVPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFE 180
            G+PEITL   P       L R +G   A +++L+GE+ITA++A + GLV+ VF  +   
Sbjct: 125 FGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTL 184

Query: 181 ESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKA 240
           E      + +   S +AL+  K+AL  S E    +       ++ + L  +ED  EG+ A
Sbjct: 185 EYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLF-TLLAATEDRHEGISA 243

Query: 241 FLEKRKPEWKGR 252
           FL+KR P++KGR
Sbjct: 244 FLQKRTPDFKGR 255


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: 136
Number of extensions: 7
Number of successful extensions: 4
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: 255
Length adjustment: 24
Effective length of query: 228
Effective length of database: 231
Effective search space:    52668
Effective search space used:    52668
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