GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Cupriavidus basilensis 4G11

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate RR42_RS19805 RR42_RS19805 enoyl-CoA hydratase

Query= BRENDA::D3RXI0
         (252 letters)



>FitnessBrowser__Cup4G11:RR42_RS19805
          Length = 258

 Score = 96.3 bits (238), Expect = 6e-25
 Identities = 83/256 (32%), Positives = 118/256 (46%), Gaps = 23/256 (8%)

Query: 12  ERVARIKIANPPV-NVLDMETMKEIISAIDEV---EGVDVIVFSGEGKSFSAGAEIKEH- 66
           E VA I +  P V N L+   + E+ +A++     E V  +V S  G+ F AGA++    
Sbjct: 11  EGVATITLNRPDVLNALNSALLLELRAAVERAAQDEAVRAVVLSANGRGFCAGADLAGRG 70

Query: 67  --FPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNA---- 120
               D    +   +  +I  +       + +V G A G G  LA+A D VLA ++A    
Sbjct: 71  TGLQDSGTLLRERYHPIILALRNMPKPVITSVNGVAAGAGMSLALAGDVVLAGRSASFLQ 130

Query: 121 ---KLG-VPEITLAHYPPVAIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFED 176
              K+G VP+    ++       LPR  G   A  L +  E I AE A  IGLV KV ED
Sbjct: 131 AFSKIGLVPDAGSTYF-------LPRYAGEMRARALAILAEKIDAEEAHRIGLVWKVHED 183

Query: 177 ENFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVE 236
           E            L +  + A  L K+AL  S + +  +  +       S+  KSED  E
Sbjct: 184 EALPAETARLAAHLAQMPTFAYGLIKEALNASLQSDLPAQLE-REATLQSRASKSEDVKE 242

Query: 237 GLKAFLEKRKPEWKGR 252
           G+ AFLEKRKP +KGR
Sbjct: 243 GVAAFLEKRKPAFKGR 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: 123
Number of extensions: 9
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