GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Rhizobium etli CFN 42

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_042119745.1 RHE_RS23495 carnitinyl-CoA dehydratase

Query= BRENDA::O87873
         (258 letters)



>NCBI__GCF_000092045.1:WP_042119745.1
          Length = 260

 Score =  116 bits (291), Expect = 4e-31
 Identities = 83/257 (32%), Positives = 124/257 (48%), Gaps = 17/257 (6%)

Query: 14  RDGSLLRLRLARPKANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFGASVDEH 73
           RDG++L + + RPKAN +D A   AM     +    P LR  ++   G  F F A  D  
Sbjct: 9   RDGAVLEVVIDRPKANAIDLATSRAMGLIFRDFRDDPELRVAIISGAGEKF-FCAGWDLK 67

Query: 74  MPDQCAQMLKSLHGL-----VREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAAPDAK 128
                   +   +G+     ++E+ D   P++ A+ G C GGGLE+A + +L+ AA  A 
Sbjct: 68  AAAS-GDAVDGDYGVGGFGGLQELRDLNKPVICAVNGLCCGGGLEIALSTDLIIAAEHAT 126

Query: 129 FGQPEIRLGVFAPAASCLLPPRVGQACAEDLLWSGRSIDGAEGHRIGLIDVLAEDPEAAA 188
           F  PEIR G  A AAS  LP R+    A D+L +GR +D  E HR G ++ +        
Sbjct: 127 FALPEIRSGTVADAASIKLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFVNEVVPAERLME 186

Query: 189 LRWFDEHIARLSAS-------SLRFAVRAARCDSVPRIKQKLDTVEALYLEELMASHDAV 241
             W    +ARL  S       +++  VR A   +      K+   +   ++ L +S D +
Sbjct: 187 RAW---ELARLLESGPPLVYAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSEDQL 243

Query: 242 EGLKAFLEKRSANWENR 258
           EG +AF EKRS  W+ R
Sbjct: 244 EGARAFAEKRSPIWKGR 260


Lambda     K      H
   0.321    0.135    0.402 

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: 158
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: 258
Length of database: 260
Length adjustment: 24
Effective length of query: 234
Effective length of database: 236
Effective search space:    55224
Effective search space used:    55224
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 Apr 09 2024. 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