GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Pseudomonas fluorescens GW456-L13

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate PfGW456L13_3427 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= BRENDA::O87873
         (258 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3427
          Length = 272

 Score = 94.0 bits (232), Expect = 3e-24
 Identities = 82/252 (32%), Positives = 122/252 (48%), Gaps = 13/252 (5%)

Query: 10  VWLERDGSLLRLRLARPKA-NIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPH-FSFG 67
           V LERD  +  + L RP+  N ++  +   + QAL    Q P +R +++  EG   F  G
Sbjct: 17  VRLERDAMVGWVVLTRPRQINAINDEIRQGVPQALALLQQDPDIRVIVIRGEGDRGFCAG 76

Query: 68  ASVDEHMPDQCAQMLKSLHGLVR--EMLDSPV-PILVALRGQCLGGGLEVAAAGNLLFAA 124
           A + E    + +  ++     VR  E LD    P++ A+ G C+GGGLE+  A ++ FAA
Sbjct: 77  ADIKERRGPESSLQVRQRMENVRWIETLDGITKPVIAAIHGYCMGGGLELVLACDIRFAA 136

Query: 125 PDAKFGQPEIRLGVFAPAASCLLPPRV---GQACAEDLLWSGRSIDGAEGHRIGLIDVLA 181
           PDA F  PE  LG+           RV   GQA   D+L +G  +   +  RIGL+  LA
Sbjct: 137 PDAVFALPETGLGLIPGGGGTQRLSRVVAPGQAL--DMLLTGDRVGAEQAQRIGLVSRLA 194

Query: 182 EDPE--AAALRWFDEHIARLSASSLRFAVRAARCDSVPRIKQKLDTVEALYLEELMASHD 239
            D       +R F + IA    ++  F  +AAR      +K+ LD +E      L  + D
Sbjct: 195 SDSANLVQEVRAFAQRIASKPPTASAFVKQAARAALEMDLKRGLD-LELDLFALLAPTKD 253

Query: 240 AVEGLKAFLEKR 251
           A E  +AF E+R
Sbjct: 254 AREAAQAFSERR 265


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: 172
Number of extensions: 9
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: 258
Length of database: 272
Length adjustment: 25
Effective length of query: 233
Effective length of database: 247
Effective search space:    57551
Effective search space used:    57551
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 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