GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Dechlorosoma suillum PS

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate Dsui_0521 Dsui_0521 enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::O87873
         (258 letters)



>FitnessBrowser__PS:Dsui_0521
          Length = 258

 Score = 82.8 bits (203), Expect = 6e-21
 Identities = 79/260 (30%), Positives = 120/260 (46%), Gaps = 29/260 (11%)

Query: 9   KVWLERDGSLLRLRLARP-KANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFG 67
           ++ + RDG +  + L+ P K N V+ AM   +  A+ E     +LR V+L   G  F+ G
Sbjct: 4   RILVSRDGDIATVTLSNPEKLNAVNYAMWCDLAAAMAELSADSSLRCVVLAGAGEAFAAG 63

Query: 68  ASVDEHMPDQCAQMLKSLH------GLVREMLDSPVPILVALRGQCLGGGLEVAAAGNLL 121
             ++E +  +   + ++LH        +  + D P P +  +RG C+GGGLE+A   +L 
Sbjct: 64  GDIEEFLVKR-TNLEQALHYHDKVGAALDAVRDCPHPTVALIRGACIGGGLEIAGNCDLR 122

Query: 122 FAAPDAKFGQPEIRLGV-FAPAASCLLPPRVGQACAEDLLWSGRSIDGAEGHRIGLIDVL 180
            A   AKFG P  RLG    P     L    G A   ++L  GR +  AE +  GL+  +
Sbjct: 123 IAGEGAKFGAPINRLGFSMYPGEMSGLLALAGPAVMSEILLEGRILSAAEAYAKGLLTRV 182

Query: 181 AEDPEAAALRWFDEHIARLSASSLRFAVRA---ARCDSVPRIKQKLDTVEALYLEELMAS 237
             D +       DE    ++A++ R A  A   AR     +  ++L +   L  EE  AS
Sbjct: 183 VADAQLE-----DE----VTATARRIAAGAPLVARWHK--QWMRRLASGAPLTQEEKAAS 231

Query: 238 H------DAVEGLKAFLEKR 251
                  D  EGL AFL KR
Sbjct: 232 FAFLDTADYKEGLDAFLAKR 251


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: 168
Number of extensions: 8
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: 258
Length adjustment: 24
Effective length of query: 234
Effective length of database: 234
Effective search space:    54756
Effective search space used:    54756
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