GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Dyella japonica UNC79MFTsu3.2

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate N515DRAFT_0416 N515DRAFT_0416 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0416
          Length = 686

 Score =  118 bits (296), Expect = 3e-31
 Identities = 70/191 (36%), Positives = 111/191 (58%), Gaps = 4/191 (2%)

Query: 11  EGNLFWITLNRPDK-LNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQ 69
           +  +  +TL+R +  +NAL+ ++L+EL + V +   +    V+I + K   F  GADI +
Sbjct: 16  DSGIVTLTLDRANSSVNALSREVLDELGQIVERLSIEKPAGVLIHSAKPGGFAVGADIKE 75

Query: 70  FNQLT-PAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAA--EE 126
           F +        +  + G+ + + +  L  PT+A I+G  +GGG EL LAC  RIAA  E+
Sbjct: 76  FVEYARDGTVLQNIENGQRVFESLARLPCPTVAAIHGACMGGGTELVLACRQRIAADDEK 135

Query: 127 AQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLAN 186
            ++GLPE+ LGI+PG+GGT RL R+IG   AL +M+TG  +  + A   G+V+R+ P   
Sbjct: 136 TRIGLPEVMLGIHPGWGGTARLPRLIGALDALPVMLTGKALSARRAAALGVVDRLAPPNE 195

Query: 187 LEQETRKLAEK 197
           L  E R L  +
Sbjct: 196 LLAEARALLRR 206


Lambda     K      H
   0.315    0.135    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: 383
Number of extensions: 21
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: 259
Length of database: 686
Length adjustment: 32
Effective length of query: 227
Effective length of database: 654
Effective search space:   148458
Effective search space used:   148458
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: 42 (22.0 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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