GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Sphingomonas koreensis DSMZ 15582

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate Ga0059261_2668 Ga0059261_2668 Enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::D3RXI0
         (252 letters)



>FitnessBrowser__Korea:Ga0059261_2668
          Length = 256

 Score = 94.0 bits (232), Expect = 3e-24
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 7/247 (2%)

Query: 12  ERVARIKIANPP-VNVLDMETMKEII---SAIDEVEGVDVIVFSGEG-KSFSAGAEIKEH 66
           + VA I +  P  +N L  E    +I   SA +  + V  +V +G G K+FSAG++I   
Sbjct: 11  DHVATITLNRPAKLNALTPEMAAALIASVSACNSSDAVRCVVITGAGEKAFSAGSDITTL 70

Query: 67  FPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKLGVPE 126
                P   R      D +  C+   VAA+ G+ALGGG E A+A D  +AS NA+   PE
Sbjct: 71  DGYATPWDFRNRDDYCDALRACRKPVVAAINGYALGGGLETAMAADIRIASTNARFAAPE 130

Query: 127 ITLAHYPPVAIAL-LPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFEESVND 185
           I L       +A  L   +G  NA  ++ TG+ I AE+A   GLV++V   +       +
Sbjct: 131 IKLGWIGGGGMAAGLTYSMGASNAALMLFTGDMIDAEKALAWGLVSEVVAPDALLARAQE 190

Query: 186 FVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKAFLEKR 245
              ++  ++ +A    K  L  +    +    +   D+  +    ++DA EG  AF EKR
Sbjct: 191 IARTIASRAPIAAETAKLNLRAAHTMPWDKAIEYERDLQ-AICFATDDAKEGRAAFAEKR 249

Query: 246 KPEWKGR 252
            P ++ R
Sbjct: 250 APVFRRR 256


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: 137
Number of extensions: 8
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: 256
Length adjustment: 24
Effective length of query: 228
Effective length of database: 232
Effective search space:    52896
Effective search space used:    52896
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