GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Marinobacter adhaerens HP15

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate GFF12 HP15_12 enoyl-CoA hydratase/isomerase

Query= BRENDA::D3RXI0
         (252 letters)



>FitnessBrowser__Marino:GFF12
          Length = 270

 Score =  100 bits (249), Expect = 3e-26
 Identities = 81/260 (31%), Positives = 130/260 (50%), Gaps = 19/260 (7%)

Query: 6   IKVEKDERVARIKIANPP-VNVLDMETMKEIISAIDEVEG---VDVIVFSGEG-KSFSAG 60
           + V +D  V  + +  P  +N ++ E    +  A+++ E    + VIV  GEG +   AG
Sbjct: 15  VNVCRDGNVGWVILNRPKQINAINDEIRVGVPEALEQFEKDKEIRVIVIRGEGERGLCAG 74

Query: 61  AEIKEHF-PD------KAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDF 113
           A+IKE   P+      K  E  RW    I+ + +     + A+ G+ +GGG ELA+ACD 
Sbjct: 75  ADIKERRGPENSLQVRKRMECARW----IESIDQTTKPVIVAIHGYCMGGGLELALACDI 130

Query: 114 VLASKNAKLGVPEITLAHYP-PVAIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNK 172
             AS NA + +PE  L   P       L R++   +A +++L+G+ + A RA  IGLV +
Sbjct: 131 RYASPNAVMALPETGLGLIPGGGGTQRLSRVVAPGHALDMLLSGDRLDAARARSIGLVTR 190

Query: 173 VFE-DENFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKS 231
           V E  E+  + V++    +  K  +A    K+A   S E E     D+  D++ + L  +
Sbjct: 191 VAETQESLLQEVSELAQKIAMKPPLATTYVKRAARASLELELKRGLDLELDLF-ALLAPT 249

Query: 232 EDAVEGLKAFLEKRKPEWKG 251
           EDA E   AF E+R P + G
Sbjct: 250 EDAREAASAFSERRSPNFIG 269


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: 132
Number of extensions: 10
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: 270
Length adjustment: 25
Effective length of query: 227
Effective length of database: 245
Effective search space:    55615
Effective search space used:    55615
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