GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Marinobacter adhaerens HP15

Align short chain enoyl-CoA hydratase subunit (EC 4.2.1.17) (characterized)
to candidate GFF12 HP15_12 enoyl-CoA hydratase/isomerase

Query= metacyc::MONOMER-11697
         (290 letters)



>FitnessBrowser__Marino:GFF12
          Length = 270

 Score =  176 bits (447), Expect = 4e-49
 Identities = 102/252 (40%), Positives = 150/252 (59%), Gaps = 10/252 (3%)

Query: 43  RNSNVGLIQLNRPKALNALCNGLIVELNQALQAFEEDPAVGAIVLTG-GEKVFAAGADIK 101
           R+ NVG + LNRPK +NA+ + + V + +AL+ FE+D  +  IV+ G GE+   AGADIK
Sbjct: 19  RDGNVGWVILNRPKQINAINDEIRVGVPEALEQFEKDKEIRVIVIRGEGERGLCAGADIK 78

Query: 102 EMQ----SLTFQNCYSGGFLSHW-DQLTRVKKPVIAAVNGYALGGGCELAMMCDIIYAGE 156
           E +    SL  +        + W + + +  KPVI A++GY +GGG ELA+ CDI YA  
Sbjct: 79  ERRGPENSLQVRKRME---CARWIESIDQTTKPVIVAIHGYCMGGGLELALACDIRYASP 135

Query: 157 KAQFGQPEILIGTIPGAGGTQRLTRAVGKSLAMEMVLTGDRISAQDAKQAGLVSKIFPV- 215
            A    PE  +G IPG GGTQRL+R V    A++M+L+GDR+ A  A+  GLV+++    
Sbjct: 136 NAVMALPETGLGLIPGGGGTQRLSRVVAPGHALDMLLSGDRLDAARARSIGLVTRVAETQ 195

Query: 216 ETVVEEAIQCAEKIASNSKIVTAMAKESVNAAFEMTLAEGVKLEKKLFYSTFATEDRKEG 275
           E++++E  + A+KIA    + T   K +  A+ E+ L  G+ LE  LF     TED +E 
Sbjct: 196 ESLLQEVSELAQKIAMKPPLATTYVKRAARASLELELKRGLDLELDLFALLAPTEDAREA 255

Query: 276 MAAFVEKRKANF 287
            +AF E+R  NF
Sbjct: 256 ASAFSERRSPNF 267


Lambda     K      H
   0.319    0.133    0.378 

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: 160
Number of extensions: 6
Number of successful extensions: 4
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: 290
Length of database: 270
Length adjustment: 26
Effective length of query: 264
Effective length of database: 244
Effective search space:    64416
Effective search space used:    64416
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 (21.8 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