GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Marinobacter adhaerens HP15

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate GFF12 HP15_12 enoyl-CoA hydratase/isomerase

Query= reanno::psRCH2:GFF2389
         (257 letters)



>FitnessBrowser__Marino:GFF12
          Length = 270

 Score =  160 bits (406), Expect = 2e-44
 Identities = 100/248 (40%), Positives = 139/248 (56%), Gaps = 10/248 (4%)

Query: 14  VALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSA-KAFAAGADIKEMAE 72
           V  + LNRP+ +NA+N ++   + +AL Q E D +I  IV+ G   +   AGADIKE   
Sbjct: 23  VGWVILNRPKQINAINDEIRVGVPEALEQFEKDKEIRVIVIRGEGERGLCAGADIKERRG 82

Query: 73  LTYPQIYLD-----DFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIFAADNARF 127
              P+  L      +     + I    KP+I A+ GY +GGG ELAL CD+ +A+ NA  
Sbjct: 83  ---PENSLQVRKRMECARWIESIDQTTKPVIVAIHGYCMGGGLELALACDIRYASPNAVM 139

Query: 128 GQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPA-ESLL 186
             PE  LG++PG GGTQRL+R V    A+DM L+G ++DAA A   GLV RV    ESLL
Sbjct: 140 ALPETGLGLIPGGGGTQRLSRVVAPGHALDMLLSGDRLDAARARSIGLVTRVAETQESLL 199

Query: 187 EETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQKEGMAAF 246
           +E  + A+ IA K   AT  +K +   + E  L  G+  E  +F  +  T D +E  +AF
Sbjct: 200 QEVSELAQKIAMKPPLATTYVKRAARASLELELKRGLDLELDLFALLAPTEDAREAASAF 259

Query: 247 SEKRKPEF 254
           SE+R P F
Sbjct: 260 SERRSPNF 267


Lambda     K      H
   0.321    0.135    0.375 

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: 127
Number of extensions: 7
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: 257
Length of database: 270
Length adjustment: 25
Effective length of query: 232
Effective length of database: 245
Effective search space:    56840
Effective search space used:    56840
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.

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