GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Rhizobium leguminosarum bv. trifolii WSM1325

Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_012757048.1 RLEG_RS07315 enoyl-CoA hydratase/isomerase family protein

Query= metacyc::MONOMER-13469
         (259 letters)



>NCBI__GCF_000023185.1:WP_012757048.1
          Length = 259

 Score =  161 bits (407), Expect = 1e-44
 Identities = 98/255 (38%), Positives = 137/255 (53%), Gaps = 7/255 (2%)

Query: 8   LEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADI 67
           ++ DG+VA++T++RP+ LNAL+   LK +  A +++  + NV A I+TG GK F AG DI
Sbjct: 8   IDVDGHVATLTISRPEKLNALDLDMLKALADAADEVEANANVRAAILTGEGKGFSAGGDI 67

Query: 68  AEMKDLTAVE-GRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSK 126
                +   E G  +   G++IF +L  L  P+IAA+NG ALGGG EL+   DIR+A  +
Sbjct: 68  KAWGGMLPQEFGHLWVRHGHRIFERLATLRVPLIAALNGHALGGGLELAGVADIRLAEEQ 127

Query: 127 AKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDK 186
            K G PE GLG+ PG+ GTQRL R       + +   G++  AEEA  +G+V+ VV    
Sbjct: 128 IKIGLPETGLGMVPGWSGTQRLVRRFSAQAVRRMALGGEIFTAEEARLLGIVDAVVPTGN 187

Query: 187 LLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFA--TEDRVEG 244
            L  A+     I    P A  + K  I      D  T V    E  G   A  T D  EG
Sbjct: 188 ALAAAREYAQRIAARGPAATEIAKLMIASANGEDNGTAV----EALGSILAAKTGDLKEG 243

Query: 245 MTAFVEKRDKAFKNK 259
           + +F EKR   FK +
Sbjct: 244 VASFSEKRPATFKGE 258


Lambda     K      H
   0.318    0.136    0.376 

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: 169
Number of extensions: 12
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: 259
Length of database: 259
Length adjustment: 24
Effective length of query: 235
Effective length of database: 235
Effective search space:    55225
Effective search space used:    55225
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 Apr 09 2024. 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