GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Williamsia sterculiae CPCC 203464

Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_076481536.1 BW971_RS16050 crotonase/enoyl-CoA hydratase family protein

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



>NCBI__GCF_900156495.1:WP_076481536.1
          Length = 264

 Score =  138 bits (348), Expect = 1e-37
 Identities = 88/251 (35%), Positives = 134/251 (53%), Gaps = 6/251 (2%)

Query: 13  NVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADIAEMKD 72
           ++A ITL+RP ALNA+N+A    +  A+   A+D +V  V++TG+G+AF AGAD+  +  
Sbjct: 16  HIAVITLDRPDALNAVNSALAVGLGNALEAAAQDMDVRVVVVTGTGRAFCAGADLKALAA 75

Query: 73  LTAVEGRKFSVLGNK-IFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKAKFGQ 131
              ++       G   I R    + KPVIAA+NGFALGGG EL L+ D+ +    A  G 
Sbjct: 76  GDRIDDPDHPERGFAGIVRHW--IPKPVIAAVNGFALGGGTELVLAADLAVIDETASLGL 133

Query: 132 PEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKLLEEA 191
           PEV  G+    GG  R+ R +   +A E+  TG+ I+A  A  +GLVN+V      L+ A
Sbjct: 134 PEVRRGLIAAAGGLLRVHRQVSPKVANEIALTGQPISAVRAHELGLVNRVARQGTALDTA 193

Query: 192 KALVDAIIVNAPIAVRMCKAAINQGLQCD---IDTGVAYEAEVFGECFATEDRVEGMTAF 248
           + L   I  NAP++V   K  +++  + +    D       E      ++ D  EG  AF
Sbjct: 194 RELAATIAANAPVSVAQSKWLMHETAKDEQGWDDRAWELNQEALVRVLSSADAREGPRAF 253

Query: 249 VEKRDKAFKNK 259
            EKR+  ++ +
Sbjct: 254 AEKREPRWEGR 264


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: 158
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: 259
Length of database: 264
Length adjustment: 25
Effective length of query: 234
Effective length of database: 239
Effective search space:    55926
Effective search space used:    55926
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 24 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