GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Marinobacter adhaerens HP15

Align crotonase (EC 4.2.1.150) (characterized)
to candidate GFF55 HP15_55 enoyl-CoA hydratase/isomerase

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



>FitnessBrowser__Marino:GFF55
          Length = 266

 Score =  160 bits (404), Expect = 3e-44
 Identities = 99/264 (37%), Positives = 147/264 (55%), Gaps = 8/264 (3%)

Query: 4   KNIILEKDGNVASITLNRPKALNALNAAT-LKEIDAAINDIAEDDNVYAVIITGSGKAFV 62
           K + +E+ GNVA + +N P+  NAL   + + EI     ++  D ++ A+++TG+GKAF 
Sbjct: 3   KFLNVERLGNVAVVRMNSPETHNALTTESQINEIVDLCAEVKADKSIRAMVLTGTGKAFC 62

Query: 63  AGADIAEMKDLTAV-EGRKFSVLG------NKIFRKLENLEKPVIAAINGFALGGGCELS 115
           AG +I +M+    +  G  + +         KI   L  L+ PVIAA+NG A+G G +L+
Sbjct: 63  AGGNIKDMQKRQGIFAGSPYDLRDVYRNGIQKIPLCLYELDIPVIAAVNGHAIGAGLDLA 122

Query: 116 LSCDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRI 175
             CDIRIAS+ AKF +  V LGI PG GG   L R +G+  A  + +TG+ I AE+AL  
Sbjct: 123 CMCDIRIASNNAKFAESFVKLGIVPGDGGAWLLPRIVGIPKASLMAFTGETIGAEQALSW 182

Query: 176 GLVNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGEC 235
           GLV +V  PD+L  EA  L   I  N   A+R+CK  + +G    +D+ +   A      
Sbjct: 183 GLVEQVCAPDELDAEALGLAQRIAENPGHALRLCKRLLREGQHMRLDSLLELSAAYQSLA 242

Query: 236 FATEDRVEGMTAFVEKRDKAFKNK 259
             T+D  E + +FVEKR   F +K
Sbjct: 243 HHTQDHQEAVDSFVEKRKPNFLDK 266


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: 176
Number of extensions: 9
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: 266
Length adjustment: 25
Effective length of query: 234
Effective length of database: 241
Effective search space:    56394
Effective search space used:    56394
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