GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Halioglobus japonicus S1-36

Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_084200593.1 C0029_RS01675 enoyl-CoA hydratase

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



>NCBI__GCF_002869505.1:WP_084200593.1
          Length = 262

 Score =  172 bits (436), Expect = 6e-48
 Identities = 101/248 (40%), Positives = 144/248 (58%), Gaps = 2/248 (0%)

Query: 12  GNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFVAGADIAEM 70
           G+VA IT++ P A N  +  +L  + A +  +  + N+YA++ITG+G K F AGAD+   
Sbjct: 15  GHVAKITVDNPAA-NTWDTESLPGLAALVEALNAEKNIYALVITGAGQKFFSAGADLKIF 73

Query: 71  KDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKAKFG 130
            D       K +    + F  L +     IAAINGFA+GGG EL+++CDIRIA  +A+  
Sbjct: 74  ADGDPEAAGKMAAYFGQAFETLADFRGVSIAAINGFAMGGGLELAMACDIRIAEEQAQLA 133

Query: 131 QPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKLLEE 190
            PE  +G+ P  GGTQRL + +G G AK +I  G+ I A++A RIGLV +VV     LE 
Sbjct: 134 LPEAKVGLLPCAGGTQRLTQLVGEGWAKRMILCGERIKADKAERIGLVEEVVATGTALER 193

Query: 191 AKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDRVEGMTAFVE 250
           A AL + +   +PI+V  CK  I+      I  G+  E   F   F+TED+ EG+ AF+E
Sbjct: 194 AMALAEQVGEQSPISVTACKKLIHSARDICIAQGLEDERSEFVALFSTEDQREGVNAFLE 253

Query: 251 KRDKAFKN 258
           KR   +KN
Sbjct: 254 KRKPEWKN 261


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: 164
Number of extensions: 6
Number of successful extensions: 2
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: 262
Length adjustment: 25
Effective length of query: 234
Effective length of database: 237
Effective search space:    55458
Effective search space used:    55458
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