GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Dechlorosoma suillum PS

Align crotonase (EC 4.2.1.150) (characterized)
to candidate Dsui_2807 Dsui_2807 enoyl-CoA hydratase/carnithine racemase

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



>FitnessBrowser__PS:Dsui_2807
          Length = 262

 Score =  137 bits (344), Expect = 3e-37
 Identities = 88/242 (36%), Positives = 130/242 (53%), Gaps = 10/242 (4%)

Query: 16  SITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADIAEMKDL-- 73
           ++ LNRP   N+L+ A L+ + A +  IA D  V  V++ G+GKAF AG D+ EM+    
Sbjct: 19  TLVLNRPAQFNSLSNAMLETLLAELQSIAADKTVRVVVLQGAGKAFCAGHDLKEMRSNHD 78

Query: 74  TAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKAKFGQPE 133
            A     F +   K+   ++ + +PVIA I+G A   GC+L   CD+ +A+  AKF    
Sbjct: 79  KAFMQALFKLCA-KVMLTIQEMPQPVIARIHGIATAAGCQLVSMCDLAVAADVAKFAVSG 137

Query: 134 VGLGI---TPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKLLEE 190
           + +G+   TP  G    LAR +G   A E++ TG+ I+A EA R GLVN+VV    L E 
Sbjct: 138 INVGLFCSTPAVG----LARNMGRKEALEMLLTGEFIDAGEAQRRGLVNRVVALGDLDEA 193

Query: 191 AKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDRVEGMTAFVE 250
            + LV +I+  +P+AV   K    + L+  I+    Y  EV        D  EG+ AF+E
Sbjct: 194 VEHLVQSILAKSPVAVATGKQMFYKQLEMGIEAAYQYAGEVMACNMMAGDAAEGIDAFIE 253

Query: 251 KR 252
           KR
Sbjct: 254 KR 255


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: 154
Number of extensions: 6
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: 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 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