GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Shewanella loihica PV-4

Align crotonase (EC 4.2.1.150) (characterized)
to candidate 5210229 Shew_2672 carnitinyl-CoA dehydratase (RefSeq)

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



>FitnessBrowser__PV4:5210229
          Length = 261

 Score =  151 bits (382), Expect = 1e-41
 Identities = 92/261 (35%), Positives = 150/261 (57%), Gaps = 7/261 (2%)

Query: 4   KNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFV 62
           +++ + ++G++  I L+RPKA NA++A T  E+        +D  +   IITG+G + F 
Sbjct: 3   ESLHVTRNGSILEIVLDRPKA-NAIDAKTSYEMGEVFLAFRDDPELRVAIITGAGARFFS 61

Query: 63  AGADIAEMKDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRI 122
           AG D+    +  A +   F   G     +L +L+KPVIAA+NG+A GGG EL+L+ D+ +
Sbjct: 62  AGWDLKAAAEGEAPDA-DFGPGGFAGLTELFDLDKPVIAAVNGYAFGGGFELALAADLIV 120

Query: 123 ASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVV 182
            +  A F  PE  LGI P  GG  RL + +   +  EL+ TG+ ++A+EALR G+VN+VV
Sbjct: 121 CADNASFALPEAKLGIVPDSGGMLRLPKLLPAPIVNELMMTGRSMDAQEALRWGVVNRVV 180

Query: 183 EPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAY----EAEVFGECFAT 238
           E + L+E A+ L + I  +AP+A+   K    +  +  ++ G A+    + + +     +
Sbjct: 181 EQEALMETARELANEISQSAPLALAAIKEIYRETGELSVEQGYAHIRGGQLKHYPSVLHS 240

Query: 239 EDRVEGMTAFVEKRDKAFKNK 259
           ED +EG  AF EKRD  ++ K
Sbjct: 241 EDALEGPAAFAEKRDPVWQGK 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: 162
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: 261
Length adjustment: 24
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
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