GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Algoriphagus aquaeductus T4

Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_111391465.1 CLV31_RS03385 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

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



>NCBI__GCF_003253485.1:WP_111391465.1
          Length = 801

 Score = 57.4 bits (137), Expect = 9e-13
 Identities = 41/139 (29%), Positives = 69/139 (49%), Gaps = 12/139 (8%)

Query: 25  LNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADIAEMKDLTAVEGRKFSVL 84
           +N++ A  ++ I+ AI     + +   ++I   G  F AGA++A +        ++F  +
Sbjct: 507 MNSMGAEVIEGINTAIG--MAEKSYKGLVIGNEGGNFSAGANLAML--FMFAGDQEFDEI 562

Query: 85  GNKIFRKLENL-------EKPVIAAINGFALGGGCELSLSCDIRIASSKAKFGQPEVGLG 137
            N +  + +N          PV+ A +  ALGGGCELSL  D   A ++   G  EVG+G
Sbjct: 563 -NLMIAQFQNTMMRARYSSVPVVVAPHNMALGGGCELSLHADHIQAHAELYMGLVEVGVG 621

Query: 138 ITPGFGGTQRLARAIGVGM 156
           + P  GGT+ + R    G+
Sbjct: 622 LIPAGGGTKEMTRRFANGV 640


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: 412
Number of extensions: 21
Number of successful extensions: 1
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: 801
Length adjustment: 33
Effective length of query: 226
Effective length of database: 768
Effective search space:   173568
Effective search space used:   173568
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: 51 (24.3 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