GapMind for catabolism of small carbon sources

 

Alignments for a candidate for KDF-hydrolase in Magnetospirillum magneticum AMB-1

Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_011383249.1 AMB_RS04120 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase

Query= reanno::Smeli:SM_b21112
         (281 letters)



>NCBI__GCF_000009985.1:WP_011383249.1
          Length = 254

 Score =  139 bits (351), Expect = 5e-38
 Identities = 77/201 (38%), Positives = 111/201 (55%), Gaps = 7/201 (3%)

Query: 71  GKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIV 130
           G    + +NY+DHA E     P +P+ F+K     VG       P  +    +E EL +V
Sbjct: 45  GTTFALAINYADHAKELAFKAPEKPLAFLKGPGTFVGHRAVTRKPADAGFMHYECELAVV 104

Query: 131 IGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGPTGPWLVTKDE 190
           IG+TA+ V   +A D+VAGY   +D + R F    +    + K+ D     GPW+V +D+
Sbjct: 105 IGRTARDVKAKDAYDFVAGYTVANDYAIRNFLQNYYRPNLRTKNRDGCTVLGPWMVDRDD 164

Query: 191 VADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMG 250
           VADP  L +   VNG  +Q G+T+ MV+G   L+ YLS FM+L PGD+I TGTP G+ + 
Sbjct: 165 VADPMSLDISTFVNGARVQSGNTRDMVFGVPALIEYLSSFMTLSPGDLILTGTPDGI-VD 223

Query: 251 MKPPRYLKAGDVVELGIEGLG 271
           +KP      GD V   +EG+G
Sbjct: 224 VKP------GDEVVTEVEGVG 238


Lambda     K      H
   0.315    0.136    0.408 

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: 252
Number of extensions: 9
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: 281
Length of database: 254
Length adjustment: 25
Effective length of query: 256
Effective length of database: 229
Effective search space:    58624
Effective search space used:    58624
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: 42 (22.0 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