GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudarthrobacter sulfonivorans Ar51

Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_058929179.1 AU252_RS01275 enoyl-CoA hydratase-related protein

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



>NCBI__GCF_001484605.1:WP_058929179.1
          Length = 262

 Score =  159 bits (402), Expect = 6e-44
 Identities = 95/261 (36%), Positives = 151/261 (57%), Gaps = 9/261 (3%)

Query: 4   KNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFV 62
           + ++ E    VA IT+NRP++ NAL+ A +  +       AED++V+A+++TG+G +AF 
Sbjct: 6   EEVLFEIRDRVAYITMNRPESRNALSQAVVARLAEVFTVAAEDNDVWAIVLTGAGDRAFC 65

Query: 63  AGADIAEMKDLTAVEGRKFSV----LGNKIFRKLENLEKPVIAAINGFALGGGCELSLSC 118
           AG D+ E+  + A EGR+F V        +F  +  + KP IA++NG A+ GG EL+L+C
Sbjct: 66  AGGDLKELNQI-AQEGRRFPVPMTGTERNLFELVLEVGKPTIASLNGPAVAGGFELALAC 124

Query: 119 DIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLV 178
           DIRIA+  +  G PE   G+   F  T  L R +   +A  ++YTG+++   EAL  GLV
Sbjct: 125 DIRIAAEHSTIGMPEAKRGMGANFA-TVLLPRLVPRSVALSMLYTGELMAPSEALHWGLV 183

Query: 179 NKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFAT 238
           N V   D+L +E +  V +I+ NAP+A+R  K  + +G +  +    A    V    + +
Sbjct: 184 NAVHPADQLAKETEEFVRSIVANAPLALRRYKEMVTKGWELSVQ--AALRLNVGPNPYLS 241

Query: 239 EDRVEGMTAFVEKRDKAFKNK 259
            DR EG+ AF+EKR   ++ K
Sbjct: 242 ADREEGVRAFIEKRAPRWEGK 262


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: 147
Number of extensions: 10
Number of successful extensions: 4
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 Apr 09 2024. 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