GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Burkholderia vietnamiensis G4

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_011881868.1 3-hydroxybutyryl-CoA dehydratase

Query= BRENDA::Q1D5Y4
         (258 letters)



>NCBI__GCF_000016205.1:WP_011881868.1
          Length = 261

 Score =  177 bits (449), Expect = 2e-49
 Identities = 103/243 (42%), Positives = 137/243 (56%)

Query: 16  TIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERATMAED 75
           T+D     NA++   L E+            V  V++TG+G+KAF AGAD+ E A ++  
Sbjct: 19  TVDRPKSLNALNFQTLTEITAAFEDARDDDAVHGVIVTGSGNKAFVAGADISEIAALSAV 78

Query: 76  EVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLTEVKL 135
               F      T   IE      IAA+NG ALGGG ELA+AC +R+A+  A+ G  EVKL
Sbjct: 79  AAEKFAGLGHSTMNLIETLGKPVIAAVNGFALGGGCELAMACTMRIASEHAKFGQPEVKL 138

Query: 136 GIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAVAYGLAE 195
           GIIPG GGTQRL RLVG G A  LILTA  I+A EA  +GL N +     L+A A  +  
Sbjct: 139 GIIPGFGGTQRLPRLVGKGIAMQLILTAALIDANEAHRIGLVNEVVEADKLIARAEQILN 198

Query: 196 SVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLRAFAEKRAPVY 255
            +  NAPIA   A  A+++G    L+ AL+LE   +     TED+ EG  AF +KRAP +
Sbjct: 199 QIAANAPIATRLAITAVNQGVEASLEQALSLERALFAVCAATEDKAEGTAAFLDKRAPTF 258

Query: 256 KGR 258
           + +
Sbjct: 259 QSK 261


Lambda     K      H
   0.319    0.136    0.380 

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: 135
Number of extensions: 4
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: 258
Length of database: 261
Length adjustment: 24
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 ( 7.4 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